You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@commons.apache.org by "Mark R. Diggory" <md...@latte.harvard.edu> on 2003/08/16 19:10:20 UTC
[math] JLink for Mathematica and Generic API's
Hey guys,
Have any of you checked out JLink for mathematica? This is a very
interesting JNI bridge for Mathematica. I find it kinda interesting
because they use a Functor pattern in the "Eval" class of this package.
http://www.wolfram.com/solutions/mathlink/jlink/
I'm also looking at the Omegahat Project for intersting usage that may
relate back to our library in our future:
http://www.omegahat.org/
Specifically, this is an interesting XML Markup for Statistics that R
and Matlab currently provide.
http://www.omegahat.org/StatDataML/
I also notice theres support for this in Octave www.octave.org as well.
I know this is actually outside of the "scope of development" for
commons math. But, I think its interesting to see where all these
projects are going in terms of Java development, cross language
interaction and the exposure of their api's. One interest to me is
defining a "subset" of functionality across all these applications that
can also applies to commons math. I'm interested in the possibility of a
"specification/api" that can be used to define statistical/mathematical
evaluations in java. A generic api that one could write an evaluation in
which could be executed against any provider, similar in nature to JAXP
or JNDI.
-Mark
RE: [math] Would code for generating IC50 curves fit here?
Posted by Eric Pugh <ep...@upstate.com>.
Al,
You are correct.. Those curves are used for testing data, looking for
"goodness of fit" when plotting a series of data points that should be on a
nice curve.
You are right about more general curve fitting would be the way to go.
I'm hoping to not reinvent the wheel on this, but if I do, I will post it to
[math] as a proposal.
Eric
-----Original Message-----
From: Al Chou [mailto:hotfusionman@yahoo.com]
Sent: Sunday, August 17, 2003 7:49 PM
To: Jakarta Commons Developers List
Subject: Re: [math] Would code for generating IC50 curves fit here?
--- Eric Pugh <ep...@upstate.com> wrote:
> Hi all,
>
> I am faced with a needing to generate IC50 (also called EC50) curves for a
> project.
>
> A) Does anyone know of any packages that do this?
>
> B) If not, would this be something of interest for Math?
I don't think we have any curve-fitting code yet. I think a set of more
widely
used curves (a brief search on Google suggests that IC50/EC50 curves are
used
primarily in pharmacology, is that right?) would be higher on the priority
list, if we were to put curve fitting in scope for some release (it probably
wouldn't be the initial release, given the situation to date).
Al
=====
Albert Davidson Chou
Get answers to Mac questions at http://www.Mac-Mgrs.org/ .
__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
RE: [math] Would code for generating IC50 curves fit here?
Posted by Eric Pugh <ep...@upstate.com>.
Al,
You are correct.. Those curves are used for testing data, looking for
"goodness of fit" when plotting a series of data points that should be on a
nice curve.
You are right about more general curve fitting would be the way to go.
I'm hoping to not reinvent the wheel on this, but if I do, I will post it to
[math] as a proposal.
Eric
-----Original Message-----
From: Al Chou [mailto:hotfusionman@yahoo.com]
Sent: Sunday, August 17, 2003 7:49 PM
To: Jakarta Commons Developers List
Subject: Re: [math] Would code for generating IC50 curves fit here?
--- Eric Pugh <ep...@upstate.com> wrote:
> Hi all,
>
> I am faced with a needing to generate IC50 (also called EC50) curves for a
> project.
>
> A) Does anyone know of any packages that do this?
>
> B) If not, would this be something of interest for Math?
I don't think we have any curve-fitting code yet. I think a set of more
widely
used curves (a brief search on Google suggests that IC50/EC50 curves are
used
primarily in pharmacology, is that right?) would be higher on the priority
list, if we were to put curve fitting in scope for some release (it probably
wouldn't be the initial release, given the situation to date).
Al
=====
Albert Davidson Chou
Get answers to Mac questions at http://www.Mac-Mgrs.org/ .
__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
Re: [math] Would code for generating IC50 curves fit here?
Posted by Al Chou <ho...@yahoo.com>.
--- Eric Pugh <ep...@upstate.com> wrote:
> Hi all,
>
> I am faced with a needing to generate IC50 (also called EC50) curves for a
> project.
>
> A) Does anyone know of any packages that do this?
>
> B) If not, would this be something of interest for Math?
I don't think we have any curve-fitting code yet. I think a set of more widely
used curves (a brief search on Google suggests that IC50/EC50 curves are used
primarily in pharmacology, is that right?) would be higher on the priority
list, if we were to put curve fitting in scope for some release (it probably
wouldn't be the initial release, given the situation to date).
Al
=====
Albert Davidson Chou
Get answers to Mac questions at http://www.Mac-Mgrs.org/ .
__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
Re: [math] Would code for generating IC50 curves fit here?
Posted by Al Chou <ho...@yahoo.com>.
--- Eric Pugh <ep...@upstate.com> wrote:
> Hi all,
>
> I am faced with a needing to generate IC50 (also called EC50) curves for a
> project.
>
> A) Does anyone know of any packages that do this?
>
> B) If not, would this be something of interest for Math?
I don't think we have any curve-fitting code yet. I think a set of more widely
used curves (a brief search on Google suggests that IC50/EC50 curves are used
primarily in pharmacology, is that right?) would be higher on the priority
list, if we were to put curve fitting in scope for some release (it probably
wouldn't be the initial release, given the situation to date).
Al
=====
Albert Davidson Chou
Get answers to Mac questions at http://www.Mac-Mgrs.org/ .
__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com
[math] Would code for generating IC50 curves fit here?
Posted by Eric Pugh <ep...@upstate.com>.
Hi all,
I am faced with a needing to generate IC50 (also called EC50) curves for a
project.
A) Does anyone know of any packages that do this?
B) If not, would this be something of interest for Math?
Eric Pugh
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
[math] Would code for generating IC50 curves fit here?
Posted by Eric Pugh <ep...@upstate.com>.
Hi all,
I am faced with a needing to generate IC50 (also called EC50) curves for a
project.
A) Does anyone know of any packages that do this?
B) If not, would this be something of interest for Math?
Eric Pugh
Re: [math] JLink for Mathematica and Generic API's
Posted by "Mark R. Diggory" <md...@latte.harvard.edu>.
Brent Worden wrote:
>
> If you're talking about creating a Service Provider Interface, I
> whole-heartedly agree. I envision we would follow the existing JAR
> service provider mechanism
>(http://java.sun.com/j2se/1.4.1/docs/guide/jar/jar.html#Service%20Provider)
> and use commons-discovery to enable it.
>
Yes, That is a technology we could take advantage of.
> The library, as it stands, wouldn't be too hard to morph into two
> separate JARs, one for the API and one for the default implementation.
> Brent Worden
> http://www.brent.worden.org
The questions for me that arise have to do with applicability to other
libraries like JLink, Omegahat, R, S-plus, Matlab etc. In an ideal
world, it would be an ambitious project that would require involvement
from all these groups to establish a standard API (in the real world,
estabilishing an example of such an API is probibly more attainable).
I'm surprised that nothing of this nature has already developed? Unless
I'm missing something in my research. There is an interesting project at
Omegahat for a standard StatDataXml markup language for transfering data
between platforms. But I have yet to locate anything suggesting a a
standard API of some sort for Java itself.
http://www.omegahat.org/StatDataML/
And Omegahat itself is a platform that has several plugins spanning many
of these applications.
http://www.omegahat.org/download/R/packages/
So in summary, so far I have the following examples for which such a
standardized API might be usefull:
SJava: JNI bridge between Java and R.
http://www.omegahat.org/download/R/packages/SJava.tar.gz
Matlab has their Bridge between Java and Matlab
http://www.mathworks.com/access/helpdesk_r12p1/help/techdoc/matlab_external/ch_java.shtml#82500
Mathematica has the following JLink API
http://www.wolfram.com/solutions/mathlink/jlink/
Finally, CERN has the COLT package
http://hoschek.home.cern.ch/hoschek/colt/
I would find it interesting to review these API's to see their
similarities and differences in relation to each other and Commons Math.
-Mark
Re: [math] JLink for Mathematica and Generic API's
Posted by "Mark R. Diggory" <md...@latte.harvard.edu>.
Brent Worden wrote:
>
> If you're talking about creating a Service Provider Interface, I
> whole-heartedly agree. I envision we would follow the existing JAR
> service provider mechanism
>(http://java.sun.com/j2se/1.4.1/docs/guide/jar/jar.html#Service%20Provider)
> and use commons-discovery to enable it.
>
Yes, That is a technology we could take advantage of.
> The library, as it stands, wouldn't be too hard to morph into two
> separate JARs, one for the API and one for the default implementation.
> Brent Worden
> http://www.brent.worden.org
The questions for me that arise have to do with applicability to other
libraries like JLink, Omegahat, R, S-plus, Matlab etc. In an ideal
world, it would be an ambitious project that would require involvement
from all these groups to establish a standard API (in the real world,
estabilishing an example of such an API is probibly more attainable).
I'm surprised that nothing of this nature has already developed? Unless
I'm missing something in my research. There is an interesting project at
Omegahat for a standard StatDataXml markup language for transfering data
between platforms. But I have yet to locate anything suggesting a a
standard API of some sort for Java itself.
http://www.omegahat.org/StatDataML/
And Omegahat itself is a platform that has several plugins spanning many
of these applications.
http://www.omegahat.org/download/R/packages/
So in summary, so far I have the following examples for which such a
standardized API might be usefull:
SJava: JNI bridge between Java and R.
http://www.omegahat.org/download/R/packages/SJava.tar.gz
Matlab has their Bridge between Java and Matlab
http://www.mathworks.com/access/helpdesk_r12p1/help/techdoc/matlab_external/ch_java.shtml#82500
Mathematica has the following JLink API
http://www.wolfram.com/solutions/mathlink/jlink/
Finally, CERN has the COLT package
http://hoschek.home.cern.ch/hoschek/colt/
I would find it interesting to review these API's to see their
similarities and differences in relation to each other and Commons Math.
-Mark
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
RE: [math] JLink for Mathematica and Generic API's
Posted by Brent Worden <br...@worden.org>.
>
> I know this is actually outside of the "scope of development" for
> commons math. But, I think its interesting to see where all these
> projects are going in terms of Java development, cross language
> interaction and the exposure of their api's. One interest to me is
> defining a "subset" of functionality across all these applications that
> can also applies to commons math. I'm interested in the possibility of a
> "specification/api" that can be used to define statistical/mathematical
> evaluations in java. A generic api that one could write an evaluation in
> which could be executed against any provider, similar in nature to JAXP
> or JNDI.
>
>
> -Mark
If you're talking about creating a Service Provider Interface, I
whole-heartedly agree. I envision we would follow the existing JAR service
provider mechanism
(http://java.sun.com/j2se/1.4.1/docs/guide/jar/jar.html#Service%20Provider)
and use commons-discovery to enable it.
The library, as it stands, wouldn't be too hard to morph into two separate
JARs, one for the API and one for the default implementation.
Brent Worden
http://www.brent.worden.org
---------------------------------------------------------------------
To unsubscribe, e-mail: commons-dev-unsubscribe@jakarta.apache.org
For additional commands, e-mail: commons-dev-help@jakarta.apache.org
RE: [math] JLink for Mathematica and Generic API's
Posted by Brent Worden <br...@worden.org>.
>
> I know this is actually outside of the "scope of development" for
> commons math. But, I think its interesting to see where all these
> projects are going in terms of Java development, cross language
> interaction and the exposure of their api's. One interest to me is
> defining a "subset" of functionality across all these applications that
> can also applies to commons math. I'm interested in the possibility of a
> "specification/api" that can be used to define statistical/mathematical
> evaluations in java. A generic api that one could write an evaluation in
> which could be executed against any provider, similar in nature to JAXP
> or JNDI.
>
>
> -Mark
If you're talking about creating a Service Provider Interface, I
whole-heartedly agree. I envision we would follow the existing JAR service
provider mechanism
(http://java.sun.com/j2se/1.4.1/docs/guide/jar/jar.html#Service%20Provider)
and use commons-discovery to enable it.
The library, as it stands, wouldn't be too hard to morph into two separate
JARs, one for the API and one for the default implementation.
Brent Worden
http://www.brent.worden.org