You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by ma...@apache.org on 2019/06/02 17:22:47 UTC
[airavata-php-gateway] branch dreg-gateway updated (e52fc97 ->
ee3df12)
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a change to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git.
from e52fc97 Merge branch 'master' into dreg-gateway
new 1fe0687 adding a prefix for output file
new c678d7c adding explanation for job failure
new 3c60e3f fix the invalid links
new fe898a2 adding document link in homepage
new 3355e29 changing document
new 62d3e66 change the link on dREG home page
new 2cdda18 update for document and faq page
new 4e8d471 change links to buttons
new 364ce0e update UI
new 6c14e1c minor change for GR paper reviewer
new 7c4ac01 dTOX 1st version
new 4024007 updates for dTOX
new 7768b4a Update dREG page
new ee3df12 Merge branch 'dreg-gateway' of https://github.com/Danko-Lab/airavata-php-gateway into dreg-gateway
The 14 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
app/libraries/CommonUtilities.php | 4 +-
app/libraries/FileTransfer.php | 113 ++++---
app/routes.php | 7 +-
app/views/account/dashboard.blade.php | 2 +-
app/views/experiment/create-complete.blade.php | 2 +-
app/views/experiment/create.blade.php | 2 +-
app/views/partials/experiment-info.blade.php | 89 +++++-
public/themes/dreg/assets/img/3d-number.jpg | Bin 0 -> 67965 bytes
public/themes/dreg/assets/img/dTOX-model.png | Bin 0 -> 99342 bytes
.../themes/dreg/assets/img/dreg-dtox-gateway.png | Bin 0 -> 132589 bytes
public/themes/dreg/assets/img/dreg.exp.summary.png | Bin 52211 -> 46929 bytes
public/themes/dreg/assets/img/dregicon.png | Bin 0 -> 2128 bytes
public/themes/dreg/assets/img/dtox.create.exp.png | Bin 0 -> 17154 bytes
public/themes/dreg/assets/img/dtox.create.exp2.png | Bin 0 -> 40049 bytes
public/themes/dreg/assets/img/failure1.png | Bin 0 -> 53330 bytes
public/themes/dreg/assets/img/failure2.png | Bin 0 -> 29925 bytes
public/themes/dreg/assets/img/failure3-reason.png | Bin 0 -> 15519 bytes
public/themes/dreg/assets/img/failure3.png | Bin 0 -> 32245 bytes
public/themes/dreg/assets/img/failure4-reason.png | Bin 0 -> 17034 bytes
public/themes/dreg/assets/img/n1.png | Bin 0 -> 15718 bytes
public/themes/dreg/assets/img/n2.png | Bin 0 -> 19546 bytes
public/themes/dreg/assets/img/n3.png | Bin 0 -> 22082 bytes
public/themes/dreg/assets/img/n4.png | Bin 0 -> 19153 bytes
public/themes/dreg/partials/about.blade.php | 23 +-
public/themes/dreg/partials/doc.blade.php | 286 ++++++++++++++++--
public/themes/dreg/partials/dtox-doc.blade.php | 331 +++++++++++++++++++++
public/themes/dreg/partials/faq.blade.php | 38 ++-
public/themes/dreg/partials/header.blade.php | 11 +-
public/themes/dreg/partials/software.blade.php | 64 ++++
public/themes/dreg/partials/template.blade.php | 152 +++++++---
30 files changed, 968 insertions(+), 156 deletions(-)
mode change 100755 => 100644 app/views/partials/experiment-info.blade.php
create mode 100644 public/themes/dreg/assets/img/3d-number.jpg
create mode 100644 public/themes/dreg/assets/img/dTOX-model.png
create mode 100644 public/themes/dreg/assets/img/dreg-dtox-gateway.png
create mode 100644 public/themes/dreg/assets/img/dregicon.png
create mode 100644 public/themes/dreg/assets/img/dtox.create.exp.png
create mode 100644 public/themes/dreg/assets/img/dtox.create.exp2.png
create mode 100644 public/themes/dreg/assets/img/failure1.png
create mode 100644 public/themes/dreg/assets/img/failure2.png
create mode 100644 public/themes/dreg/assets/img/failure3-reason.png
create mode 100644 public/themes/dreg/assets/img/failure3.png
create mode 100644 public/themes/dreg/assets/img/failure4-reason.png
create mode 100644 public/themes/dreg/assets/img/n1.png
create mode 100644 public/themes/dreg/assets/img/n2.png
create mode 100644 public/themes/dreg/assets/img/n3.png
create mode 100644 public/themes/dreg/assets/img/n4.png
create mode 100755 public/themes/dreg/partials/dtox-doc.blade.php
create mode 100755 public/themes/dreg/partials/software.blade.php
[airavata-php-gateway] 02/14: adding explanation for job failure
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit c678d7caa6af3c716e1b0aa34bdfca6c1da3d95c
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Jun 18 19:04:07 2018 +0000
adding explanation for job failure
---
public/themes/dreg/assets/img/failure1.png | Bin 0 -> 53330 bytes
public/themes/dreg/assets/img/failure2.png | Bin 0 -> 29925 bytes
public/themes/dreg/assets/img/failure3-reason.png | Bin 0 -> 15519 bytes
public/themes/dreg/assets/img/failure3.png | Bin 0 -> 31908 bytes
public/themes/dreg/assets/img/failure4-reason.png | Bin 0 -> 17034 bytes
public/themes/dreg/partials/doc.blade.php | 39 ++++++++++++++++++++++
public/themes/dreg/partials/faq.blade.php | 12 +++++--
7 files changed, 49 insertions(+), 2 deletions(-)
diff --git a/public/themes/dreg/assets/img/failure1.png b/public/themes/dreg/assets/img/failure1.png
new file mode 100644
index 0000000..64e08cc
Binary files /dev/null and b/public/themes/dreg/assets/img/failure1.png differ
diff --git a/public/themes/dreg/assets/img/failure2.png b/public/themes/dreg/assets/img/failure2.png
new file mode 100644
index 0000000..8dd9e28
Binary files /dev/null and b/public/themes/dreg/assets/img/failure2.png differ
diff --git a/public/themes/dreg/assets/img/failure3-reason.png b/public/themes/dreg/assets/img/failure3-reason.png
new file mode 100644
index 0000000..42131b9
Binary files /dev/null and b/public/themes/dreg/assets/img/failure3-reason.png differ
diff --git a/public/themes/dreg/assets/img/failure3.png b/public/themes/dreg/assets/img/failure3.png
new file mode 100644
index 0000000..a4a9f3a
Binary files /dev/null and b/public/themes/dreg/assets/img/failure3.png differ
diff --git a/public/themes/dreg/assets/img/failure4-reason.png b/public/themes/dreg/assets/img/failure4-reason.png
new file mode 100644
index 0000000..158146c
Binary files /dev/null and b/public/themes/dreg/assets/img/failure4-reason.png differ
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index ae77e01..74c54ce 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -71,6 +71,45 @@ the user can click <b>'Open Folder'</b> link in the experiment summary page to c
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.folder.png"></img></div>
+<a name="failure"></a>
+ <p class="description" style="padding:16px">
+ 10) <b>When you meet failure</b><br>
+
+Currently when you run the dREG jobs, there are two types of errors you may have. One error may come from the system, called a system error, such as no computing time on specific GPU nodes or an internal errors in Apache Airavata. The other type of error is caused by the users' bigwig, called bigwig error, which can occur when read counts are normalized, each read is mapped to a region, or read counts in minus strand are positive values. The following figures show how to identify the err [...]
+
+
+ <p class="description" style="padding:16px">
+ a) <b>System error</b><br>
+When users submit the experiment, the failure will be shown in the experiment summary page soon as figure 10-S1 or 10-S2. The <b>experiment status</b> is "Failed" and many java errors are shown in the <b>"Errors"</b> item. Users can't solve this problem and should report this error the web master.</p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="System error(1)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure1.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S1</center></div>
+
+<br>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="System error(2)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure2.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S2</center></div>
+
+<br>
+ <p class="description" style="padding:16px">
+ b) <b>Bigwig error</b><br>
+After the experiment is complete, no results can be downloaded and job status shows a failure (see Figure 10-S3). Users can find the dREG log file or task log file to identify the problem. Enter into <b>"storage directory"</b> by clicking the <b>"open"</b> link. The users can find <b>"ARCHIVE"</b> folder where Apache Airavata copy back all files from the computing node. Check the dREG log file (<b>out.dREG.log</b>) to see the bigwig problem or check the task log file ("slurm-tasknoxxx.ou [...]
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure3.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S3</center></div>
+<BR>
+
+<p>This figure shows the bigWig problems in the dREG log file.</p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error(1)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure3-reason.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S4</center></div>
+<BR>
+
+<p>This figure shows the task log file in which explains the task was killed due to time limit.</p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error(2)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure4-reason.png"></img></div>
+<div style="clear:both;text-align:center;"><center>Figure 10-S5</center></div>
+<BR>
</div>
</div>
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index e92be49..ea4b3a9 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -8,6 +8,10 @@
<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> here </A>.</p>
+
+<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
+<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
+
<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called ‘active’ class of enhancers and promoters. </p>
<p><b>Q: Will the dREG gateway work with my data type?</b></p>
@@ -18,8 +22,12 @@
<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
-<A href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
-Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
+(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">
+(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P>
+
+
<p><b>Q: Do I have to create account before using this service?</b></p>
<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
<p><b>Q: How do I know the status of the computational nodes? </b></p>
[airavata-php-gateway] 03/14: fix the invalid links
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 3c60e3fddee12c035beb19b9049c68c76294ccb8
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Jun 18 19:34:48 2018 +0000
fix the invalid links
---
public/themes/dreg/partials/template.blade.php | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index 643ed78..8810661 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -54,7 +54,7 @@ Registered users need only upload experimental data in the required format and p
</p>
<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>See our <A href="https://osboxes/pages/faq">FAQ</A> for additional questions.
+<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A> for additional questions.
</p>
<img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img>
<p class="text-center"><small>Click the figure to enlarge it</small></p>
[airavata-php-gateway] 05/14: changing document
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 3355e295345c31027ad70910afd33a1c7a94af52
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Jun 25 16:46:28 2018 +0000
changing document
---
public/themes/dreg/assets/img/dreg.exp.summary.png | Bin 52211 -> 31052 bytes
public/themes/dreg/partials/doc.blade.php | 20 ++++++++++++--------
public/themes/dreg/partials/faq.blade.php | 4 ++++
3 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/public/themes/dreg/assets/img/dreg.exp.summary.png b/public/themes/dreg/assets/img/dreg.exp.summary.png
index 183f5c3..28604fe 100755
Binary files a/public/themes/dreg/assets/img/dreg.exp.summary.png and b/public/themes/dreg/assets/img/dreg.exp.summary.png differ
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index 74c54ce..9859deb 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -54,14 +54,14 @@ The user can check the status of their 'experiment' by clicking the menu 'Saved
<p class="description" style="padding:16px">
7) <b>Check the results</b><br>
-Once a job is completed, the user can click <B>'Download All Results'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list.
+Once a job is completed, the user can select 'Full results' in the drop-down list and then click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed by th [...]
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div>
<p class="description" style="padding:16px">
8) <b>Switch to Genome Browser</b><br>
-The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Genome Browser'</B> link. </p>
+The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Switch to genome browser'</B> link. </p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.gbview.png"></img></div>
@@ -154,17 +154,21 @@ dREG run generates a compressed file including the dREG and dREG.HD results as f
<th>Description</th>
</tr>
<tr>
- <td>out.dREG.infp.bed.gz</td>
- <td>Informative positions with the scores predicted by the dREG model</td>
+ <td>$PREFIX.dREG.infp.bed.gz</td>
+ <td>Informative positions with the scores predicted by the dREG model. <BR>Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
- <td>out.dREG.peak.full.bed.gz</td>
- <td>dREG peaks calling results with score, probability and center position information. </td>
+ <td>$PREFIX.dREG.peak.full.bed.gz</td>
+ <td>dREG peaks calling results with score, probability and center position information. <BR>Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
- <td>out.dREG.peak.score.bed.gz</td>
- <td>dREG peaks calling results only with score.</td>
+ <td>$PREFIX.dREG.peak.score.bed.gz</td>
+ <td>dREG peaks calling results only with score. <BR>Decompress it with 'gunzip' in Linux.</td>
</tr>
+ <tr>
+ <td>$PREFIX.tar.gz</td>
+ <td>Including above 3 files, can be decompressed by 'tar -xvzf' in Linux.</td>
+ </tr>
</table>
</div>
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index ea4b3a9..fd0bb4e 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -5,6 +5,8 @@
<div class="post-entry">
<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
+<p><b>Q: Which browser works well with the dREG gateway?</b></p>
+<p>A: We have tested in the Firefox and Google Chrome so far. In IE (version 10 or 11) or Safari, WashU geneome browser doesn't work.</p>
<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> here </A>.</p>
@@ -20,6 +22,8 @@
<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species . We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p>
<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
+<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
+<p>A: One month.</p>
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
[airavata-php-gateway] 04/14: adding document link in homepage
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit fe898a227533497dc32fb5943e98484bdb0466c0
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Jun 18 19:51:23 2018 +0000
adding document link in homepage
---
public/themes/dreg/partials/template.blade.php | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index 8810661..9951895 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -54,7 +54,7 @@ Registered users need only upload experimental data in the required format and p
</p>
<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A> for additional questions.
+<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A> or <A href="{{ URL::to('/') }}/pages/doc">document</a> for additional questions.
</p>
<img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img>
<p class="text-center"><small>Click the figure to enlarge it</small></p>
[airavata-php-gateway] 11/14: dTOX 1st version
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 7c4ac016feaf359d0b08343da128e22f4e94d85e
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Dec 3 22:12:09 2018 +0000
dTOX 1st version
---
app/libraries/CommonUtilities.php | 4 +-
app/libraries/ExperimentUtilities.php | 1 +
app/libraries/FileTransfer.php | 117 ++++++++--------
app/routes.php | 7 +-
app/views/account/dashboard.blade.php | 2 +-
app/views/experiment/create-complete.blade.php | 2 +-
app/views/experiment/create.blade.php | 2 +-
app/views/partials/experiment-info.blade.php | 36 ++++-
public/themes/dreg/assets/img/dTOX-model.png | Bin 0 -> 99342 bytes
.../themes/dreg/assets/img/dreg-dtox-gateway.png | Bin 0 -> 132589 bytes
public/themes/dreg/assets/img/dtox.create.exp.png | Bin 0 -> 17154 bytes
public/themes/dreg/assets/img/dtox.create.exp2.png | Bin 0 -> 42088 bytes
public/themes/dreg/partials/about.blade.php | 23 +++-
public/themes/dreg/partials/doc.blade.php | 95 +++++++++----
.../partials/{doc.blade.php => dtox-doc.blade.php} | 153 ++++++++++++---------
public/themes/dreg/partials/header.blade.php | 7 +-
public/themes/dreg/partials/software.blade.php | 58 ++++++++
public/themes/dreg/partials/template.blade.php | 130 +++++++++++------
18 files changed, 427 insertions(+), 210 deletions(-)
diff --git a/app/libraries/CommonUtilities.php b/app/libraries/CommonUtilities.php
index c2df0df..e8dba9d 100644
--- a/app/libraries/CommonUtilities.php
+++ b/app/libraries/CommonUtilities.php
@@ -199,7 +199,7 @@ class CommonUtilities
|| Session::has('admin-read-only'))){
if( Session::get("nav-active") == "experiment" && $_SERVER['REQUEST_URI']== "/xperiment/create")
$active = "active";
- $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/create"><span class="glyphicon glyphicon-plus-sign"></span> Start dREG</a></li>';
+ $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/create"><span class="glyphicon glyphicon-plus-sign"></span> Start dREG/dTOX</a></li>';
}
$active = "";
@@ -207,7 +207,7 @@ class CommonUtilities
|| Session::has('admin-read-only'))){
if( Session::get("nav-active") == "experiment" && $_SERVER['REQUEST_URI']== "/experiment/browse")
$active = "active";
- $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/browse"><span class="glyphicon glyphicon-list"></span> Saved dREG runs</a></li>';
+ $navbar .= '<li class="' . $active . '"><a href="' . URL::to("/") . '/experiment/browse"><span class="glyphicon glyphicon-list"></span> Saved runs</a></li>';
}
// <<- dREG
diff --git a/app/libraries/ExperimentUtilities.php b/app/libraries/ExperimentUtilities.php
index ade7873..89f5809 100755
--- a/app/libraries/ExperimentUtilities.php
+++ b/app/libraries/ExperimentUtilities.php
@@ -829,6 +829,7 @@ class ExperimentUtilities
echo '<option value="'.$vals[$i].'">'.$vals[$i] .'</option>';
}
echo '</select>';
+ echo '</div>';
}else{
echo '<input '.$disabled . ' value="' . $input->value . '" type="text" class="form-control" name="' . $input->sanitizedFormName .
'" id="' . $input->sanitizedFormName .
diff --git a/app/libraries/FileTransfer.php b/app/libraries/FileTransfer.php
index 73882a6..470139c 100644
--- a/app/libraries/FileTransfer.php
+++ b/app/libraries/FileTransfer.php
@@ -13,7 +13,7 @@ use \TusServer\TusServer;
class FileTransfer {
- public static function gbrowser($filelist ){
+ public static function gbrowser_dREG($filelist ){
$protocol = 'http';
if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https')
$protocol = 'https';
@@ -42,7 +42,7 @@ class FileTransfer {
$content = $content . ' {
type:"bigwig",
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[2]). '",
- name: "'. $filelist[3] .'",
+ name: "'. $filelist[2] .'",
#fixedscale:{min:0,max:20},
summarymethod:"min",
colorpositive:"#C5000B",
@@ -76,64 +76,61 @@ class FileTransfer {
},'. "\n";
- #$content = $content . '{
- # type:"bedgraph",
- # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.infp.bed.gz').'",
- # name: "dREG Info. Sites:",
- # mode: "show",
- # colorpositive:"#B30086",
- # colornegative:"#0000e5",
- # backgroundcolor:"#ffffe5",
- # height:40,
- # fixedscale:{min:0, max:1},
- #},'. "\n";
-
- #$content = $content . '{
- # type:"bedgraph",
- # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.peak.score.bed.gz').'",
- # name: "dREG Peak Calling:",
- # mode: "show",
- # colorpositive:"#B30086",
- # colornegative:"#0000e5",
- # backgroundcolor:"#ffffe5",
- # height:40,
- # fixedscale:{min:0.2, max:1.0},
- #},'. "\n";
-
-
- #$content = $content . '{
- # type:"bigwig",
- # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
- # name: "imputed DNase-I signal:",
- # #fixedscale:{min:0,max:20},
- # summarymethod:"max",
- # colorpositive:"#00B306",
- # backgroundcolor:"#ffffe5",
- # height:100,
- # mode: "show",
- #},'. "\n";
-
- #$content = $content . '{
- # type:"bedgraph",
- # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.relaxed.bed.gz').'",
- # name: "dREG.HD relaxed peaks:",
- # mode: "show",
- # colorpositive:"#0000e5/#B30086",
- # backgroundcolor:"#ffffe5",
- # height:40,
- # fixedscale:{min:0, max:1},
- #},'. "\n";
-
- #$content = $content . '{
- # type:"bedgraph",
- # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.stringent.bed.gz').'",
- # name: "dREG.HD stringent peaks:",
- # mode: "show",
- # colorpositive:"#0000e5/#B30086",
- # backgroundcolor:"#ffffe5",
- # height:40,
- # fixedscale:{min:0, max:1},
- #},'. "\n";
+ $content = $content . ']';
+ return Response::make($content, 200)
+ ->header('Content-Type', 'text/plain');
+ }
+
+ public static function gbrowser_dTOX($filelist ){
+ $protocol = 'http';
+ if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https')
+ $protocol = 'https';
+
+ include("basecode.php");
+
+ $dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"];
+ $filelist = explode("\n", RBase64::decode( $filelist ) );
+ $folder_path=$filelist[0]. "ARCHIVE" ;
+ $content = "[ \n";
+ $out_prefix = $filelist[3];
+
+ $content = $content . ' {
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[1]). '",
+ name: "'. $filelist[1] .'",
+ #fixedscale:{min:0,max:20},
+ summarymethod:"max",
+ colorpositive:"#C5000B",
+ colornegative:"#0084D1",
+ height:100,
+ mode: "show",
+ },'. "\n" ;
+
+
+ $content = $content . ' {
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[2]). '",
+ name: "'. $filelist[2] .'",
+ #fixedscale:{min:0,max:20},
+ summarymethod:"min",
+ colorpositive:"#C5000B",
+ colornegative:"#0084D1",
+ height:100,
+ mode: "show",
+ },'. "\n" ;
+
+ $content = $content . '{
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dTOX.bound.bed.gz').'",
+ name: "dTOX bound status:",
+ mode: "show",
+ colorpositive:"#B30086",
+ colornegative:"#0000e5",
+ backgroundcolor:"#ffffe5",
+ height:40,
+ fixedscale:{min:0, max:1},
+ },'. "\n";
+
$content = $content . ']';
return Response::make($content, 200)
diff --git a/app/routes.php b/app/routes.php
index 1ab5acd..e201de3 100755
--- a/app/routes.php
+++ b/app/routes.php
@@ -178,7 +178,12 @@ Route::get("files/get","FilemanagerController@get");
// Added by dREG
Route::get("gbrowser/{filelist}", function($filelist){
- return FileTransfer::gbrowser($filelist);
+ return FileTransfer::gbrowser_dREG($filelist);
+});
+
+//Added by dTOX
+Route::get("gbrowser1/{filelist}", function($filelist){
+ return FileTransfer::gbrowser_dTOX($filelist);
});
Route::get("gbfile/{file}", function($file){
diff --git a/app/views/account/dashboard.blade.php b/app/views/account/dashboard.blade.php
index 8cc8501..d6c7eae3 100644
--- a/app/views/account/dashboard.blade.php
+++ b/app/views/account/dashboard.blade.php
@@ -250,7 +250,7 @@
<span class="glyphicon glyphicon-plus-sign console-icon"></span>
</div>
<div class="col-md-12">
- <h4>Start dREG</h4>
+ <h4>Start dREG/dTOX</h4>
</div>
</div>
</a>
diff --git a/app/views/experiment/create-complete.blade.php b/app/views/experiment/create-complete.blade.php
index 7b1ab36..7dafa54 100755
--- a/app/views/experiment/create-complete.blade.php
+++ b/app/views/experiment/create-complete.blade.php
@@ -11,7 +11,7 @@
{{-- Commented by dREG
<h1>Create a new experiment</h1>
--}}
- <h1>Create a new dREG experiment</h1>
+ <h1>Create a new dREG or dTOX experiment</h1>
<!-- <form action="{{URL::to('/')}}/experiment/create" method="POST" role="form" enctype="multipart/form-data"> -->
<form action="{{URL::to('/')}}/experiment/create" method="POST" role="form" >
diff --git a/app/views/experiment/create.blade.php b/app/views/experiment/create.blade.php
index 0a1ce01..cc4e215 100755
--- a/app/views/experiment/create.blade.php
+++ b/app/views/experiment/create.blade.php
@@ -18,7 +18,7 @@
{{-- Added by dREG
<h1>Create a new experiment</h1>
--}}
- <h1>Create a new dREG experiment</h1>
+ <h1>Create a new dREG or dTOX experiment</h1>
<form action="{{URL::to('/')}}/experiment/create" method="POST" role="form" enctype="multipart/form-data">
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
old mode 100755
new mode 100644
index 55c4c3f..4715e6d
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -220,6 +220,8 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d
}
?>
<td>
+
+@if( $expVal["applicationInterface"]->applicationName !== "dTOX prediction" )
<select id="download">
<option value=''>Select results</option>
@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') )
@@ -235,20 +237,46 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d
<option value=<?php echo $param_prefix.".dREG.peak.score.bed.gz"?>>dREG peak(only with scores)</option>
@endif
</select>
+@else
+ <select id="download">
+ <option value=''>Select results</option>
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') )
+ <option value=<?php echo $param_prefix.".tar.gz" ?>>Full results</option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTOX.full.bed.gz') )
+ <option value=<?php echo $param_prefix.".dTOX.full.bed.gz"?>>all dTOX regions</option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTox.bound.bed.gz') )
+ <option value=<?php echo $param_prefix.".dTOX.bound.bed.gz"?>>dTOX bound regions </option>
+@endif
+ </select>
+
+
+@endif
+
-<!-- <a href="" target="_blank" id="retLinks">Download <span class="glyphicon glyphicon-save" style="width:20px"></span></a> -->
<button id="retLinks" style="color: #fff; background-color: #3e5a43; border-color: #46b8da; border: 1px solid transparent;" >Download <span class="glyphicon glyphicon-save" style="width:20px"></span></button>
</td>
</tr>
<tr>
<td><strong>Genome Browser</strong></td>
<td>
+
+@if( $expVal["applicationInterface"]->applicationName !== "dTOX prediction" )
<select id="genomebuilder">
<option value="">Select genome </option>
<option value="hg19">hg19</option>
<option value="hg38">hg38</option>
<option value="mm10">mm10</option>
- </select>
+ </select>
+@else
+ <select id="genomebuilder">
+ <option value="">Select genome </option>
+ <option value="hg19">hg19</option>
+ <option value="mm10">mm10</option>
+ </select>
+@endif
+
or input
<input type="text" id="customeGB" style="width:40px"/>
<!-- <a href="#1" target="_blank" id="gbLinks">Switch to genome browser <span class="glyphicon glyphicon-new-window" style="width:20px"></span></a> -->
@@ -547,7 +575,11 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d
if (gb == '')
return false;
+@if( $expVal["applicationInterface"]->applicationName !== "dTOX prediction" )
var gbUrl = "http://epigenomegateway.wustl.edu/browser/?datahub={{ $protocol .'://'. $_SERVER['HTTP_HOST']. '/gbrowser/'. RBase64::encode( $filelist ) }}&genome=";
+@else
+ var gbUrl = "http://epigenomegateway.wustl.edu/browser/?datahub={{ $protocol .'://'. $_SERVER['HTTP_HOST']. '/gbrowser1/'. RBase64::encode( $filelist ) }}&genome=";
+@endif
window.open(gbUrl + gb);
return false;
});
diff --git a/public/themes/dreg/assets/img/dTOX-model.png b/public/themes/dreg/assets/img/dTOX-model.png
new file mode 100644
index 0000000..906fa45
Binary files /dev/null and b/public/themes/dreg/assets/img/dTOX-model.png differ
diff --git a/public/themes/dreg/assets/img/dreg-dtox-gateway.png b/public/themes/dreg/assets/img/dreg-dtox-gateway.png
new file mode 100644
index 0000000..798a04e
Binary files /dev/null and b/public/themes/dreg/assets/img/dreg-dtox-gateway.png differ
diff --git a/public/themes/dreg/assets/img/dtox.create.exp.png b/public/themes/dreg/assets/img/dtox.create.exp.png
new file mode 100644
index 0000000..3601c78
Binary files /dev/null and b/public/themes/dreg/assets/img/dtox.create.exp.png differ
diff --git a/public/themes/dreg/assets/img/dtox.create.exp2.png b/public/themes/dreg/assets/img/dtox.create.exp2.png
new file mode 100644
index 0000000..c4d0843
Binary files /dev/null and b/public/themes/dreg/assets/img/dtox.create.exp2.png differ
diff --git a/public/themes/dreg/partials/about.blade.php b/public/themes/dreg/partials/about.blade.php
index 53b8c4e..d485a2d 100755
--- a/public/themes/dreg/partials/about.blade.php
+++ b/public/themes/dreg/partials/about.blade.php
@@ -3,14 +3,27 @@
<h1 class="text-center top-space">About dREG gateway</h1>
<p dir="ltr">
The <A title="dREG gateway" href="http://dreg.dnasequence.org">dREG gateway</A>
-is a cloud service that predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The hosted service is developed by the Danko lab at the Baker Institute and Cornell University and supported by the <A title="SciGaP" href="http://www.scigap.org">SciGap</A> (Science Gateway Platform as a Service) and <A title="XSEDE" href="http://www.xsede.org">XSEDE</A> (Extreme Science and Engineering Discovery Environment).
+is a cloud platform that hosts two bioinformatics online services for functional analysis of sequencing data, dREG transcriptional regulatory element peak calling and dTOX transcription factor binding prediction. These online services are developed by the Danko lab at the Baker Institute and Cornell University and supported by the <A title="SciGaP" target=_blank href="http://www.scigap.org">SciGap</A> (Science Gateway Platform as a Service) and <A title="XSEDE" target=_blank href="http: [...]
</p>
- <p dir="ltr"><A title="SciGaP" href="http://www.scigap.org">SciGaP</A> supports access to core infrastructure services required by Science Gateways, including: user identity, accounts, authorization, and access to multiple computational resources from XSEDE. </p>
- <p dir="ltr"><A title="XSEDE" href="http://www.xsede.org">XSEDE</A> provides GPU resources under the project (TG-BIO160048: dREG Science Gateway).</p>
+ <p dir="ltr">The gateway is built on the infrastructure services of SciGaP and the computional resources of XSEDE as the following architecture, the details can be found in this paper: <A target=_blank href="https://dl.acm.org/citation.cfm?id=3219141">"Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata"</A>. In PEARC 2018: Practice and Experience in Advanced Research Computing, July 22-26, 2018, Pittsburgh, PA, USA.
+
+ <p dir="ltr"><A title="SciGaP" target=_blank href="http://www.scigap.org">SciGaP</A> supports access to core infrastructure services required by Science Gateways, including: user identity, accounts, authorization, and access to multiple computational resources from XSEDE. </p>
+ <p dir="ltr"><A title="XSEDE" target=_blank href="http://www.xsede.org">XSEDE</A> provides GPU resources under the project (TG-BIO160048 and TG-BIO180027: dREG Science Gateway).</p>
+
+ <div>
+ <img id="myImg" alt="dREG Gateway" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg-dtox-gateway.png" style="display: block;margin-left: auto; margin-right: auto; width:80%"></img>
+ <p class="text-center"><small> Gateway Architecture</small></p>
+
+ <div id="myModal" class="modal" onkeypress="document.getElementById('myModal').style.display='none'" >
+ <span class="close" onclick="document.getElementById('myModal').style.display='none'">×</span>
+ <img class="modal-content" id="img01">
+ <div id="caption"></div>
+ </div>
<h1 class="text-center top-space">About Danko Lab</h1>
- <p dir="ltr"><A title="Danko Lab" href="http://www.dankolab.org">Danko Lab</A> at the Cornell University studies how gene expression programs are encoded in mammalian DNA sequences, and how these ‘regulatory codes’ contribute to evolution, development, and disease. Our specialty is developing statistics and machine-learning approaches to analyze genomic sequencing data, prepared using DNase-I-seq, ATAC-seq, PRO-seq, RNA-seq, and related assays. Our tools borrow a wide variety of ideas [...]
-
+ <p dir="ltr"><A title="Danko Lab" href="http://www.dankolab.org">Danko Lab</A>
+at Cornell University studies how gene expression programs are encoded in mammalian DNA sequences, and how these 'regulatory codes' contribute to evolution, development, and disease. Our specialty is developing statistics and machine-learning approaches to analyze genomic sequencing data, prepared using DNase-I-seq, ATAC-seq, PRO-seq, RNA-seq, and related assays. Our tools borrow a wide variety of ideas from the fields of statistics and machine-learning, including recent uses of hidden M [...]
+
<h1 class="text-center top-space">About Apache Airavata</h1>
<p dir="ltr"><A title="Apache Airavata" href="http://airavata.apache.org/">Apache Airavata</A>
is a software framework that enables you to compose, manage, execute, and monitor large scale applications and workflows on distributed computing resources such as local clusters, supercomputers, computational grids, and computing clouds. </p>
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index edb984b..dd70744 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -1,15 +1,15 @@
<div class="container">
<div class="content">
<div class="text-center">
- <h2 class="title top-space">Documentation</h2>
+ <h2 class="title top-space">dREG Documentation</h2>
</div>
<ul class="nav nav-tabs nav-justified" role="tablist">
<li role="presentation" class="active"><a href="#instructure" role="tab" data-toggle="tab">Instructions</a></li>
- <li role="presentation"><a href="#sp" role="tab" data-toggle="tab">Software/Package</a></li>
<li role="presentation"><a href="#input" role="tab" data-toggle="tab">Input</a></li>
<li role="presentation"><a href="#output" role="tab" data-toggle="tab">Output</a></li>
- </ul>
+ <li role="presentation"><a href="#faq" role="tab" data-toggle="tab">FAQ</a></li>
+</ul>
<div class="tab-content">
<div role="tabpanel" class="tab-pane active" id="instructure">
@@ -49,7 +49,7 @@ Click the 'save and launch' button. BigWig file are transferred to the XSEDE se
<p class="description" style="padding:16px">
6) <b>Check the status</b><br>
-The user can check the status of their 'experiment' by clicking the menu 'Saved dREG runs' below the dREG logo.
+The user can check the status of their 'experiment' by clicking the menu 'Saved runs' below the dREG logo.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment browse" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.list.png"></img></div>
@@ -119,28 +119,6 @@ After the experiment is complete, no results can be downloaded and job status sh
</div>
-<!---- SOFTWARE PANEL -->
- <div role="tabpanel" class="tab-pane" id="sp">
- <div class="row">
- <div class="col-sm-offset-1 col-sm-10 col-xs-12">
- <p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p>
-
- <p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG">https://github.com/Danko-Lab/dREG</A>.</p>
- <p class="description">
-The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p>
- <p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD">https://github.com/Danko-Lab/dREG.HD</A>.</p>
- <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p>
- <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm">https://github.com/Danko-Lab/Rgtsvm</A>.</p>
- <p class="description">
-Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p>
-
- <p class="description">[4] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p> <p class="description">
-Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE.
-</p>
-
- </div>
- </div>
- </div>
<!---- INPUT PANEL -->
@@ -308,6 +286,71 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
</div>
</div>
+<!---- FAQ PANEL -->
+
+
+ <div role="tabpanel" class="tab-pane" id="faq">
+ <div class="row">
+ <div class="col-sm-offset-1 col-sm-10 col-xs-12">
+
+<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
+
+<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
+<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0"> here </A>.</p>
+
+<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
+<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
+
+<p><b>Q: Which browser works well with the dREG gateway?</b></p>
+<p>A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.</p>
+
+
+<p><b>Q: What should the Safari users be aware of?</b></p>
+<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br>
+Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab".
+</p>
+
+<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
+<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p>
+
+<p><b>Q: Will the dREG gateway work with my data type?</b></p>
+<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p>
+
+<p><b>Q: Will the pre-trained models work using data from my species?</b></p>
+<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
+
+<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p>
+<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
+
+<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
+<p>A: One month.</p>
+
+<p><b>Q: How to I cite the dREG gateway?</b></p>
+<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
+<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
+(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">
+(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P>
+
+
+<p><b>Q: Do I have to create account before using this service?</b></p>
+<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
+
+<p><b>Q: How do I know the status of the computational nodes? </b></p>
+<p>A: Since we can't update this web site very often, the gateway status is updated <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md">here</A> on the dREG page based on the notifications of the XSEDE community. </p>
+
+<p><b>Q: Who do I thank for the computing power? </b></p>
+<p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org">SciGaP</A> and <A title="Apache Airavata" href="http://airavata.apache.org/">Apache Airavata</A> and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>.</p>
+
+<p><b>Q: I have another question that is not on this FAQ. How can I contact you?</b></p>
+<p>A: Yes, please contact us with any questions! Zhong(zw355 at cornell.edu). Charles(cgd24 at cornell.edu).</p>
+
+
+ </div>
+ </div>
+</div>
+
+<!---- OUTPUT PANEL -->
</div><!-- /.content -->
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/dtox-doc.blade.php
similarity index 72%
copy from public/themes/dreg/partials/doc.blade.php
copy to public/themes/dreg/partials/dtox-doc.blade.php
index edb984b..d54bdea 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/dtox-doc.blade.php
@@ -1,46 +1,46 @@
<div class="container">
<div class="content">
<div class="text-center">
- <h2 class="title top-space">Documentation</h2>
+ <h2 class="title top-space">dTOX Documentation</h2>
</div>
<ul class="nav nav-tabs nav-justified" role="tablist">
<li role="presentation" class="active"><a href="#instructure" role="tab" data-toggle="tab">Instructions</a></li>
- <li role="presentation"><a href="#sp" role="tab" data-toggle="tab">Software/Package</a></li>
<li role="presentation"><a href="#input" role="tab" data-toggle="tab">Input</a></li>
<li role="presentation"><a href="#output" role="tab" data-toggle="tab">Output</a></li>
- </ul>
+ <li role="presentation"><a href="#faq" role="tab" data-toggle="tab">FAQ</a></li>
+</ul>
<div class="tab-content">
<div role="tabpanel" class="tab-pane active" id="instructure">
<div class="row">
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
<p class="description" style="padding:16px">
- 1) <b>Login</b>:<br>
+ 1) <b>Login</b>:(same as dREG)<br>
The user needs to log in by clicking 'login' link at the top-right corner of the page. Having an account provides a number of benefits, and is free and easy.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG login" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.login.png" ></img></div>
<p class="description" style="padding:16px">
- 2) <b>Create a new project (optional)</b><br>
-Optionally, users can choose to make a new 'project' in the dREG gateway to archive a collection of dREG data from related experiments. This will allow a collection of experiments to be stored in close proximity to each other.</p>
+ 2) <b>Create a new project (optional, same as dREG)</b><br>
+Optionally, users can choose to make a new 'project' in the dREG/dTOX gateway to archive a collection of sequencing data from related experiments. This will allow a collection of experiments to be stored in close proximity to each other.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG project" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.project.png" ></img></div>
<p class="description" style="padding:16px">
- 3) <b>Start new dREG</b><br>
-Select the menu 'Start dREG' below the dREG logo to create an data analysis for your data, as the following screenshot.
+ 3) <b>Start new dTOX</b><br>
+Select the menu 'Start dREG/dTOX' below the dREG logo to create an data analysis for your data, as the following screenshot. Please notice to select the "dTOX prediction" Application.
</p>
-<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.exp.png" ></img></div>
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dtox.create.exp.png" ></img></div>
<p class="description" style="padding:16px">
- 4) <b>Select bigWig files</b><br>
-Select bigWig files representing PRO-seq, GRO-seq, or ChRO-seq signal on the plus and minus strand. Please notice that two GPU resources are available now, currently it is easier to get the computation resources on <A href="http://comet.sdsc.xsede.org/">Comet.sdsc.xsede.org</A> than <A href="https://www.psc.edu/index.php/bridges">Bridges.psc.edu</A>.
+ 4) <b>Fill experiment form</b><br>
+Select bigWig files representing PRO-seq, ATAC-seq, or dNase-I-seq signal on the plus and minus strand. Please notice that two GPU resources are available now, currently it is easier to get the computation resources on <A href="http://comet.sdsc.xsede.org/">Comet.sdsc.xsede.org</A> than <A href="https://www.psc.edu/index.php/bridges">Bridges.psc.edu</A>.
</p>
-<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment create" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.exp2.png" ></img></div>
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment create" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dtox.create.exp2.png" ></img></div>
<p class="description" style="padding:16px">
5) <b>Submit the job</b><br>
@@ -49,7 +49,7 @@ Click the 'save and launch' button. BigWig file are transferred to the XSEDE se
<p class="description" style="padding:16px">
6) <b>Check the status</b><br>
-The user can check the status of their 'experiment' by clicking the menu 'Saved dREG runs' below the dREG logo.
+The user can check the status of their 'experiment' by clicking the menu 'Saved runs' below the dREG logo.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment browse" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.list.png"></img></div>
@@ -119,29 +119,6 @@ After the experiment is complete, no results can be downloaded and job status sh
</div>
-<!---- SOFTWARE PANEL -->
- <div role="tabpanel" class="tab-pane" id="sp">
- <div class="row">
- <div class="col-sm-offset-1 col-sm-10 col-xs-12">
- <p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p>
-
- <p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG">https://github.com/Danko-Lab/dREG</A>.</p>
- <p class="description">
-The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p>
- <p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD">https://github.com/Danko-Lab/dREG.HD</A>.</p>
- <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p>
- <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm">https://github.com/Danko-Lab/Rgtsvm</A>.</p>
- <p class="description">
-Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p>
-
- <p class="description">[4] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p> <p class="description">
-Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE.
-</p>
-
- </div>
- </div>
- </div>
-
<!---- INPUT PANEL -->
<div role="tabpanel" class="tab-pane" id="input">
@@ -209,26 +186,17 @@ Airavata PHP Gateway provides an API to build web sites which interact with high
<th>Description</th>
</tr>
<tr>
- <td>$PREFIX.dREG.infp.bed.gz</td>
- <td>Informative positions with dREG scores predicted by the dREG model. Decompress it with 'gunzip' in Linux.</td>
+ <td>$PREFIX.dTOX.full.bed.gz</td>
+ <td>TFBS regions with full information including chromosome, start, ending, MOTIF ID, RTFBSDB score, strand, Transcription factor, dTOX score, bound status. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
- <td>$PREFIX.dREG.peak.full.bed.gz</td>
- <td>Significant peaks (FDR < 0.05) with dREG scores, p-values and center positions where the maximum dREG scores are located. Decompress it with 'gunzip' in Linux.</td>
- </tr>
- <tr>
- <td>$PREFIX.dREG.peak.score.bed.gz</td>
- <td>Significant peaks (FDR < 0.05) only with dREG scores. Decompress it with 'gunzip' in Linux.</td>
- </tr>
-
- <tr>
- <td>$PREFIX.dREG.peak.prob.bed.gz</td>
- <td>Significant peaks (FDR < 0.05) only with p-values. Decompress it with 'gunzip' in Linux.</td>
+ <td>$PREFIX.dTOX.bound.bed.gz</td>
+ <td>TFBS regions only with bound status. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
- <td>$PREFIX.dREG.raw.peak.bed.gz</td>
- <td>All raw peaks generated by dREG peak calling, including dREG scores, uncorrected p-values, center positions where the maximum are located in smoothed curves, center positions where the maximim are lcoated in original curve, centroid. Only available in the Web storage.</td>
+ <td>$PREFIX.dTOX.rtfbsdb.bed.gz</td>
+ <td>>TFBS regions only with RTFBSDB score. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
@@ -249,11 +217,11 @@ border-color: #dadada;" data-expandable-box-container="true">
<p><b>Informative position:</b>
Loci denoted as "informative positions" meet the following criteria: contain more than 3 reads in 100 bp interval on either strand, or more than 1 read in 1Kbp interval on both strands. Informative positions are used to predict the dREG scores for TRE (Transcription Regulatory Element) identification. </p>
-<p><b>dREG score:</b>
+<p><b>dTOX score:</b>
Training and prediction is done using a Support Vector Regression model where a label of 1 indicates RNA polymerase II initialization or transciption through the informative position. The predicted values from the pre-trained model are called dREG scores. A dREG score close to 1 indicates that a position likely a TRE.
</p>
-<p><b>Peak p-value:</b>
+<p><b>RTFBSDB score:</b>
We test 5 dREG scores around each candidate peak center using the NULL hypothesis that each point within this peak is drawn from the non-TRE distribution. This test estimates the statistical confidence of each candidate dREG peak. In the final result, FDR is applied to do multiple correction and only the peaks with adjusted p-value < 0.05 are reported.
</p>
@@ -270,19 +238,11 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
<tr>
<th>File name</th> <th>Description</th> </tr>
<tr>
- <td>$PREFIX.dREG.infp.bw</td>
- <td>The bigWig file converted from the bed file of informative positions ($PREFIX.dREG.infp.bed.gz).</td>
- </tr>
<tr>
- <td>$PREFIX.dREG.peak.score.bw</td>
+ <td>$PREFIX.dTOX.bound.bw</td>
<td>The bigWig file converted from the significant peaks (FDR < 0.05) with dREG scores ($PREFIX.dREG.peak.score.bed.gz).</td>
</tr>
- <tr>
- <td>$PREFIX.dREG.peak.prob.bw</td>
- <td>The bigWig file converted from the significant peaks (FDR < 0.05) with p-values ($PREFIX.dREG.peak.prob.bed.gz). </td>
- </tr>
-
- <tr>
+ <tr>
<td>*.bed.gz.tbi</td>
<td> The index files generated from the corresponding bed files. Please ignore them if you download the results.</td>
</tr>
@@ -295,7 +255,7 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
<tr>
<th>File name</th> <th>Description</th> </tr>
<tr>
- <td>$PREFIX.dREG.log</td>
+ <td>$PREFIX.dTOX.log</td>
<td>Print the summary information after peak calling. If the bigWigs don't meet the requirements of dREG, the warning information will be outputted in this file.
</td>
</tr>
@@ -308,6 +268,71 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
</div>
</div>
+<!---- FAQ PANEL -->
+
+
+ <div role="tabpanel" class="tab-pane" id="faq">
+ <div class="row">
+ <div class="col-sm-offset-1 col-sm-10 col-xs-12">
+
+<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
+
+<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
+<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0"> here </A>.</p>
+
+<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
+<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
+
+<p><b>Q: Which browser works well with the dREG gateway?</b></p>
+<p>A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.</p>
+
+
+<p><b>Q: What should the Safari users be aware of?</b></p>
+<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br>
+Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab".
+</p>
+
+<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
+<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p>
+
+<p><b>Q: Will the dREG gateway work with my data type?</b></p>
+<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p>
+
+<p><b>Q: Will the pre-trained models work using data from my species?</b></p>
+<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
+
+<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p>
+<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
+
+<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
+<p>A: One month.</p>
+
+<p><b>Q: How to I cite the dREG gateway?</b></p>
+<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
+<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
+(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">
+(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P>
+
+
+<p><b>Q: Do I have to create account before using this service?</b></p>
+<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
+
+<p><b>Q: How do I know the status of the computational nodes? </b></p>
+<p>A: Since we can't update this web site very often, the gateway status is updated <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md">here</A> on the dREG page based on the notifications of the XSEDE community. </p>
+
+<p><b>Q: Who do I thank for the computing power? </b></p>
+<p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org">SciGaP</A> and <A title="Apache Airavata" href="http://airavata.apache.org/">Apache Airavata</A> and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>.</p>
+
+<p><b>Q: I have another question that is not on this FAQ. How can I contact you?</b></p>
+<p>A: Yes, please contact us with any questions! Zhong(zw355 at cornell.edu). Charles(cgd24 at cornell.edu).</p>
+
+
+ </div>
+ </div>
+</div>
+
+<!---- OUTPUT PANEL -->
</div><!-- /.content -->
diff --git a/public/themes/dreg/partials/header.blade.php b/public/themes/dreg/partials/header.blade.php
index 043860d..a470341 100755
--- a/public/themes/dreg/partials/header.blade.php
+++ b/public/themes/dreg/partials/header.blade.php
@@ -19,11 +19,12 @@ color:blue;
<div class="collapse navbar-collapse" >
<ul class="nav navbar-nav navbar-right">
<li><a class="scroll hidden" href="#home"></a></li>
-
<li><a class="scroll" @if( $_SERVER['REQUEST_URI'] === "/" ) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/">Home</a></li>
+ <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">dREG Documentation</a></li>
+ <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/dtox-doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/dtox-doc">dTOX dcumentation</a></li>
+ <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/software") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/software">Software/Package</a></li>
<li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/about") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/about">About</a></li>
- <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">Documentation</a></li>
- <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/faq") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/faq">FAQ</a></li>
+
<!--
@if(! Session::has('loggedin'))
<li><a class="scroll" href="{{ URL::to('/') }}/create">Create Account</a></li>
diff --git a/public/themes/dreg/partials/software.blade.php b/public/themes/dreg/partials/software.blade.php
new file mode 100755
index 0000000..686983c
--- /dev/null
+++ b/public/themes/dreg/partials/software.blade.php
@@ -0,0 +1,58 @@
+<div class="container">
+
+
+<h1 class="text-center top-space">Software/Package</h1>
+<div class="post-entry">
+
+ <p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p>
+
+ <p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG">https://github.com/Danko-Lab/dREG</A>.</p>
+ <p class="description">
+The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p>
+
+ <p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD">https://github.com/Danko-Lab/dREG.HD</A>.</p>
+ <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p>
+
+ <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm">https://github.com/Danko-Lab/Rgtsvm</A>.</p>
+ <p class="description">
+Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p>
+
+ <p class="description">[4] <B>rtfbsdb package</B>: <A href="https://github.com/Danko-Lab/rtfbs_db">https://github.com/Danko-Lab/rtfbs_db</A>.</p>
+ <p class="description">
+Rtfbsdb implements TFBS scaning acorss whole genome and TF enrichment test with the aid of CIS-BP, Jolma and other TF databases.
+ </p>
+
+ <p class="description">[5] <B>tfTarget package</B>: <A href="https://github.com/Danko-Lab/tfTarget">https://github.com/Danko-Lab/tfTarget</A>.</p>
+ <p class="description">
+Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data.
+ </p>
+
+ <p class="description">[6] <B>Proseq 2.0</B>: <A href="https://github.com/Danko-Lab/proseq2.0">https://github.com/Danko-Lab/proseq2.0</A>.</p>
+ <p class="description">
+Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing.
+ </p>
+
+ <p class="description">[7] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p>
+ <p class="description">
+Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE.
+ </p>
+
+</div>
+<!-- end of .post-entry -->
+
+<br style="clear:both"/>
+<hr style="color:green"/>
+
+</div>
+
+<div class="col-md-12 text-center" style=" padding: 20px 0 20px 0; background-color:#FFFFFF">
+ <a href="http://airavata.apache.org/" target="_blank">
+ <img width="200px" src="{{URL::to('/')}}/themes/{{Session::get('theme')}}/assets/img/poweredby-airavata-logo.png">
+ </a>
+ <a href="http://www.nsf.gov/" target="_blank" class="logo-seperation">
+ <img width="200px" src="{{URL::to('/')}}/themes/{{Session::get('theme')}}/assets/img/nsf-logo.png">
+ </a>
+ <a href="https://www.xsede.org/" target="_blank" class="logo-seperation">
+ <img width="200px" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/powered-by-xsede.gif">
+ </a>
+</div>
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index 8dff7b8..0110898 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -1,28 +1,64 @@
<link media="all" type="text/css" rel="stylesheet" href="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/css/zoom.css"/>
<div class="col-md-offset-2 col-md-8 breathing-space scigap-info" >
- <h1 class="text-center">Welcome to dREG gateway!</h1>
- <p class="text-center" style="color:#cccccc;">
- Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.<br/>
- </p>
- <p class="text-center" style="color:#444444;">
-The gateway status and updates are <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md"><B>here!</b></A>
-</p>
- <hr/>
-
- <div class="col-md-5" style="margin-left: 5%">
- <H2> How does it work?</H2>
- <p style="font-size:14px; margin-top:20px; text-align:justify">
-The dREG gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses pre-trained dREG and dREG-HD models to identify divergent transcript start sites and impute the predicted DNase-1 hypersensitivity signal across the genome. The dREG gateway uses pre-trained models that work in any mammalian organism (other or [...]
-<img id="myImg" alt="dREG Gateway" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-works.png" style="width:100%"></img>
-<p class="text-center"><small>Click the figure to enlarge it</small></p>
-
-<div id="myModal" class="modal" onkeypress="document.getElementById('myModal').style.display='none'" >
- <span class="close" onclick="document.getElementById('myModal').style.display='none'">×</span>
- <img class="modal-content" id="img01">
- <div id="caption"></div>
+ <h1 class="text-center">Welcome to dREG and dTOX gateway!</h1>
+ <p class="text-center" style="color:#cccccc;">
+ Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.<br/>
+ </p>
+ <p class="text-center" style="color:#444444;">
+ The gateway status and updates are <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md"><B>here!</b></A>
+ </p>
+ <hr/>
+
+<div class="col-md-offset-1 col-md-5" style="margin-left: 5%" >
+ <H2> How is dREG used?</H2>
+ <p style="font-size:14px; margin-top:10px; text-align:justify">
+ The dREG model in the gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses pre-trained dREG model to identify divergent transcript start sites and impute the predicted DNase-1 hypersensitivity signal across the genome. The current dREG model works in any mammalian organism.</p>
+ <p style="font-size:14px; margin-top:10px;text-align:justify">
+Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p>
+
+ <p style="font-size:14px; margin-top:5px;text-align:justify">
+ <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
+ Use the Danko lab's <b>mapping pipeline</b> (<A target=_blank href="https://github.com/Danko-Lab/proseq2.0">here</A>) to prepare bigWig files from fastq files or <b>convert BAM files</b> of mapped reads to bigWig (<A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">here</A>).
+ </p>
+
+ <p style="font-size:14px; margin-top:5px;text-align:justify">
+ <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
+ See our <A href="{{ URL::to('/') }}/pages/doc#faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/doc">documentation</a> or <A target=_blank href="https://www.dropbox.com/s/jzlamnd0mej0z76/Chu.dREG_protocol.pdf?dl=0">dREG protocol manuscript</A> for additional questions.</p>
+
+ <img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img>
+ <p class="text-center"><small>Click the figure to enlarge it</small></p>
+ <div id="myModal2" class="modal" onkeypress="document.getElementById('myModal2').style.display='none'" >
+ <span class="close" onclick="document.getElementById('myModal2').style.display='none'">×</span>
+ <img class="modal-content" id="img02">
+ <div id="caption"></div>
+ </div>
+</div>
+
+
+<div class="col-md-offset-1 col-md-5" style="margin-left: 5%">
+ <H2> How is dTOX used? </H2>
+ <p color="red">Under construction, please ignore this section! </p>
+ <p style="font-size:14px; margin-top:10px;text-align:justify">
+The dTOX models in the gateway predict the binding status of transcription factor binding sites using PRO-seq, ATAC-seq, or DNase-1-seq data. The server takes as input bigWig files provided by the user, which represent the PRO-seq, ATAC-seq, or DNase-1-seq signal on the plus and minus strand. Once the user selects the transcription factors to predict on, the gateway uses a pre-trained dTOX model to identify transcription factor binding patterns. The current dTOX models work in any mammal [...]
+ <p style="font-size:14px; margin-top:10px;text-align:justify">
+The web operations are same as the dREG model. Users need to login -> upload data -> run data. Results can be downloaded or viewed in the WashU Genome browser.</p>
+
+ <p style="font-size:14px; margin-top:5px;text-align:justify">
+ <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
+ See our <A href="{{ URL::to('/') }}/pages/dtox-doc#faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/dtox-doc">documentation</a> for additional questions.
+ </p>
+
+ <img id="myImg3" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dTOX-model.png" style="width:100%"></img>
+ <p class="text-center"><small>Click the figure to enlarge it</small></p>
+ <div id="myModal3" class="modal" onkeypress="document.getElementById('myModal3').style.display='none'" >
+ <span class="close" onclick="document.getElementById('myModal3').style.display='none'">×</span>
+ <img class="modal-content" id="img03">
+ <div id="caption"></div>
+ </div>
</div>
+
<script>
// Get the modal
var modal = document.getElementById('myModal');
@@ -43,29 +79,6 @@ span.onclick = function() {
}
</script>
- </div>
-
- <div class="col-md-offset-1 col-md-5" style="margin-left: 5%">
- <H2> How is it used?</H2>
- <p style="font-size:14px; margin-top:20px;text-align:justify">
-Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p>
-
-<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
-Use the Danko lab's <b>mapping pipeline</b> (<A target=_blank href="https://github.com/Danko-Lab/proseq2.0">here</A>) to prepare bigWig files from fastq files or <b>convert BAM files</b> of mapped reads to bigWig (<A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">here</A>).
-</p>
-
-<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
-See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/doc">documentation</a> or <A target=_blank href="https://www.dropbox.com/s/jzlamnd0mej0z76/Chu.dREG_protocol.pdf?dl=0">dREG protocol manuscript</A> for additional questions.
-</p>
-<img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img>
-<p class="text-center"><small>Click the figure to enlarge it</small></p>
-<div id="myModal2" class="modal" onkeypress="document.getElementById('myModal2').style.display='none'" >
- <span class="close" onclick="document.getElementById('myModal2').style.display='none'">×</span>
- <img class="modal-content" id="img02">
- <div id="caption"></div>
-</div>
<script>
// Get the modal
@@ -87,11 +100,40 @@ span.onclick = function() {
}
</script>
- </div>
+<script>
+// Get the modal
+var modal = document.getElementById('myModal3');
+// Get the image and insert it inside the modal - use its "alt" text as a caption
+var img = document.getElementById('myImg3');
+var modalImg = document.getElementById("img03");
+var captionText = document.getElementById("caption");
+img.onclick = function(){
+ modal.style.display = "block";
+ modalImg.src = this.src;
+ captionText.innerHTML = this.alt;
+}
+// Get the <span> element that closes the modal
+var span = document.getElementsByClassName("close")[0];
+// When the user clicks on <span> (x), close the modal
+span.onclick = function() {
+ modal.style.display = "none";
+}
+</script>
+
<br style="clear:both"/>
<hr style="color:green"/>
+<h1 class="text-center">Gateway Introduction</h1>
+
+<div style="width: 92%; margin-left: 5%; padding-left:15px">
+<p>
+The dREG gateway is a cloud platform developed by the <A target=_blank href="http://www.dankolab.org/">Danko lab</a> at the <A target=_blank href="https://www2.vet.cornell.edu/departments-centers-and-institutes/baker-institute">Baker Institute</A>, <A target=_blank href="http://www.cornell.edu">Cornell University</A> and supported by the <A target=_blank href="https://www.scigap.org/">SciGap</A> (Science Gateway Platform as a Service) and <A target=_blank href="https://www.xsede.org/">XS [...]
+Currently, this gateway hosts two bioinformatics services for functional analysis of sequencing data, dREG transcriptional regulatory element peak calling and dTOX transcription factor binding prediction. Both services take as input files (either PRO-seq, GRO-seq, ATAC-seq or DNase-1-seq) provided by the user, and then uses pre-trained models to conduct prediction and post-processing on GPU computing nodes. The architecture and details are <A href="{{ URL::to('/') }}/pages/about">here</a>.
+</div>
+
+<hr style="color:green"/>
+
<h1 class="text-center">Publications</h1>
<div style="width: 92%; margin-left: 5%; padding-left:15px">
<table>
[airavata-php-gateway] 07/14: update for document and faq page
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 2cdda18ac7490943581b4ecd4b434518ae08faac
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Sep 24 20:04:36 2018 +0000
update for document and faq page
---
public/themes/dreg/partials/doc.blade.php | 76 ++++++++++++++++++++++++++-----
public/themes/dreg/partials/faq.blade.php | 26 ++++++++---
2 files changed, 85 insertions(+), 17 deletions(-)
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index 9859deb..007ce1b 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -54,20 +54,22 @@ The user can check the status of their 'experiment' by clicking the menu 'Saved
<p class="description" style="padding:16px">
7) <b>Check the results</b><br>
-Once a job is completed, the user can select 'Full results' in the drop-down list and then click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed by th [...]
-
-</p>
+Once a job is completed, the user can select 'Full results' in the drop-down list and then LEFT-click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed [...]
+</br>
+In <font color="RED">Safari</font>, it could be problematic because Safari tries to unzip the compressed results automatically using a non-compatible compress method. Please check <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature.</p>
+
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div>
<p class="description" style="padding:16px">
8) <b>Switch to Genome Browser</b><br>
-The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Switch to genome browser'</B> link. </p>
+The convenient tool provided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Switch to genome browser'</B> link. The genome identifier must be specified by two ways, 1) select from the drop-down list or 2) fill the identifier in the textbox. Please use LEFT-click to open a genome browser window.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.gbview.png"></img></div>
<p class="description" style="padding:16px">
9) <b>Check the storage</b><br>
-the user can click <b>'Open Folder'</b> link in the experiment summary page to check the storage for the current job or click the menu 'Storage' under the dREG logo to check the folders and files for all jobs(experiments). The following figure shows the data files in the job's folder, including two bigWig files, one result in bedgraph format, two outputs of job scheduler on GPU nodes.</p>
+The user can LEFT-click <b>'Open Folder'</b> link in the experiment summary page to check the storage for the current job or click the menu 'Storage' under the dREG logo to check the folders and files for all jobs(experiments).
+The following figure shows the data files in the job's folder, including two bigWig files, one result in bedgraph format, two outputs of job scheduler on GPU nodes.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.folder.png"></img></div>
@@ -144,7 +146,7 @@ Airavata PHP Gateway provides an API to build web sites which interact with high
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
<p class="description">
-dREG run generates a compressed file including the dREG and dREG.HD results as follows:
+1) dREG run generates a compressed file including the <font color="green"> dREG results </font> as follows:
</p>
<p class="description"> </p>
@@ -155,23 +157,75 @@ dREG run generates a compressed file including the dREG and dREG.HD results as f
</tr>
<tr>
<td>$PREFIX.dREG.infp.bed.gz</td>
- <td>Informative positions with the scores predicted by the dREG model. <BR>Decompress it with 'gunzip' in Linux.</td>
+ <td>Informative positions with dREG scores predicted by the dREG model. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
<td>$PREFIX.dREG.peak.full.bed.gz</td>
- <td>dREG peaks calling results with score, probability and center position information. <BR>Decompress it with 'gunzip' in Linux.</td>
+ <td>Significant peaks (FDR < 0.05) with dREG scores, p-values and center positions where the maximum dREG scores are located. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
<td>$PREFIX.dREG.peak.score.bed.gz</td>
- <td>dREG peaks calling results only with score. <BR>Decompress it with 'gunzip' in Linux.</td>
+ <td>Significant peaks (FDR < 0.05) only with dREG scores. Decompress it with 'gunzip' in Linux.</td>
+ </tr>
+
+ <tr>
+ <td>$PREFIX.dREG.peak.prob.bed.gz</td>
+ <td>Significant peaks (FDR < 0.05) only with p-values. Decompress it with 'gunzip' in Linux.</td>
</tr>
+
+ <tr>
+ <td>$PREFIX.dREG.raw.peak.bed.gz</td>
+ <td>All raw peaks generated by dREG peak calling, including dREG scores, uncorrected p-values, center positions where the maximum are located in smoothed curves, center positions where the maximim are lcoated in original curve, centroid. Only available in the Web storage.</td>
+ </tr>
+
<tr>
<td>$PREFIX.tar.gz</td>
- <td>Including above 3 files, can be decompressed by 'tar -xvzf' in Linux.</td>
+ <td>Including above 5 files, can be decompressed by 'tar -xvzf' in Linux.</td>
</tr>
</table>
+ <p class="description">
+2) In the Web storage folder there are <font color="green">some files required by the WashU</font> genome browser:
+</p>
+<p class="description"> </p>
+ <table class="table">
+ <tr>
+ <th>File name</th> <th>Description</th> </tr>
+ <tr>
+ <td>$PREFIX.dREG.infp.bw</td>
+ <td>The bigWig file converted from the bed file of informative positions ($PREFIX.dREG.infp.bed.gz).</td>
+ </tr>
+ <tr>
+ <td>$PREFIX.dREG.peak.score.bw</td>
+ <td>The bigWig file converted from the significant peaks (FDR < 0.05) with dREG scores ($PREFIX.dREG.peak.score.bed.gz).</td>
+ </tr>
+ <tr>
+ <td>$PREFIX.dREG.peak.prob.bw</td>
+ <td>The bigWig file converted from the significant peaks (FDR < 0.05) with p-values ($PREFIX.dREG.peak.prob.bed.gz). </td>
+ </tr>
- </div>
+ <tr>
+ <td>*.bed.gz.tbi</td>
+ <td> The index files generated from the corresponding bed files. Please ignore them if you download the results.</td>
+ </tr>
+ </table>
+
+ <p class="description">
+3) There are <font color="green">two log files </font> in the Web storage folder:</p>
+<p class="description"> </p>
+ <table class="table">
+ <tr>
+ <th>File name</th> <th>Description</th> </tr>
+ <tr>
+ <td>$PREFIX.dREG.log</td>
+ <td>Print the summary information after peak calling. If the bigWigs don't meet the requirements of dREG, the warning information will be outputted in this file.
+ </td>
+ </tr>
+ <tr>
+ <td>slurm-??????.out</td>
+ <td>The verbose logging output of dREG package.</td>
+ </tr>
+ </table>
+ </div>
</div>
</div>
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index fd0bb4e..7550bc9 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -5,25 +5,36 @@
<div class="post-entry">
<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
-<p><b>Q: Which browser works well with the dREG gateway?</b></p>
-<p>A: We have tested in the Firefox and Google Chrome so far. In IE (version 10 or 11) or Safari, WashU geneome browser doesn't work.</p>
-
<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
-<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> here </A>.</p>
+<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0"> here </A>.</p>
<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
+<p><b>Q: Which browser works well with the dREG gateway?</b></p>
+<p>A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.</p>
+
+
+<p><b>Q: What should the Safari users be aware of?</b></p>
+<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br>
+Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab".
+</p>
+
<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
-<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called ‘active’ class of enhancers and promoters. </p>
+<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p>
+
<p><b>Q: Will the dREG gateway work with my data type?</b></p>
<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p>
+
<p><b>Q: Will the pre-trained models work using data from my species?</b></p>
-<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species . We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
+<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
+
<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p>
<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
+
<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
<p>A: One month.</p>
+
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
@@ -34,10 +45,13 @@
<p><b>Q: Do I have to create account before using this service?</b></p>
<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
+
<p><b>Q: How do I know the status of the computational nodes? </b></p>
<p>A: Since we can't update this web site very often, the gateway status is updated <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md">here</A> on the dREG page based on the notifications of the XSEDE community. </p>
+
<p><b>Q: Who do I thank for the computing power? </b></p>
<p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org">SciGaP</A> and <A title="Apache Airavata" href="http://airavata.apache.org/">Apache Airavata</A> and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>.</p>
+
<p><b>Q: I have another question that is not on this FAQ. How can I contact you?</b></p>
<p>A: Yes, please contact us with any questions! Zhong(zw355 at cornell.edu). Charles(cgd24 at cornell.edu).</p>
[airavata-php-gateway] 01/14: adding a prefix for output file
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 1fe068716937b1695479f890e0a3e7e1c5b7e345
Author: root <ro...@osboxes>
AuthorDate: Wed Mar 14 16:09:31 2018 +0000
adding a prefix for output file
---
app/libraries/FileTransfer.php | 46 ++++++++++++++++++++++------
app/views/partials/experiment-info.blade.php | 38 ++++++++++++++++++-----
2 files changed, 66 insertions(+), 18 deletions(-)
diff --git a/app/libraries/FileTransfer.php b/app/libraries/FileTransfer.php
index c59b280..73882a6 100644
--- a/app/libraries/FileTransfer.php
+++ b/app/libraries/FileTransfer.php
@@ -24,15 +24,16 @@ class FileTransfer {
$filelist = explode("\n", RBase64::decode( $filelist ) );
$folder_path=$filelist[0]. "ARCHIVE" ;
$content = "[ \n";
+ $out_prefix = $filelist[3];
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[2]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[1]). '",
name: "'. $filelist[1] .'",
#fixedscale:{min:0,max:20},
summarymethod:"max",
- colorpositive:"#B30086",
- colornegative:"#0000e5",
+ colorpositive:"#C5000B",
+ colornegative:"#0084D1",
height:100,
mode: "show",
},'. "\n" ;
@@ -40,19 +41,19 @@ class FileTransfer {
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[4]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[2]). '",
name: "'. $filelist[3] .'",
#fixedscale:{min:0,max:20},
summarymethod:"min",
- colorpositive:"#B30086",
- colornegative:"#0000e5",
+ colorpositive:"#C5000B",
+ colornegative:"#0084D1",
height:100,
mode: "show",
},'. "\n" ;
$content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.infp.bed.gz').'",
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dREG.infp.bw').'",
name: "dREG Info. Sites:",
mode: "show",
colorpositive:"#B30086",
@@ -63,8 +64,8 @@ class FileTransfer {
},'. "\n";
$content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.peak.score.bed.gz').'",
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dREG.peak.score.bw').'",
name: "dREG Peak Calling:",
mode: "show",
colorpositive:"#B30086",
@@ -76,6 +77,31 @@ class FileTransfer {
#$content = $content . '{
+ # type:"bedgraph",
+ # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.infp.bed.gz').'",
+ # name: "dREG Info. Sites:",
+ # mode: "show",
+ # colorpositive:"#B30086",
+ # colornegative:"#0000e5",
+ # backgroundcolor:"#ffffe5",
+ # height:40,
+ # fixedscale:{min:0, max:1},
+ #},'. "\n";
+
+ #$content = $content . '{
+ # type:"bedgraph",
+ # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.peak.score.bed.gz').'",
+ # name: "dREG Peak Calling:",
+ # mode: "show",
+ # colorpositive:"#B30086",
+ # colornegative:"#0000e5",
+ # backgroundcolor:"#ffffe5",
+ # height:40,
+ # fixedscale:{min:0.2, max:1.0},
+ #},'. "\n";
+
+
+ #$content = $content . '{
# type:"bigwig",
# url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
# name: "imputed DNase-I signal:",
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
index 4f43aee..268058b 100755
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -200,16 +200,32 @@
}
$dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"];
+
+
+ $param_prefix = "out";
+ if( count( $experiment->experimentInputs) > 0 )
+ foreach( $experiment->experimentInputs as $input)
+ {
+ if ($input->applicationArgument == "prefix") {
+ $param_prefix = $input->value;
+ }
+ }
?>
<td>
<select id="download">
<option value=''>Select results</option>
-@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/out.dREG.tar.gz') )
- <option value="out.dREG.tar.gz">Full results</option>
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') )
+ <option value=<?php echo $param_prefix.".tar.gz" ?>>Full results</option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.infp.bed.gz') )
+ <option value=<?php echo $param_prefix.".dREG.infp.bed.gz"?>>dREG informative sites</option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.peak.full.bed.gz') )
+ <option value=<?php echo $param_prefix.".dREG.peak.full.bed.gz"?>>dREG peaks </option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.peak.score.bed.gz') )
+ <option value=<?php echo $param_prefix.".dREG.peak.score.bed.gz"?>>dREG peak(only with scores)</option>
@endif
- <option value="out.dREG.infp.bed.gz">dREG informative sites</option>
- <option value="out.dREG.peak.full.bed.gz">dREG peaks </option>
- <option value="out.dREG.peak.score.bed.gz">dREG peak(only with scores)</option>
</select>
<a href="" target="_blank" id="retLinks">Download <span class="glyphicon glyphicon-save" style="width:20px"></span></a>
@@ -497,12 +513,18 @@
$currentOutputPath = $rp->filePath;
break;
}
-
- $path = str_replace($dataRoot, "", parse_url($currentOutputPath, PHP_URL_PATH));
- $filelist = $filelist . $input->name . "\n". $path. "\n";
+ $path = str_replace($dataRoot.$expDataDir, "", parse_url($currentOutputPath, PHP_URL_PATH));
+ $filelist = $filelist . $path. "\n";
+ }
+ else
+ {
+ $filelist = $filelist . $input->value. "\n";
}
$filelist = $expDataDir ."\n". $filelist;
+ // in case no prefix label for output file in the interface, put "out" at the end
+ $filelist = $filelist . "out\n";
+
$protocol = 'http';
if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https')
$protocol = 'https';
[airavata-php-gateway] 13/14: Update dREG page
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 7768b4a03c8517d4e52241c7efca0cb2c07577d7
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Sat Feb 9 20:59:41 2019 +0000
Update dREG page
---
public/themes/dreg/partials/doc.blade.php | 7 ++++---
public/themes/dreg/partials/template.blade.php | 8 +++++---
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index dd70744..9b5d2be 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -327,10 +327,11 @@ Secondly, when you click the genome browser link, please use the Left-Click, don
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
+<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
+<A target="_blank" href="https://genome.cshlp.org/content/29/2/293.short">
+(1) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2019). Identification of regulatory elements from nascent transcription using dREG. Genome research, 29(2), 293-303. </A></P>
<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
-(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
-<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">
-(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P>
+(2) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
<p><b>Q: Do I have to create account before using this service?</b></p>
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index 1325121..ccae7dc 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -143,11 +143,13 @@ Currently, this gateway hosts two bioinformatics services for functional analysi
<h1 class="text-center">Publications</h1>
<div style="width: 92%; margin-left: 5%; padding-left:15px">
<table>
+
<tr>
<td width="50px"><img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/n1.png" style="width:100%"></img></td>
<td>
<p class="text-left" style="margin-left: 5px; margin-top:10px;">
-Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). <A target=_blank href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">Identification of active transcriptional regulatory elements from GRO-seq data.</A> Nature methods, 12(5), 433-438.</p>
+Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2019). <A target=_blank href="https://genome.cshlp.org/content/29/2/293.short">Identification of regulatory elements from nascent transcription using dREG.</A> Genome research, 29(2), 293-303.
+</p>
</td>
</tr>
@@ -155,12 +157,12 @@ Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H.
<td width="50px"><img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/n2.png" style="width:100%"></img></td>
<td>
<p class="text-left" style="margin-left: 5px; margin-top:10px;">
-Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). <A target=_blank href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">Identification of regulatory elements from nascent transcription using dREG.</A> bioRxiv, 321539.
-</p>
+Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). <A target=_blank href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">Identification of active transcriptional regulatory elements from GRO-seq data.</A> Nature methods, 12(5), 433-438.</p>
</td>
</tr>
+
</table>
</div>
[airavata-php-gateway] 10/14: minor change for GR paper reviewer
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 6c14e1ce30788492a239e56471efaab7d687485d
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Tue Nov 6 18:11:59 2018 +0000
minor change for GR paper reviewer
---
app/views/partials/experiment-info.blade.php | 10 ++-
public/themes/dreg/assets/img/3d-number.jpg | Bin 0 -> 67965 bytes
public/themes/dreg/assets/img/n1.png | Bin 0 -> 15718 bytes
public/themes/dreg/assets/img/n2.png | Bin 0 -> 19546 bytes
public/themes/dreg/assets/img/n3.png | Bin 0 -> 22082 bytes
public/themes/dreg/assets/img/n4.png | Bin 0 -> 19153 bytes
public/themes/dreg/partials/doc.blade.php | 93 +++++++++++++++++++++++--
public/themes/dreg/partials/header.blade.php | 2 +-
public/themes/dreg/partials/template.blade.php | 26 +++++--
9 files changed, 116 insertions(+), 15 deletions(-)
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
index ece374c..55c4c3f 100755
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -88,13 +88,21 @@
@endif
<tr>
<td><strong>Experiment Status</strong></td>
- <td class="exp-status">{{{ $expVal["experimentStatusString"] }}}</td>
+ <td class="exp-status">
+{{{ $expVal["experimentStatusString"] }}} <br/>
+@if( $expVal["experimentStatusString"]!="COMPLETED" && $expVal["experimentStatusString"]!="COMPLETE")
+ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/doc#failure">here</A> to find the reasons.<br/>
+@endif
+</td>
</tr>
@foreach( $expVal["jobDetails"] as $index => $jobDetail)
<tr>
<th>Job</th>
<td>
+@if( $jobDetail->jobStatuses[0]->jobStateName == "FAILED" )
+If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/doc#failure">here</A> to find the reasons. <br/>
+@endif
<table class="table table-bordered">
<tr>
<td>Name</td>
diff --git a/public/themes/dreg/assets/img/3d-number.jpg b/public/themes/dreg/assets/img/3d-number.jpg
new file mode 100644
index 0000000..9a4671c
Binary files /dev/null and b/public/themes/dreg/assets/img/3d-number.jpg differ
diff --git a/public/themes/dreg/assets/img/n1.png b/public/themes/dreg/assets/img/n1.png
new file mode 100644
index 0000000..35ae2e8
Binary files /dev/null and b/public/themes/dreg/assets/img/n1.png differ
diff --git a/public/themes/dreg/assets/img/n2.png b/public/themes/dreg/assets/img/n2.png
new file mode 100644
index 0000000..8714846
Binary files /dev/null and b/public/themes/dreg/assets/img/n2.png differ
diff --git a/public/themes/dreg/assets/img/n3.png b/public/themes/dreg/assets/img/n3.png
new file mode 100644
index 0000000..1ee636c
Binary files /dev/null and b/public/themes/dreg/assets/img/n3.png differ
diff --git a/public/themes/dreg/assets/img/n4.png b/public/themes/dreg/assets/img/n4.png
new file mode 100644
index 0000000..72c9421
Binary files /dev/null and b/public/themes/dreg/assets/img/n4.png differ
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index 007ce1b..edb984b 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -1,12 +1,13 @@
<div class="container">
<div class="content">
<div class="text-center">
- <h2 class="title top-space">Documents</h2>
+ <h2 class="title top-space">Documentation</h2>
</div>
<ul class="nav nav-tabs nav-justified" role="tablist">
<li role="presentation" class="active"><a href="#instructure" role="tab" data-toggle="tab">Instructions</a></li>
<li role="presentation"><a href="#sp" role="tab" data-toggle="tab">Software/Package</a></li>
+ <li role="presentation"><a href="#input" role="tab" data-toggle="tab">Input</a></li>
<li role="presentation"><a href="#output" role="tab" data-toggle="tab">Output</a></li>
</ul>
@@ -118,22 +119,22 @@ After the experiment is complete, no results can be downloaded and job status sh
</div>
+<!---- SOFTWARE PANEL -->
<div role="tabpanel" class="tab-pane" id="sp">
<div class="row">
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
<p class="description">The <B>dREG gateway</B> is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:</p>
<p class="description">[1] <B>dREG package</B>: <A href="https://github.com/Danko-Lab/dREG">https://github.com/Danko-Lab/dREG</A>.</p>
- <p class="description">
+ <p class="description">
The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).</p>
<p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD">https://github.com/Danko-Lab/dREG.HD</A>.</p>
- <p class="description">The dREG.HD package refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p>
+ <p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p>
<p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm">https://github.com/Danko-Lab/Rgtsvm</A>.</p>
<p class="description">
Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p>
-
- <p class="description">[4] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p>
- <p class="description">
+
+ <p class="description">[4] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p> <p class="description">
Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE.
</p>
@@ -141,6 +142,58 @@ Airavata PHP Gateway provides an API to build web sites which interact with high
</div>
</div>
+<!---- INPUT PANEL -->
+
+ <div role="tabpanel" class="tab-pane" id="input">
+ <div class="row">
+ <div class="col-sm-offset-1 col-sm-10 col-xs-12">
+
+<p class="description" align="justify">The input to dREG consists of two bigWig files which represent the position of RNA polymerase on the positive and negative strands. The sequence alignment and processing steps to make the input bigWig files are a major factor influencing how accurately dREG predicts TIRs. dREG makes several assumptions about data processing that are critical for success. </p>
+
+<p class="description" align="justify">Critical elements of a bioinformatics pipeline that is compatible with dREG will include:</p>
+<ul>
+<li class="description" style="align:justify"><b>Representing RNA polymerase location using a single base.</b><br/>
+<p class="description" align="justify">PRO-seq measures the location of the RNA polymerase active site, in many cases at nearly single nucleotide resolution. Therefore, it is logical to represent the coordinate of RNA polymerase using the genomic position that best represents the polymerase location, rather than representing the entire read. dREG assumes that each read is represented in the bigWig file by a single base. We have noted poor performance when reads are extended. It is critic [...]
+</li>
+
+<li class="description"><b>Include a copy of the Pol I transcription unit in the reference genome. </b><br/>
+<p class="description" align="justify">PRO-seq data resolves the location of all four RNA polymerases found in Metazoan cells (Pol I, II, III, and Mt). DNA encoding the Pol I transcription unit is highly repetitive, and is not included in most mammalian reference genomes. Nevertheless, the Pol I transcription unit is a substantial source of reads in a typical PRO-seq experiment (10-30%). Many of these reads will align spuriously to retrotransposed and non-functional copies of the Pol I t [...]
+</li>
+
+<li class="description"><b>Trim 3' adapters, but leave the fragments. </b><br/>
+<p class="description" align="justify">Much of the signal for dREG comes from paused RNA polymerase. RNA polymerase pauses 30-60 bp downstream of the transcription start site. Due to this short RNA fragment length, paused reads in most PRO-seq libraries will sequence a substantial amount of adapter. This leads to poor mapping rates in full-length reads. Therefore, it is crucial to remove contaminating 3' adapters so that paused fragments will map to the reference genome properly.</p>
+</li>
+
+<li class="description"><b>Data represents unnormalized raw counts. </b><br/>
+<p class="description" align="justify">dREG assumes that data represents the number of individual sequence tags that are located at each genomic position. For this reason, it is critical that input data is not normalized. The dREG server checks to ensure that input data is expressed as integers, and will return an error if this is not the case.</p>
+</li>
+</ul>
+
+<p class="description"> Users can also use scripts generated in the Danko lab to create compatible bigWig files. Options for scripts at different starting points in the analysis are given below: </p>
+
+<ul>
+<li class="description"><b>Convert raw fastq files into bigWig</b>.<br/>
+<p class="description" align="justify">Our pipeline produces bigWig files that are compatible with dREG, and can be found at the following URL: <A target=_blank href="https://github.com/Danko-Lab/proseq_2.0">https://github.com/Danko-Lab/proseq_2.0</A>. Our PRO-seq pipeline takes single-end or pair-ended sequencing reads (fastq format) as input. The pipeline automates routine pre-processing and alignment steps, including pre-processing reads to remove the adapter sequences and trim based [...]
+</li>
+
+<li><b>Convert mapped reads in BAM files into bigWigs</b>.<br/>
+<p class="description" align="justify">We provide a tool that converts mapped reads from a BAM file into bigWig files that are compatible with dREG. This tool is available here: <A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">https://github.com/Danko-Lab/RunOnBamToBigWig</A>.</p>
+</li>
+</ul>
+
+<p class="description">Other considerations:</p>
+<ul>
+<p class="description" style="justify"> The quality and quantity of the experimental data are major factors in determining how sensitive dREG will be in detecting TREs. We have found that dREG has a reasonable statistical power for discovering TREs with as few as ~40M uniquely mappable reads, and saturates detection of TREs in well-studied ENCODE cell lines with >80M reads. To increase the number of reads available for TRE discovery, we encourage users to merge biological replicates in o [...]
+
+<p class="description" style="justify">We have found that visualizing aligned data in a genome browser prior (e.g., IGV or UCSC) to downstream analysis is a useful way to catch any data quality or alignment issues.</p>
+
+</ul>
+ </div>
+ </div>
+ </div>
+
+<!---- OUTPUT PANEL -->
+
<div role="tabpanel" class="tab-pane" id="output">
<div class="row">
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
@@ -183,7 +236,33 @@ Airavata PHP Gateway provides an API to build web sites which interact with high
<td>Including above 5 files, can be decompressed by 'tar -xvzf' in Linux.</td>
</tr>
</table>
- <p class="description">
+
+<div style="padding:20px;
+border-style: solid;
+border-width: 5;
+border-color: #dadada;" data-expandable-box-container="true">
+<figcaption>
+<div style="padding-bottom:15px" id="Sec2">Box 1:<b> Brief description of key terms</b></div>
+</figcaption>
+
+<div class="suppress-bottom-margin add-top-margin">
+<p><b>Informative position:</b>
+Loci denoted as "informative positions" meet the following criteria: contain more than 3 reads in 100 bp interval on either strand, or more than 1 read in 1Kbp interval on both strands. Informative positions are used to predict the dREG scores for TRE (Transcription Regulatory Element) identification. </p>
+
+<p><b>dREG score:</b>
+Training and prediction is done using a Support Vector Regression model where a label of 1 indicates RNA polymerase II initialization or transciption through the informative position. The predicted values from the pre-trained model are called dREG scores. A dREG score close to 1 indicates that a position likely a TRE.
+</p>
+
+<p><b>Peak p-value:</b>
+We test 5 dREG scores around each candidate peak center using the NULL hypothesis that each point within this peak is drawn from the non-TRE distribution. This test estimates the statistical confidence of each candidate dREG peak. In the final result, FDR is applied to do multiple correction and only the peaks with adjusted p-value < 0.05 are reported.
+</p>
+
+
+</div></div>
+
+<br/>
+
+<p class="description">
2) In the Web storage folder there are <font color="green">some files required by the WashU</font> genome browser:
</p>
<p class="description"> </p>
diff --git a/public/themes/dreg/partials/header.blade.php b/public/themes/dreg/partials/header.blade.php
index c0ee6cc..043860d 100755
--- a/public/themes/dreg/partials/header.blade.php
+++ b/public/themes/dreg/partials/header.blade.php
@@ -22,7 +22,7 @@ color:blue;
<li><a class="scroll" @if( $_SERVER['REQUEST_URI'] === "/" ) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/">Home</a></li>
<li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/about") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/about">About</a></li>
- <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">Documents</a></li>
+ <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">Documentation</a></li>
<li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/faq") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/faq">FAQ</a></li>
<!--
@if(! Session::has('loggedin'))
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index e15d313..8dff7b8 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -49,12 +49,15 @@ span.onclick = function() {
<H2> How is it used?</H2>
<p style="font-size:14px; margin-top:20px;text-align:justify">
Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p>
-<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>Click <A href="https://github.com/Danko-Lab/proseq2.0"> this link </A> to check <B>how to prepare your PRO-seq, GRO-seq, or ChRO-seq data in bigWig format</B>.
+<p style="font-size:14px; margin-top:5px;text-align:justify">
+<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
+Use the Danko lab's <b>mapping pipeline</b> (<A target=_blank href="https://github.com/Danko-Lab/proseq2.0">here</A>) to prepare bigWig files from fastq files or <b>convert BAM files</b> of mapped reads to bigWig (<A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">here</A>).
</p>
+
<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A> or <A href="{{ URL::to('/') }}/pages/doc">document</a> for additional questions.
+<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
+See our <A href="{{ URL::to('/') }}/pages/faq">FAQ</A>, <A href="{{ URL::to('/') }}/pages/doc">documentation</a> or <A target=_blank href="https://www.dropbox.com/s/jzlamnd0mej0z76/Chu.dREG_protocol.pdf?dl=0">dREG protocol manuscript</A> for additional questions.
</p>
<img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG-model.png" style="width:100%"></img>
<p class="text-center"><small>Click the figure to enlarge it</small></p>
@@ -93,12 +96,23 @@ span.onclick = function() {
<div style="width: 92%; margin-left: 5%; padding-left:15px">
<table>
<tr>
-<td width="100px"><img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dREG.Preprint.png" style="width:100%"></img></td>
+<td width="50px"><img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/n1.png" style="width:100%"></img></td>
<td>
-<p class="text-left" style="margin-left: 25px"><A href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
-Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438.</A></p>
+<p class="text-left" style="margin-left: 5px; margin-top:10px;">
+Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). <A target=_blank href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">Identification of active transcriptional regulatory elements from GRO-seq data.</A> Nature methods, 12(5), 433-438.</p>
</td>
</tr>
+
+<tr>
+<td width="50px"><img id="myImg2" alt="dREG model" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/n2.png" style="width:100%"></img></td>
+<td>
+<p class="text-left" style="margin-left: 5px; margin-top:10px;">
+Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). <A target=_blank href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">Identification of regulatory elements from nascent transcription using dREG.</A> bioRxiv, 321539.
+</p>
+</td>
+</tr>
+
+
</table>
</div>
[airavata-php-gateway] 06/14: change the link on dREG home page
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 62d3e664ed3628b91cf853946f4da8065901f472
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Wed Aug 29 21:35:02 2018 +0000
change the link on dREG home page
---
public/themes/dreg/partials/template.blade.php | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index 9951895..e15d313 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -50,7 +50,7 @@ span.onclick = function() {
<p style="font-size:14px; margin-top:20px;text-align:justify">
Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p>
<p style="font-size:14px; margin-top:5px;text-align:justify">
-<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>Click <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> this link </A> to check <B>how to prepare your PRO-seq, GRO-seq, or ChRO-seq data in bigWig format</B>.
+<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>Click <A href="https://github.com/Danko-Lab/proseq2.0"> this link </A> to check <B>how to prepare your PRO-seq, GRO-seq, or ChRO-seq data in bigWig format</B>.
</p>
<p style="font-size:14px; margin-top:5px;text-align:justify">
[airavata-php-gateway] 08/14: change links to buttons
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 4e8d471b1899ebfe4467fc2e1587cf72cd68c519
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Fri Oct 5 20:17:17 2018 +0000
change links to buttons
---
app/views/partials/experiment-info.blade.php | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
index 268058b..ece374c 100755
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -226,9 +226,10 @@
@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.peak.score.bed.gz') )
<option value=<?php echo $param_prefix.".dREG.peak.score.bed.gz"?>>dREG peak(only with scores)</option>
@endif
- </select>
+ </select>
- <a href="" target="_blank" id="retLinks">Download <span class="glyphicon glyphicon-save" style="width:20px"></span></a>
+<!-- <a href="" target="_blank" id="retLinks">Download <span class="glyphicon glyphicon-save" style="width:20px"></span></a> -->
+<button id="retLinks" style="color: #fff; background-color: #3e5a43; border-color: #46b8da; border: 1px solid transparent;" >Download <span class="glyphicon glyphicon-save" style="width:20px"></span></button>
</td>
</tr>
<tr>
@@ -241,8 +242,9 @@
<option value="mm10">mm10</option>
</select>
or input
- <input type="text" id="customeGB" style="width:40px"/>
- <a href="#1" target="_blank" id="gbLinks">Switch to genome browser <span class="glyphicon glyphicon-new-window" style="width:20px"></span></a>
+ <input type="text" id="customeGB" style="width:40px"/>
+<!-- <a href="#1" target="_blank" id="gbLinks">Switch to genome browser <span class="glyphicon glyphicon-new-window" style="width:20px"></span></a> -->
+<button id="gbLinks" style="color: #fff; background-color: #3e5a43; border-color: #46b8da; border: 1px solid transparent;">Switch to genome browser <span class="glyphicon glyphicon-new-window" style="width:20px"></span></button>
</td>
</tr>
{{-- dREG --}}
[airavata-php-gateway] 12/14: updates for dTOX
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 40240074ee5731e8f4e42d77404659dc47e1436f
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Thu Jan 17 22:16:22 2019 +0000
updates for dTOX
---
app/libraries/FileTransfer.php | 2 +-
app/views/partials/experiment-info.blade.php | 5 +-
public/themes/dreg/assets/img/dregicon.png | Bin 0 -> 2128 bytes
public/themes/dreg/assets/img/dtox.create.exp2.png | Bin 42088 -> 40049 bytes
public/themes/dreg/partials/dtox-doc.blade.php | 126 +++++++++------------
public/themes/dreg/partials/header.blade.php | 6 +-
public/themes/dreg/partials/software.blade.php | 16 ++-
public/themes/dreg/partials/template.blade.php | 14 ++-
8 files changed, 79 insertions(+), 90 deletions(-)
diff --git a/app/libraries/FileTransfer.php b/app/libraries/FileTransfer.php
index 470139c..1dd6dd9 100644
--- a/app/libraries/FileTransfer.php
+++ b/app/libraries/FileTransfer.php
@@ -120,7 +120,7 @@ class FileTransfer {
},'. "\n" ;
$content = $content . '{
- type:"bigwig",
+ type:"bedgraph",
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dTOX.bound.bed.gz').'",
name: "dTOX bound status:",
mode: "show",
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
index 4715e6d..1e88c0b 100644
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -243,10 +243,7 @@ If the job is failed, please refer <A href="https://dreg.dnasequence.org/pages/d
@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') )
<option value=<?php echo $param_prefix.".tar.gz" ?>>Full results</option>
@endif
-@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTOX.full.bed.gz') )
- <option value=<?php echo $param_prefix.".dTOX.full.bed.gz"?>>all dTOX regions</option>
-@endif
-@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTox.bound.bed.gz') )
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dTOX.bound.bed.gz') )
<option value=<?php echo $param_prefix.".dTOX.bound.bed.gz"?>>dTOX bound regions </option>
@endif
</select>
diff --git a/public/themes/dreg/assets/img/dregicon.png b/public/themes/dreg/assets/img/dregicon.png
new file mode 100644
index 0000000..1af0e6e
Binary files /dev/null and b/public/themes/dreg/assets/img/dregicon.png differ
diff --git a/public/themes/dreg/assets/img/dtox.create.exp2.png b/public/themes/dreg/assets/img/dtox.create.exp2.png
index c4d0843..5af3f6d 100644
Binary files a/public/themes/dreg/assets/img/dtox.create.exp2.png and b/public/themes/dreg/assets/img/dtox.create.exp2.png differ
diff --git a/public/themes/dreg/partials/dtox-doc.blade.php b/public/themes/dreg/partials/dtox-doc.blade.php
index d54bdea..cabdf82 100755
--- a/public/themes/dreg/partials/dtox-doc.blade.php
+++ b/public/themes/dreg/partials/dtox-doc.blade.php
@@ -37,27 +37,27 @@ Select the menu 'Start dREG/dTOX' below the dREG logo to create an data analysis
<p class="description" style="padding:16px">
4) <b>Fill experiment form</b><br>
-Select bigWig files representing PRO-seq, ATAC-seq, or dNase-I-seq signal on the plus and minus strand. Please notice that two GPU resources are available now, currently it is easier to get the computation resources on <A href="http://comet.sdsc.xsede.org/">Comet.sdsc.xsede.org</A> than <A href="https://www.psc.edu/index.php/bridges">Bridges.psc.edu</A>.
+Select bigWig files representing PRO-seq, ATAC-seq, or DNase-I-seq signal on the plus and minus strand.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment create" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dtox.create.exp2.png" ></img></div>
<p class="description" style="padding:16px">
5) <b>Submit the job</b><br>
-Click the 'save and launch' button. BigWig file are transferred to the XSEDE server and a GPU queue is scheduled to run dREG. After submitting, the user can check the status in the next web page, as shown below. Depend on the queue status, the job maybe wait for a long time to start prediction. Once started, it will only take 1-4 hours to complete.</p>
+Click the 'save and launch' button. BigWig file are transferred to the XSEDE server and a GPU queue is scheduled to run dTOX. After submitting, the user can check the status in the next web page, as shown below. Depending on the queue status, the job may wait for some time to start prediction. Once started, it will take 6-10 hours to complete depending on the genome used.</p>
<p class="description" style="padding:16px">
6) <b>Check the status</b><br>
-The user can check the status of their 'experiment' by clicking the menu 'Saved runs' below the dREG logo.
+The user can check the status of their 'experiment' by clicking the 'Saved runs' button on the top menu.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment browse" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.list.png"></img></div>
<p class="description" style="padding:16px">
7) <b>Check the results</b><br>
-Once a job is completed, the user can select 'Full results' in the drop-down list and then LEFT-click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed [...]
+Once a job is completed, the user can select 'dTOX Bound Regions' in the drop-down list and then LEFT-click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page. The downloaded file has a 'gz' extension and can be decompressed by the 'gunzip' command in Linux. Please <font color="red">don't use RIGHT-click </font> to open a tab for downloading. To extract bound [...]
</br>
-In <font color="RED">Safari</font>, it could be problematic because Safari tries to unzip the compressed results automatically using a non-compatible compress method. Please check <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature.</p>
+In <font color="RED">Safari</font>, it could be problematic because Safari tries to unzip the compressed results automatically using a non-compatible compression method. Please check <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div>
@@ -76,9 +76,9 @@ The following figure shows the data files in the job's folder, including two big
<a name="failure"></a>
<p class="description" style="padding:16px">
- 10) <b>When you meet failure</b><br>
+ 10) <b>If your job fails</b><br>
-Currently when you run the dREG jobs, there are two types of errors you may have. One error may come from the system, called a system error, such as no computing time on specific GPU nodes or an internal errors in Apache Airavata. The other type of error is caused by the users' bigwig, called bigwig error, which can occur when read counts are normalized, each read is mapped to a region, or read counts in minus strand are positive values. The following figures show how to identify the err [...]
+When you run dTOX, there are two main types of errors you may encounter. One error may come from the system, called a system error, such as no computing time on specific GPU nodes or an internal errors in Apache Airavata. The other type of error is caused by the users' bigWig file, called a bigWig error, which can occur when read counts are normalized, each read is mapped to a region, or read counts in minus strand are positive values. The following figures show how to identify the error [...]
<p class="description" style="padding:16px">
@@ -96,14 +96,15 @@ When users submit the experiment, the failure will be shown in the experiment su
<br>
<p class="description" style="padding:16px">
b) <b>Bigwig error</b><br>
-After the experiment is complete, no results can be downloaded and job status shows a failure (see Figure 10-S3). Users can find the dREG log file or task log file to identify the problem. Enter into <b>"storage directory"</b> by clicking the <b>"open"</b> link. The users can find <b>"ARCHIVE"</b> folder where Apache Airavata copy back all files from the computing node. Check the dREG log file (<b>out.dREG.log</b>) to see the bigwig problem or check the task log file ("slurm-tasknoxxx.ou [...]
+After the experiment is complete, no results can be downloaded and job status shows a failure (see Figure 10-S3). Users can find the dTOX log file or task log file to identify the problem. Enter into <b>"storage directory"</b> by clicking the <b>"open"</b> link. The users can find <b>"ARCHIVE"</b> folder where Apache Airavata copies back all files from the computing node. Check the dTOX log file (<b>run.dTOX.log</b>) to see the bigwig problem or check the task log file ("slurm-tasknoxxx. [...]
+tps://github.com/Danko-Lab/utils/dnase/BamToBigWig">link for DNase-I-seq</a>, or <A href="ht
+tps://github.com/Danko-Lab/utils/atacseq/BamToBigWig">link for ATAC-seq</a> to solve the problems.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure3.png"></img></div>
<div style="clear:both;text-align:center;"><center>Figure 10-S3</center></div>
<BR>
<p>This figure shows the bigWig problems in the dREG log file.</p>
-
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="Bigwig error(1)" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/failure3-reason.png"></img></div>
<div style="clear:both;text-align:center;"><center>Figure 10-S4</center></div>
<BR>
@@ -125,42 +126,26 @@ After the experiment is complete, no results can be downloaded and job status sh
<div class="row">
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
-<p class="description" align="justify">The input to dREG consists of two bigWig files which represent the position of RNA polymerase on the positive and negative strands. The sequence alignment and processing steps to make the input bigWig files are a major factor influencing how accurately dREG predicts TIRs. dREG makes several assumptions about data processing that are critical for success. </p>
-
-<p class="description" align="justify">Critical elements of a bioinformatics pipeline that is compatible with dREG will include:</p>
-<ul>
-<li class="description" style="align:justify"><b>Representing RNA polymerase location using a single base.</b><br/>
-<p class="description" align="justify">PRO-seq measures the location of the RNA polymerase active site, in many cases at nearly single nucleotide resolution. Therefore, it is logical to represent the coordinate of RNA polymerase using the genomic position that best represents the polymerase location, rather than representing the entire read. dREG assumes that each read is represented in the bigWig file by a single base. We have noted poor performance when reads are extended. It is critic [...]
-</li>
-
-<li class="description"><b>Include a copy of the Pol I transcription unit in the reference genome. </b><br/>
-<p class="description" align="justify">PRO-seq data resolves the location of all four RNA polymerases found in Metazoan cells (Pol I, II, III, and Mt). DNA encoding the Pol I transcription unit is highly repetitive, and is not included in most mammalian reference genomes. Nevertheless, the Pol I transcription unit is a substantial source of reads in a typical PRO-seq experiment (10-30%). Many of these reads will align spuriously to retrotransposed and non-functional copies of the Pol I t [...]
-</li>
+<p class="description" align="justify">The input to dTOX consists of two bigWig files which represent either the position of RNA polymerase on the positive and negative strands (PRO-seq) or the accessibility on the positive and negative strands (DNase-I-seq or ATAC-seq). The sequence alignment and processing steps to make the input bigWig files are a major factor influencing how accurately dTOX predicts transcription factor binding.</p>
-<li class="description"><b>Trim 3' adapters, but leave the fragments. </b><br/>
-<p class="description" align="justify">Much of the signal for dREG comes from paused RNA polymerase. RNA polymerase pauses 30-60 bp downstream of the transcription start site. Due to this short RNA fragment length, paused reads in most PRO-seq libraries will sequence a substantial amount of adapter. This leads to poor mapping rates in full-length reads. Therefore, it is crucial to remove contaminating 3' adapters so that paused fragments will map to the reference genome properly.</p>
-</li>
+<p class="description" align="justify">A key component of all datatypes is that data represents unnormalized raw counts. dTOX assumes that data represents the number of individual sequence tags that are located at each genomic position. For this reason, it is critical that input data is not normalized. The server checks to ensure that input data is expressed as integers, and will return an error if this is not the case.</p>
-<li class="description"><b>Data represents unnormalized raw counts. </b><br/>
-<p class="description" align="justify">dREG assumes that data represents the number of individual sequence tags that are located at each genomic position. For this reason, it is critical that input data is not normalized. The dREG server checks to ensure that input data is expressed as integers, and will return an error if this is not the case.</p>
-</li>
-</ul>
<p class="description"> Users can also use scripts generated in the Danko lab to create compatible bigWig files. Options for scripts at different starting points in the analysis are given below: </p>
<ul>
<li class="description"><b>Convert raw fastq files into bigWig</b>.<br/>
-<p class="description" align="justify">Our pipeline produces bigWig files that are compatible with dREG, and can be found at the following URL: <A target=_blank href="https://github.com/Danko-Lab/proseq_2.0">https://github.com/Danko-Lab/proseq_2.0</A>. Our PRO-seq pipeline takes single-end or pair-ended sequencing reads (fastq format) as input. The pipeline automates routine pre-processing and alignment steps, including pre-processing reads to remove the adapter sequences and trim based [...]
+<p class="description" align="justify">Our pipeline produces bigWig files that are compatible with dREG, and can be found at the following URLs: <A target=_blank href="https://github.com/Danko-Lab/proseq_2.0">https://github.com/Danko-Lab/proseq_2.0</A> (PRO-seq), <A target=_blank href="https://github.com/Danko-Lab/atac">https://github.com/Danko-Lab/atac</A> (ATAC-seq), <A target=_blank href="https://github.com/Danko-Lab/dnase">https://github.com/Danko-Lab/dnase</A> (DNase-I-seq). The pip [...]
</li>
<li><b>Convert mapped reads in BAM files into bigWigs</b>.<br/>
-<p class="description" align="justify">We provide a tool that converts mapped reads from a BAM file into bigWig files that are compatible with dREG. This tool is available here: <A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">https://github.com/Danko-Lab/RunOnBamToBigWig</A>.</p>
+<p class="description" align="justify">We provide scripts that convert mapped reads from a BAM file into bigWig files that are compatible with dTOX. The scripts are avavailable on our GitHub page. For PRO-seq: <A target=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">https://github.com/Danko-Lab/RunOnBamToBigWig</A>. For DNase-I-seq: <A target=_blank href="https://github.com/Danko-Lab/utils/dnase/BamToBigWig">https://github.com/Danko-Lab/utils/dnase/BamToBigWig</A>. For ATA [...]
</li>
</ul>
<p class="description">Other considerations:</p>
<ul>
-<p class="description" style="justify"> The quality and quantity of the experimental data are major factors in determining how sensitive dREG will be in detecting TREs. We have found that dREG has a reasonable statistical power for discovering TREs with as few as ~40M uniquely mappable reads, and saturates detection of TREs in well-studied ENCODE cell lines with >80M reads. To increase the number of reads available for TRE discovery, we encourage users to merge biological replicates in o [...]
+<p class="description" style="justify">The quality and quantity of the experimental data are major factors in determining how sensitive dTOX will be in detecting transcription factor binding. To increase the number of reads available for transcription factor binding detection, we encourage users to merge biological replicates in order to improve statistical power prior to running dTOX. Additionally, to compare binding predictions between conditions we recommend comparing samples at simil [...]
<p class="description" style="justify">We have found that visualizing aligned data in a genome browser prior (e.g., IGV or UCSC) to downstream analysis is a useful way to catch any data quality or alignment issues.</p>
@@ -176,7 +161,7 @@ After the experiment is complete, no results can be downloaded and job status sh
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
<p class="description">
-1) dREG run generates a compressed file including the <font color="green"> dREG results </font> as follows:
+1) A dTOX run generates a compressed file including the following files:
</p>
<p class="description"> </p>
@@ -186,23 +171,9 @@ After the experiment is complete, no results can be downloaded and job status sh
<th>Description</th>
</tr>
<tr>
- <td>$PREFIX.dTOX.full.bed.gz</td>
- <td>TFBS regions with full information including chromosome, start, ending, MOTIF ID, RTFBSDB score, strand, Transcription factor, dTOX score, bound status. Decompress it with 'gunzip' in Linux.</td>
- </tr>
- <tr>
<td>$PREFIX.dTOX.bound.bed.gz</td>
- <td>TFBS regions only with bound status. Decompress it with 'gunzip' in Linux.</td>
+ <td>TFBS regions that are predicted as bound. The file includes chromosome, start, ending, MOTIF ID, RTFBSDB score, strand, dTOX score, bound status. Decompress it with 'gunzip' in Linux.</td>
</tr>
-
- <tr>
- <td>$PREFIX.dTOX.rtfbsdb.bed.gz</td>
- <td>>TFBS regions only with RTFBSDB score. Decompress it with 'gunzip' in Linux.</td>
- </tr>
-
- <tr>
- <td>$PREFIX.tar.gz</td>
- <td>Including above 5 files, can be decompressed by 'tar -xvzf' in Linux.</td>
- </tr>
</table>
<div style="padding:20px;
@@ -215,21 +186,37 @@ border-color: #dadada;" data-expandable-box-container="true">
<div class="suppress-bottom-margin add-top-margin">
<p><b>Informative position:</b>
-Loci denoted as "informative positions" meet the following criteria: contain more than 3 reads in 100 bp interval on either strand, or more than 1 read in 1Kbp interval on both strands. Informative positions are used to predict the dREG scores for TRE (Transcription Regulatory Element) identification. </p>
+Loci denoted as "informative positions" meet the following criteria: contain more than 1 reads in 400 bp interval on either strand. Informative positions are used to predict transcription factor binding. </p>
-<p><b>dTOX score:</b>
-Training and prediction is done using a Support Vector Regression model where a label of 1 indicates RNA polymerase II initialization or transciption through the informative position. The predicted values from the pre-trained model are called dREG scores. A dREG score close to 1 indicates that a position likely a TRE.
+<p><b>dTOX decision value:</b>
+Training and prediction is done using a Support Vector Regression model where a label of 1 indicates transcription factor binding. The predicted values from the pre-trained model are called dTOX decision values. A dTOX decision value close to 1 indicates that a position likely to be bound.
</p>
+</div></div>
-<p><b>RTFBSDB score:</b>
-We test 5 dREG scores around each candidate peak center using the NULL hypothesis that each point within this peak is drawn from the non-TRE distribution. This test estimates the statistical confidence of each candidate dREG peak. In the final result, FDR is applied to do multiple correction and only the peaks with adjusted p-value < 0.05 are reported.
-</p>
+<br/>
+<div style="padding:20px;
+border-style: solid;
+border-width: 5;
+border-color: #dadada;" data-expandable-box-container="true">
+<figcaption>
+<div style="padding-bottom:15px" id="Sec2">Box 2:<b> Extracting bound motifs for a specific transcription factor. </b></div>
+</figcaption>
+
+<div class="suppress-bottom-margin add-top-margin">
+<p>The dTOX output file contains the binding status of our entire set of motifs with PWMs. To find the binding status of the motifs you are interested in, you can run our R script that extracts the Motif IDs that belong to a particular transcription factor. The script is located <A target=_blank href="https://github.com/Danko-Lab/dTOX/blob/master/extract_TF.bsh">here.</A> This script requires 3 arguments: the name of the file with the dTOX results, the transcription factor you want to ex [...]
+<br/>
+<br/>
+R --vanilla --slave --args out.dTOX.bound.bed.gz TF outputFile.bed.gz < extract-bound-TF.R
+</p>
</div></div>
<br/>
+
+
+
<p class="description">
2) In the Web storage folder there are <font color="green">some files required by the WashU</font> genome browser:
</p>
@@ -240,7 +227,7 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
<tr>
<tr>
<td>$PREFIX.dTOX.bound.bw</td>
- <td>The bigWig file converted from the significant peaks (FDR < 0.05) with dREG scores ($PREFIX.dREG.peak.score.bed.gz).</td>
+ <td>The bigWig file converted from bound motifs ($PREFIX.dTOX.bound.bed.gz).</td>
</tr>
<tr>
<td>*.bed.gz.tbi</td>
@@ -249,19 +236,14 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
</table>
<p class="description">
-3) There are <font color="green">two log files </font> in the Web storage folder:</p>
+3) There are <font color="green">one log file </font> in the Web storage folder:</p>
<p class="description"> </p>
<table class="table">
<tr>
<th>File name</th> <th>Description</th> </tr>
<tr>
- <td>$PREFIX.dTOX.log</td>
- <td>Print the summary information after peak calling. If the bigWigs don't meet the requirements of dREG, the warning information will be outputted in this file.
- </td>
- </tr>
- <tr>
<td>slurm-??????.out</td>
- <td>The verbose logging output of dREG package.</td>
+ <td>The verbose log output of dTOX package.</td>
</tr>
</table>
</div>
@@ -275,10 +257,10 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
<div class="row">
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
-<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
+<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. Below are frequent questions about the dREG Gateway and the dTOX program.</p>
-<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
-<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0"> here </A>.</p>
+<p><b>Q: How should I prepare bigWig files for use with dTOX?</b></p>
+<p>A: Information about how to prepare files can be found on the Danko lab github page here for<A href="https://github.com/Danko-Lab/proseq2.0"> PRO-seq </A>, <A href="https://github.com/Danko-Lab/utils/tree/master/dnase"> DNase </A>, and <A href="https://github.com/Danko-Lab/utils/tree/master/atacseq"> ATAC-seq </A>.</p>
<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
@@ -288,15 +270,12 @@ We test 5 dREG scores around each candidate peak center using the NULL hypothesi
<p><b>Q: What should the Safari users be aware of?</b></p>
-<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br>
+<p>A: By default, Safari unzips a zip file automatically when you download it. However dTOX results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be problematic when you download dTOX results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br>
Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab".
</p>
-<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
-<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p>
-
-<p><b>Q: Will the dREG gateway work with my data type?</b></p>
-<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p>
+<p><b>Q: Will dTOX work with my data type?</b></p>
+<p>A: dTOX was trained and tested on PRO-seq, ATAC-seq, and DNase-I-seq. dTOX will also work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p>
<p><b>Q: Will the pre-trained models work using data from my species?</b></p>
<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
@@ -307,13 +286,10 @@ Secondly, when you click the genome browser link, please use the Left-Click, don
<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
<p>A: One month.</p>
-<p><b>Q: How to I cite the dREG gateway?</b></p>
-<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
-<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
-(1) Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438. </A></p>
+<p><b>Q: How do I cite dTOX?</b></p>
+<p>A: Please cite our papers if you use dTOX results in your publication:<BR/>
<A target="_blank" href="https://www.biorxiv.org/content/early/2018/05/14/321539.abstract">
-(2) Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539. </A></P>
-
+(1) ADD CITATION. Choate, L. A., Wang, Z., & Danko, C. G. (2018). Identification of transcription factor binding using genome-wide accessibility and transcription. bioRxiv. </A></P>
<p><b>Q: Do I have to create account before using this service?</b></p>
<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
diff --git a/public/themes/dreg/partials/header.blade.php b/public/themes/dreg/partials/header.blade.php
index a470341..e532620 100755
--- a/public/themes/dreg/partials/header.blade.php
+++ b/public/themes/dreg/partials/header.blade.php
@@ -1,4 +1,8 @@
<title>dREG Gateway</title>
+<link rel="icon"
+ type="image/png"
+ href="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dregicon.png">
+
<div id="navbar" class="navbar navbar-inverse">
<div class="container-fluid" style="background:white;">
<div class="navbar-header" style="background:white;">
@@ -21,7 +25,7 @@ color:blue;
<li><a class="scroll hidden" href="#home"></a></li>
<li><a class="scroll" @if( $_SERVER['REQUEST_URI'] === "/" ) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/">Home</a></li>
<li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/doc">dREG Documentation</a></li>
- <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/dtox-doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/dtox-doc">dTOX dcumentation</a></li>
+ <li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/dtox-doc") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/dtox-doc">dTOX documentation</a></li>
<li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/software") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/software">Software/Package</a></li>
<li><a class="scroll" @if(strpos($_SERVER['REQUEST_URI'], "pages/about") !== false) style="color:blue" @else style="color:black" @endif href="{{ URL::to('/') }}/pages/about">About</a></li>
diff --git a/public/themes/dreg/partials/software.blade.php b/public/themes/dreg/partials/software.blade.php
index 686983c..892e515 100755
--- a/public/themes/dreg/partials/software.blade.php
+++ b/public/themes/dreg/partials/software.blade.php
@@ -13,26 +13,32 @@ The dREG package is developed to detect the divergently oriented RNA polymerase
<p class="description">[2] <B>dREG.HD package</B>: <A href="https://github.com/Danko-Lab/dREG.HD">https://github.com/Danko-Lab/dREG.HD</A>.</p>
<p class="description">The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.</p>
- <p class="description">[3] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm">https://github.com/Danko-Lab/Rgtsvm</A>.</p>
+
+
+ <p class="description">[3] <B>dTOX package</B>: <A href="https://github.com/Danko-Lab/dTOX">https://github.com/Danko-Lab/dTOX</A>.</p>
+ <p class="description">The dTOX package detects transcription factor binding in PRO-seq, DNase-I-seq, and ATAC-seq using support vector machines and random forests. </p>
+
+
+ <p class="description">[4] <B>Rgtsvm package</B>: <A href="https://github.com/Danko-Lab/Rgtsvm">https://github.com/Danko-Lab/Rgtsvm</A>.</p>
<p class="description">
Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models. </p>
- <p class="description">[4] <B>rtfbsdb package</B>: <A href="https://github.com/Danko-Lab/rtfbs_db">https://github.com/Danko-Lab/rtfbs_db</A>.</p>
+ <p class="description">[5] <B>rtfbsdb package</B>: <A href="https://github.com/Danko-Lab/rtfbs_db">https://github.com/Danko-Lab/rtfbs_db</A>.</p>
<p class="description">
Rtfbsdb implements TFBS scaning acorss whole genome and TF enrichment test with the aid of CIS-BP, Jolma and other TF databases.
</p>
- <p class="description">[5] <B>tfTarget package</B>: <A href="https://github.com/Danko-Lab/tfTarget">https://github.com/Danko-Lab/tfTarget</A>.</p>
+ <p class="description">[6] <B>tfTarget package</B>: <A href="https://github.com/Danko-Lab/tfTarget">https://github.com/Danko-Lab/tfTarget</A>.</p>
<p class="description">
Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data.
</p>
- <p class="description">[6] <B>Proseq 2.0</B>: <A href="https://github.com/Danko-Lab/proseq2.0">https://github.com/Danko-Lab/proseq2.0</A>.</p>
+ <p class="description">[7] <B>Proseq 2.0</B>: <A href="https://github.com/Danko-Lab/proseq2.0">https://github.com/Danko-Lab/proseq2.0</A>.</p>
<p class="description">
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing.
</p>
- <p class="description">[7] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p>
+ <p class="description">[8] <B>Airavata PHP Gateway</B>: <A href="https://github.com/apache/airavata-php-gateway.git">https://github.com/apache/airavata-php-gateway.git</A>.</p>
<p class="description">
Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE.
</p>
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index 0110898..1325121 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -3,7 +3,7 @@
<div class="col-md-offset-2 col-md-8 breathing-space scigap-info" >
<h1 class="text-center">Welcome to dREG and dTOX gateway!</h1>
<p class="text-center" style="color:#cccccc;">
- Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.<br/>
+ Find the location of transcriptional regulatory elements and transcription factoring binding using genomic data.<br/>
</p>
<p class="text-center" style="color:#444444;">
The gateway status and updates are <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md"><B>here!</b></A>
@@ -13,7 +13,7 @@
<div class="col-md-offset-1 col-md-5" style="margin-left: 5%" >
<H2> How is dREG used?</H2>
<p style="font-size:14px; margin-top:10px; text-align:justify">
- The dREG model in the gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses pre-trained dREG model to identify divergent transcript start sites and impute the predicted DNase-1 hypersensitivity signal across the genome. The current dREG model works in any mammalian organism.</p>
+ The dREG model in the gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses a pre-trained dREG model to identify divergent transcript start sites and impute the predicted DNase-I hypersensitivity signal across the genome. The current dREG model works in any mammalian organism.</p>
<p style="font-size:14px; margin-top:10px;text-align:justify">
Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link. </p>
@@ -38,11 +38,17 @@ Registered users need only upload experimental data in the required format and p
<div class="col-md-offset-1 col-md-5" style="margin-left: 5%">
<H2> How is dTOX used? </H2>
- <p color="red">Under construction, please ignore this section! </p>
<p style="font-size:14px; margin-top:10px;text-align:justify">
-The dTOX models in the gateway predict the binding status of transcription factor binding sites using PRO-seq, ATAC-seq, or DNase-1-seq data. The server takes as input bigWig files provided by the user, which represent the PRO-seq, ATAC-seq, or DNase-1-seq signal on the plus and minus strand. Once the user selects the transcription factors to predict on, the gateway uses a pre-trained dTOX model to identify transcription factor binding patterns. The current dTOX models work in any mammal [...]
+The dTOX models in the gateway predict the binding status of transcription factor binding sites using PRO-seq, ATAC-seq, or DNase-I-seq data. The server takes as input bigWig files provided by the user, which represent the PRO-seq, ATAC-seq, or DNase-1-seq signal on the plus and minus strand. The gateway uses two pre-trained dTOX models to identify transcription factor binding patterns genome-wide. The current dTOX models work in any mammalian organism and on any motif that has an associ [...]
<p style="font-size:14px; margin-top:10px;text-align:justify">
The web operations are same as the dREG model. Users need to login -> upload data -> run data. Results can be downloaded or viewed in the WashU Genome browser.</p>
+ <p style="font-size:14px; margin-top:5px;text-align:justify">
+ <img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
+ Use the Danko lab's pipeline to <b>convert BAM files</b> of mapped reads to bigWig (<A ta
+rget=_blank href="https://github.com/Danko-Lab/RunOnBamToBigWig">here for PRO-seq</A>), (<A ta
+rget=_blank href="https://github.com/Danko-Lab/utils/dnase/BamToBigWig">here for DNase-I-seq</A>), and (<A ta
+rget=_blank href="https://github.com/Danko-Lab/utils/atacseq/BamToBigWig">here for ATAC-seq</A>).
+ </p>
<p style="font-size:14px; margin-top:5px;text-align:justify">
<img src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/webdev-bullet-icon.png" style="height:20px"></img>
[airavata-php-gateway] 14/14: Merge branch 'dreg-gateway' of
https://github.com/Danko-Lab/airavata-php-gateway into dreg-gateway
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit ee3df12bb6a375ff97a071201965074878ff1b9c
Merge: e52fc97 7768b4a
Author: Marcus Christie <ma...@iu.edu>
AuthorDate: Sun Jun 2 13:22:20 2019 -0400
Merge branch 'dreg-gateway' of https://github.com/Danko-Lab/airavata-php-gateway into dreg-gateway
app/libraries/CommonUtilities.php | 4 +-
app/libraries/FileTransfer.php | 113 ++++---
app/routes.php | 7 +-
app/views/account/dashboard.blade.php | 2 +-
app/views/experiment/create-complete.blade.php | 2 +-
app/views/experiment/create.blade.php | 2 +-
app/views/partials/experiment-info.blade.php | 89 +++++-
public/themes/dreg/assets/img/3d-number.jpg | Bin 0 -> 67965 bytes
public/themes/dreg/assets/img/dTOX-model.png | Bin 0 -> 99342 bytes
.../themes/dreg/assets/img/dreg-dtox-gateway.png | Bin 0 -> 132589 bytes
public/themes/dreg/assets/img/dreg.exp.summary.png | Bin 52211 -> 46929 bytes
public/themes/dreg/assets/img/dregicon.png | Bin 0 -> 2128 bytes
public/themes/dreg/assets/img/dtox.create.exp.png | Bin 0 -> 17154 bytes
public/themes/dreg/assets/img/dtox.create.exp2.png | Bin 0 -> 40049 bytes
public/themes/dreg/assets/img/failure1.png | Bin 0 -> 53330 bytes
public/themes/dreg/assets/img/failure2.png | Bin 0 -> 29925 bytes
public/themes/dreg/assets/img/failure3-reason.png | Bin 0 -> 15519 bytes
public/themes/dreg/assets/img/failure3.png | Bin 0 -> 32245 bytes
public/themes/dreg/assets/img/failure4-reason.png | Bin 0 -> 17034 bytes
public/themes/dreg/assets/img/n1.png | Bin 0 -> 15718 bytes
public/themes/dreg/assets/img/n2.png | Bin 0 -> 19546 bytes
public/themes/dreg/assets/img/n3.png | Bin 0 -> 22082 bytes
public/themes/dreg/assets/img/n4.png | Bin 0 -> 19153 bytes
public/themes/dreg/partials/about.blade.php | 23 +-
public/themes/dreg/partials/doc.blade.php | 286 ++++++++++++++++--
public/themes/dreg/partials/dtox-doc.blade.php | 331 +++++++++++++++++++++
public/themes/dreg/partials/faq.blade.php | 38 ++-
public/themes/dreg/partials/header.blade.php | 11 +-
public/themes/dreg/partials/software.blade.php | 64 ++++
public/themes/dreg/partials/template.blade.php | 152 +++++++---
30 files changed, 968 insertions(+), 156 deletions(-)
diff --cc app/views/partials/experiment-info.blade.php
index 046fb32,1e88c0b..867aeca
mode 100755,100644..100644
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
[airavata-php-gateway] 09/14: update UI
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 364ce0e0b43a65231b207dfa580318f4636e16a1
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Oct 29 17:57:50 2018 +0000
update UI
---
public/themes/dreg/assets/img/dreg.exp.summary.png | Bin 31052 -> 46929 bytes
public/themes/dreg/assets/img/failure3.png | Bin 31908 -> 32245 bytes
2 files changed, 0 insertions(+), 0 deletions(-)
diff --git a/public/themes/dreg/assets/img/dreg.exp.summary.png b/public/themes/dreg/assets/img/dreg.exp.summary.png
index 28604fe..3571f72 100755
Binary files a/public/themes/dreg/assets/img/dreg.exp.summary.png and b/public/themes/dreg/assets/img/dreg.exp.summary.png differ
diff --git a/public/themes/dreg/assets/img/failure3.png b/public/themes/dreg/assets/img/failure3.png
index a4a9f3a..6a1198b 100644
Binary files a/public/themes/dreg/assets/img/failure3.png and b/public/themes/dreg/assets/img/failure3.png differ