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Posted to dev@taverna.apache.org by "Stian Soiland-Reyes (JIRA)" <ji...@apache.org> on 2016/01/11 17:09:39 UTC
[jira] [Created] (TAVERNA-882) Publications page
Stian Soiland-Reyes created TAVERNA-882:
-------------------------------------------
Summary: Publications page
Key: TAVERNA-882
URL: https://issues.apache.org/jira/browse/TAVERNA-882
Project: Apache Taverna
Issue Type: New Feature
Components: Website
Reporter: Stian Soiland-Reyes
Priority: Minor
It would be good to have a Publications page with academic publications that are about Taverna or use Taverna.
The older http://www.taverna.org.uk/cite/ refers to the latest canonical citations about Taverna, http://dx.doi.org/10.1093/nar/gkt328
but even after moving to Apache we have gathered new citations:
https://scholar.google.co.uk/scholar?hl=en&q=%22Apache+Taverna%22&btnG=&as_sdt=1%2C5&as_sdtp=
Some searches (must be filtered further):
https://scholar.google.co.uk/scholar?q=Taverna+workflow&btnG=&hl=en&as_sdt=0%2C5
https://scholar.google.co.uk/scholar?q=Taverna+workbench&btnG=&hl=en&as_sdt=0%2C5
Also anything with Taverna on http://dev.mygrid.org.uk/wiki/display/about/myGrid+Publications
In addition to listing the master citation http://dx.doi.org/10.1093/nar/gkt328 I would propose a single chronological text page along the style we have used on http://www.esciencelab.org.uk/publications/ with links to the DOI and a preprint if it's not Open Access. (I guess those links can be tricky for older papers).
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Re: [jira] [Created] (TAVERNA-882) Publications page
Posted by Gale Naylor <Ga...@noventussolutions.com>.
I mocked up a Publications page on my blog.
https://galenaylor.wordpress.com/2016/01/11/references-and-publications/
(Wordpress
did not like the 4th level headers (e.g., ####2015), so I would fix that,
of course.)
It seems like this should be two pages: one for how to reference Taverna
and the website, and one to list relevant publications.
Also, I wasn't sure what to do about the reference to the latest canonical
citations.
Does this seem like a good start, or what should be changed?
(Sorry for the long emails with abstracts. I just now found the direct
links to the papers.)
Gale
On Mon, Jan 11, 2016 at 1:48 PM Gale Naylor <Ga...@noventussolutions.com>
wrote:
> What about this paper from October 2014? Would you want to include this on
> a publications page?
>
> Title: BIFI: a Taverna plugin for a simplified and user-friendly workflow
> platform.
>
> Authors: Yildiz A; Dilaveroglu E; Visne I; Günay B; Sefer E; Weinhausel
> A; Rattay F; Goble CA; Pandey RV; Kriegner A (Health & Environment
> Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria.
> albert.kriegner@ait.ac.at.)
>
> Source: BMC Research Notes [BMC Res Notes] 2014 Oct 20; Vol. 7, pp. 740.
> Date of Electronic Publication: 2014 Oct 20.
>
> Journal Info: Publisher: Biomed Central Country of Publication: England
> NLM ID: 101462768 Publication Model: Electronic Cited Medium: Internet
> ISSN: 1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation:
> BMC Res Notes Subsets: MEDLINE
>
> Abstract: Background: Heterogeneity in the features, input-output
> behaviour and user interface for available bioinformatics tools and
> services is still a bottleneck for both expert and non-expert users.
> Advancement in providing common interfaces over such tools and services are
> gaining interest among researchers. However, the lack of (meta-)
> information about input-output data and parameter prevents to provide
> automated and standardized solutions, which can assist users in setting the
> appropriate parameters. These limitations must be resolved especially in
> the workflow-based solution in order to ease the integration of software.
>
> Findings: We report a Taverna Workbench plugin: the XworX BIFI (Beautiful
> Interfaces for Inputs) implemented as a solution for the aforementioned
> issues. BIFI provides a Graphical User Interface (GUI) definition language
> used to layout the user interface and to define parameter options for
> Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF)
> directly or discover appropriate instances from a configured repository. In
> the absence of a GDF, BIFI generates a default interface.
>
> Conclusion: The Taverna Workbench is an open source software providing the
> ability to combine various services within a workflow. Nevertheless, users
> can supply input data to the workflow via a simple user interface providing
> only a text area to enter the input in text form. The workflow may contain
> meta-information in human readable form such as description text for the
> port and an example value. However, not all workflow ports are documented
> so well or have all the required information.BIFI uses custom user
> interface components for ports which give users feedback on the parameter
> data type or structure to be used for service execution and enables
> client-side data validations. Moreover, BIFI offers user interfaces that
> allow users to interactively construct workflow views and share them with
> the community, thus significantly increasing usability of heterogeneous,
> distributed service consumption.
>
> DOI: 10.1186/1756-0500-7-740
>
>
> On Mon, Jan 11, 2016 at 1:01 PM Gale Naylor <Ga...@noventussolutions.com>
> wrote:
>
>> On the other hand, I found this September 2015 paper on EBSCOHost, and it
>> looks promising:
>>
>> Title: Scientific workflow optimization for improved peptide and protein
>> identification.
>> Authors: Holl, Sonja; Mohammed, Yassene; Zimmermann, Olav; Palmblad,
>> Magnus (n.m.palmblad@lumc.nl)
>>
>> Source: BMC Bioinformatics. 9/3/2015, Vol. 16 Issue 1, p1-13. 13p. 1
>> Color Photograph, 1 Diagram, 3 Charts, 4 Graphs.
>>
>> Author-Supplied Keywords: Optimization, Scientific workflow, Tandem mass
>> spectrometry, Taverna workbench, X!Tandem
>>
>> Abstract: Background: Peptide-spectrum matching is a common step in most
>> data processing workflows for mass spectrometry-based proteomics. Many
>> algorithms and software packages, both free and commercial, have been
>> developed to address this task. However, these algorithms typically require
>> the user to select instrument- and sample-dependent parameters, such as
>> mass measurement error tolerances and number of missed enzymatic cleavages.
>> In order to select the best algorithm and parameter set for a particular
>> dataset, in-depth knowledge about the data as well as the algorithms
>> themselves is needed. Most researchers therefore tend to use default
>> parameters, which are not necessarily optimal. Results: *We have applied
>> a new optimization framework for the Taverna scientific workflow management
>> system* (http://ms-utils.org/Taverna_Optimization.pdf) to find the best
>> combination of parameters for a given scientific workflow to perform
>> peptide-spectrum matching. The optimizations themselves are non-trivial, as
>> demonstrated by several phenomena that can be observed when allowing for
>> larger mass measurement errors in sequence database searches. On-the-fly
>> parameter optimization embedded in scientific workflow management systems
>> enables experts and non-experts alike to extract the maximum amount of
>> information from the data. The same workflows could be used for exploring
>> the parameter space and compare algorithms, not only for peptide-spectrum
>> matching, but also for other tasks, such as retention time prediction.
>> Conclusion: Using the optimization framework, we were able to learn about
>> how the data was acquired as well as the explored algorithms. We observed a
>> phenomenon identifying many ammonia-loss b-ion spectra as peptides with
>> N-terminal pyroglutamate and a large precursor mass measurement error.
>> These insights could only be gained with the extension of the common range
>> for the mass measurement error tolerance parameters explored by the
>> optimization framework. [ABSTRACT FROM AUTHOR]
>>
>> Copyright of BMC Bioinformatics is the property of BioMed Central and its
>> content may not be copied or emailed to multiple sites or posted to a
>> listserv without the copyright holder's express written permission.
>> However, users may print, download, or email articles for individual use.
>> This abstract may be abridged. No warranty is given about the accuracy of
>> the copy. Users should refer to the original published version of the
>> material for the full abstract. (Copyright applies to all Abstracts.)
>>
>> DOI: 10.1186/s12859-015-0714-x
>>
>>
>> On Mon, Jan 11, 2016 at 12:42 PM Gale Naylor <Ga...@noventussolutions.com>
>> wrote:
>>
>>> I looked at the links to the Google scholar searches above and mostly
>>> found oblique references to Apache Taverna, along the lines of what Alan
>>> mentioned. The only one that looked promising to me was this one:
>>>
>>> Local Graph Patterns for Scientific Workflow Similarity Search
>>>
>>>
>>> https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf
>>>
>>>
>>> But, it looked more like a detailed abstract and not a compete paper.
>>>
>>>
>>> The other searches seemed only to return older references to Taverna
>>> (2013 and earlier).
>>>
>>>
>>> I can make an Apache Taverna page for citations, but I will need help
>>> with what publications you think are good to include.
>>>
>>>
>>> Gale
>>>
>>>
>>>
>>> On Mon, Jan 11, 2016 at 8:21 AM alaninmcr <al...@googlemail.com>
>>> wrote:
>>>
>>>> Just a warning that you need to be careful when doing a search. A lot of
>>>> the citations will be unhelpful like "Popular workflow systems include
>>>> X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z
>>>> because ...".
>>>>
>>>> Alan
>>>>
>>>
Re: [jira] [Created] (TAVERNA-882) Publications page
Posted by Gale Naylor <Ga...@noventussolutions.com>.
What about this paper from October 2014? Would you want to include this on
a publications page?
Title: BIFI: a Taverna plugin for a simplified and user-friendly workflow
platform.
Authors: Yildiz A; Dilaveroglu E; Visne I; Günay B; Sefer E; Weinhausel A;
Rattay F; Goble CA; Pandey RV; Kriegner A (Health & Environment Department,
AIT Austrian Institute of Technology GmbH, Vienna, Austria.
albert.kriegner@ait.ac.at.)
Source: BMC Research Notes [BMC Res Notes] 2014 Oct 20; Vol. 7, pp. 740.
Date of Electronic Publication: 2014 Oct 20.
Journal Info: Publisher: Biomed Central Country of Publication: England NLM
ID: 101462768 Publication Model: Electronic Cited Medium: Internet ISSN:
1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation: BMC Res
Notes Subsets: MEDLINE
Abstract: Background: Heterogeneity in the features, input-output behaviour
and user interface for available bioinformatics tools and services is still
a bottleneck for both expert and non-expert users. Advancement in providing
common interfaces over such tools and services are gaining interest among
researchers. However, the lack of (meta-) information about input-output
data and parameter prevents to provide automated and standardized
solutions, which can assist users in setting the appropriate parameters.
These limitations must be resolved especially in the workflow-based
solution in order to ease the integration of software.
Findings: We report a Taverna Workbench plugin: the XworX BIFI (Beautiful
Interfaces for Inputs) implemented as a solution for the aforementioned
issues. BIFI provides a Graphical User Interface (GUI) definition language
used to layout the user interface and to define parameter options for
Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF)
directly or discover appropriate instances from a configured repository. In
the absence of a GDF, BIFI generates a default interface.
Conclusion: The Taverna Workbench is an open source software providing the
ability to combine various services within a workflow. Nevertheless, users
can supply input data to the workflow via a simple user interface providing
only a text area to enter the input in text form. The workflow may contain
meta-information in human readable form such as description text for the
port and an example value. However, not all workflow ports are documented
so well or have all the required information.BIFI uses custom user
interface components for ports which give users feedback on the parameter
data type or structure to be used for service execution and enables
client-side data validations. Moreover, BIFI offers user interfaces that
allow users to interactively construct workflow views and share them with
the community, thus significantly increasing usability of heterogeneous,
distributed service consumption.
DOI: 10.1186/1756-0500-7-740
On Mon, Jan 11, 2016 at 1:01 PM Gale Naylor <Ga...@noventussolutions.com>
wrote:
> On the other hand, I found this September 2015 paper on EBSCOHost, and it
> looks promising:
>
> Title: Scientific workflow optimization for improved peptide and protein
> identification.
> Authors: Holl, Sonja; Mohammed, Yassene; Zimmermann, Olav; Palmblad,
> Magnus (n.m.palmblad@lumc.nl)
>
> Source: BMC Bioinformatics. 9/3/2015, Vol. 16 Issue 1, p1-13. 13p. 1
> Color Photograph, 1 Diagram, 3 Charts, 4 Graphs.
>
> Author-Supplied Keywords: Optimization, Scientific workflow, Tandem mass
> spectrometry, Taverna workbench, X!Tandem
>
> Abstract: Background: Peptide-spectrum matching is a common step in most
> data processing workflows for mass spectrometry-based proteomics. Many
> algorithms and software packages, both free and commercial, have been
> developed to address this task. However, these algorithms typically require
> the user to select instrument- and sample-dependent parameters, such as
> mass measurement error tolerances and number of missed enzymatic cleavages.
> In order to select the best algorithm and parameter set for a particular
> dataset, in-depth knowledge about the data as well as the algorithms
> themselves is needed. Most researchers therefore tend to use default
> parameters, which are not necessarily optimal. Results: *We have applied
> a new optimization framework for the Taverna scientific workflow management
> system* (http://ms-utils.org/Taverna_Optimization.pdf) to find the best
> combination of parameters for a given scientific workflow to perform
> peptide-spectrum matching. The optimizations themselves are non-trivial, as
> demonstrated by several phenomena that can be observed when allowing for
> larger mass measurement errors in sequence database searches. On-the-fly
> parameter optimization embedded in scientific workflow management systems
> enables experts and non-experts alike to extract the maximum amount of
> information from the data. The same workflows could be used for exploring
> the parameter space and compare algorithms, not only for peptide-spectrum
> matching, but also for other tasks, such as retention time prediction.
> Conclusion: Using the optimization framework, we were able to learn about
> how the data was acquired as well as the explored algorithms. We observed a
> phenomenon identifying many ammonia-loss b-ion spectra as peptides with
> N-terminal pyroglutamate and a large precursor mass measurement error.
> These insights could only be gained with the extension of the common range
> for the mass measurement error tolerance parameters explored by the
> optimization framework. [ABSTRACT FROM AUTHOR]
>
> Copyright of BMC Bioinformatics is the property of BioMed Central and its
> content may not be copied or emailed to multiple sites or posted to a
> listserv without the copyright holder's express written permission.
> However, users may print, download, or email articles for individual use.
> This abstract may be abridged. No warranty is given about the accuracy of
> the copy. Users should refer to the original published version of the
> material for the full abstract. (Copyright applies to all Abstracts.)
>
> DOI: 10.1186/s12859-015-0714-x
>
>
> On Mon, Jan 11, 2016 at 12:42 PM Gale Naylor <Ga...@noventussolutions.com>
> wrote:
>
>> I looked at the links to the Google scholar searches above and mostly
>> found oblique references to Apache Taverna, along the lines of what Alan
>> mentioned. The only one that looked promising to me was this one:
>>
>> Local Graph Patterns for Scientific Workflow Similarity Search
>>
>>
>> https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf
>>
>>
>> But, it looked more like a detailed abstract and not a compete paper.
>>
>>
>> The other searches seemed only to return older references to Taverna
>> (2013 and earlier).
>>
>>
>> I can make an Apache Taverna page for citations, but I will need help
>> with what publications you think are good to include.
>>
>>
>> Gale
>>
>>
>>
>> On Mon, Jan 11, 2016 at 8:21 AM alaninmcr <al...@googlemail.com>
>> wrote:
>>
>>> Just a warning that you need to be careful when doing a search. A lot of
>>> the citations will be unhelpful like "Popular workflow systems include
>>> X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z
>>> because ...".
>>>
>>> Alan
>>>
>>
Re: [jira] [Created] (TAVERNA-882) Publications page
Posted by Gale Naylor <Ga...@noventussolutions.com>.
On the other hand, I found this September 2015 paper on EBSCOHost, and it
looks promising:
Title: Scientific workflow optimization for improved peptide and protein
identification.
Authors: Holl, Sonja; Mohammed, Yassene; Zimmermann, Olav; Palmblad, Magnus
(n.m.palmblad@lumc.nl)
Source: BMC Bioinformatics. 9/3/2015, Vol. 16 Issue 1, p1-13. 13p. 1 Color
Photograph, 1 Diagram, 3 Charts, 4 Graphs.
Author-Supplied Keywords: Optimization, Scientific workflow, Tandem mass
spectrometry, Taverna workbench, X!Tandem
Abstract: Background: Peptide-spectrum matching is a common step in most
data processing workflows for mass spectrometry-based proteomics. Many
algorithms and software packages, both free and commercial, have been
developed to address this task. However, these algorithms typically require
the user to select instrument- and sample-dependent parameters, such as
mass measurement error tolerances and number of missed enzymatic cleavages.
In order to select the best algorithm and parameter set for a particular
dataset, in-depth knowledge about the data as well as the algorithms
themselves is needed. Most researchers therefore tend to use default
parameters, which are not necessarily optimal. Results: *We have applied a
new optimization framework for the Taverna scientific workflow management
system* (http://ms-utils.org/Taverna_Optimization.pdf) to find the best
combination of parameters for a given scientific workflow to perform
peptide-spectrum matching. The optimizations themselves are non-trivial, as
demonstrated by several phenomena that can be observed when allowing for
larger mass measurement errors in sequence database searches. On-the-fly
parameter optimization embedded in scientific workflow management systems
enables experts and non-experts alike to extract the maximum amount of
information from the data. The same workflows could be used for exploring
the parameter space and compare algorithms, not only for peptide-spectrum
matching, but also for other tasks, such as retention time prediction.
Conclusion: Using the optimization framework, we were able to learn about
how the data was acquired as well as the explored algorithms. We observed a
phenomenon identifying many ammonia-loss b-ion spectra as peptides with
N-terminal pyroglutamate and a large precursor mass measurement error.
These insights could only be gained with the extension of the common range
for the mass measurement error tolerance parameters explored by the
optimization framework. [ABSTRACT FROM AUTHOR]
Copyright of BMC Bioinformatics is the property of BioMed Central and its
content may not be copied or emailed to multiple sites or posted to a
listserv without the copyright holder's express written permission.
However, users may print, download, or email articles for individual use.
This abstract may be abridged. No warranty is given about the accuracy of
the copy. Users should refer to the original published version of the
material for the full abstract. (Copyright applies to all Abstracts.)
DOI: 10.1186/s12859-015-0714-x
On Mon, Jan 11, 2016 at 12:42 PM Gale Naylor <Ga...@noventussolutions.com>
wrote:
> I looked at the links to the Google scholar searches above and mostly
> found oblique references to Apache Taverna, along the lines of what Alan
> mentioned. The only one that looked promising to me was this one:
>
> Local Graph Patterns for Scientific Workflow Similarity Search
>
>
> https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf
>
>
> But, it looked more like a detailed abstract and not a compete paper.
>
>
> The other searches seemed only to return older references to Taverna (2013
> and earlier).
>
>
> I can make an Apache Taverna page for citations, but I will need help with
> what publications you think are good to include.
>
>
> Gale
>
>
>
> On Mon, Jan 11, 2016 at 8:21 AM alaninmcr <al...@googlemail.com>
> wrote:
>
>> Just a warning that you need to be careful when doing a search. A lot of
>> the citations will be unhelpful like "Popular workflow systems include
>> X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z
>> because ...".
>>
>> Alan
>>
>
Re: [jira] [Created] (TAVERNA-882) Publications page
Posted by Gale Naylor <Ga...@noventussolutions.com>.
I looked at the links to the Google scholar searches above and mostly found
oblique references to Apache Taverna, along the lines of what Alan
mentioned. The only one that looked promising to me was this one:
Local Graph Patterns for Scientific Workflow Similarity Search
https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/teaching/studienDiplomArbeiten/running/expose_wiegandt_151116.pdf
But, it looked more like a detailed abstract and not a compete paper.
The other searches seemed only to return older references to Taverna (2013
and earlier).
I can make an Apache Taverna page for citations, but I will need help with
what publications you think are good to include.
Gale
On Mon, Jan 11, 2016 at 8:21 AM alaninmcr <al...@googlemail.com> wrote:
> Just a warning that you need to be careful when doing a search. A lot of
> the citations will be unhelpful like "Popular workflow systems include
> X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z
> because ...".
>
> Alan
>
Re: [jira] [Created] (TAVERNA-882) Publications page
Posted by alaninmcr <al...@googlemail.com>.
Just a warning that you need to be careful when doing a search. A lot of
the citations will be unhelpful like "Popular workflow systems include
X, Y, Taverna and Z" or "Our system is better than X, Y, Taverna and Z
because ...".
Alan