Menu
▾
▴
sbfc-devel — Mailing list to discuss SBFC code
You can subscribe to this list here.
| 2012 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(2) |
Jul
(1) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2013 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(1) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2015 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(2) |
Jun
(3) |
Jul
|
Aug
|
Sep
(2) |
Oct
|
Nov
|
Dec
|
| 2018 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(2) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Rashid S. <ras...@gm...> - 2018-05-18 15:14:34
|
Hello,
I have been trying to use rbiopaxparser(R package) to parse
biopax models that I got from biomodels (https://www.ebi.ac.
uk/biomodels-main/ <https://www.ebi.ac.uk/biomodels-main/> <
https://www.ebi.ac.uk/biomodels-main/
<https://www.ebi.ac.uk/biomodels-main/>>).
I wanted the ACTIVATION/INHIBITION data(adjacency matrix) from the models
for pathways and as far as I have read in the documenation for biopax,
there has to be a "control" class which I don't get from biopax models in
the biomodels database. How do I get the ACTIVATION/INHIBITION data?
I found this slide http://co.mbine.org/events/COM
BINE_2016/agenda?q=system/files/tramy-combine-2016.pdf which mentioned
about the different conversion tools from SBML to biopax. What I did was
convert one of the SBML files from biomodels database to a biopax model
using SBML2Biopax web tool:https://www.ebi.ac.uk/biomodels/tools/converters/
I didn't get the control class in the new biopax model. Maybe it doesn't
have/create the control object at all? I don't have much idea on how to go
about solving this or creating my own controls. Previously I used
biopax models from NCI_pid, NCI_reactome, NCI_kegg to get the
activation/inhibition data and I was trying to do the same thing with the
biopax model in biomodels and I still haven't been able to figure out how
to solve this.
Also, how can I get the actual pathway names from the biopax models in
biomodels database? They don't have a NAME identifier for the pathway and
it's encoded based on MIRIAM.
Thank you.
Rashid
University of Cincinnati
|
|
From: Nicolas Le N. <n.l...@gm...> - 2018-05-17 20:56:28
|
Hello,
I am forwarding that on the behalf of a user of BioModels' BioPAX files. I believe some work has been done during a GSoC on the SBML to BioPAX converter?
-------- Forwarded Message --------
Subject: [biopax-discuss] Re: No biopax "control" class in biomodels and getting pathway information
Date: Thu, 17 May 2018 12:57:53 -0700 (PDT)
From: Igo R <ro...@gm...>
Reply-To: bio...@go...
To: BioPAX discussion group <bio...@go...>
There is nothing wrong with BioPAX in this regard - 'control' (BioPAX Level2 class) and 'Control' (and Catalysis, Modulation subclasses in BioPAX Level3) are still there, in the specification.
This does not require every data provider generate all the available in the BioPAX ontology classes and properties every time, alright.
You're dealing with BioPAX instance data (models of pathways/interactions), such as from BioModels, BioPAX Level2 I suppose, where there can no 'control' objects at all, which is ok as long as authors meant that.
They exported to BioPAX what they wanted or could. There might be other semantic problems, such as with identifiers, controlled vocabularies, etc., - critical or not so (you can tell some is you'd run it through the BioPAX Validator, or summarize with Paxtools app, etc.)
On Thursday, May 17, 2018 at 3:44:26 PM UTC-4, Rashid Saadman wrote:
Hello,
I'm currently a PhD candidate at the University of Cincinnati and I have been trying to use rbiopaxparser(R package) to parse biopax models that I got from biomodels (https://www.ebi.ac.uk/biomodels-main/ <https://www.ebi.ac.uk/biomodels-main/>). I wanted the ACTIVATION/INHIBITION data(adjacency matrix) from the models for pathways and as far as I have read in the documenation for biopax, there has to be a "control" class which I don't get from biopax models in the biomodels database. How do I get the ACTIVATION/INHIBITION data?
Also, how can I get the actual pathway names from the biopax models in biomodels database? They don't have a NAME identifier for the pathway and it's encoded based on MIRIAM.
Thank you
Rashid Saadman Karim
--
You received this message because you are subscribed to the Google Groups "BioPAX discussion group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bio...@go... <mailto:bio...@go...>.
Visit this group at https://groups.google.com/group/biopax-discuss.
To view this discussion on the web visit https://groups.google.com/d/msgid/biopax-discuss/22bbc4af-a5d4-46d5-b302-53a87828a539%40googlegroups.com <https://groups.google.com/d/msgid/biopax-discuss/22bbc4af-a5d4-46d5-b302-53a87828a539%40googlegroups.com?utm_medium=email&utm_source=footer>.
For more options, visit https://groups.google.com/d/optout.
|
|
From: Nicolas Le N. <n.l...@gm...> - 2015-09-25 12:33:20
|
Hello, Preparing a course on pathways, I noticed a glitch in SBML to BioPAX L3 generation. I am using the model 10 (Kholodenko 2000). http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010 In the reaction MKK (Mek1)->MKK-P (Mek1-P); MKKK-P (Mos-P) The control by Mos-P is listed as INHIBITION, and not ACTIVATION <bp:Control rdf:about="control_J2_MKKK_P_0"> <bp:controlled rdf:resource="conversion_J2" /> <bp:controlType rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType> <bp:controller rdf:resource="PEP0_control_J2MKKK_P" /> </bp:Control> Actually, this should even be directly a CATALYSIS (rather than a Control) The problem is also present in Level 2. All controls are INHIBITION :-( -- Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere n.l...@gm..., http://orcid.org/0000-0002-6309-7327 http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/ |
|
From: Nicolas R. <rod...@eb...> - 2015-09-18 15:20:02
|
Hello, I just deployed a new version of the SBFC online app at: http://www.ebi.ac.uk/biomodels/tools/ Please have a look and play around with it to see if everything is working fine. We have added some new converters from BioPAX and GPML in this release. If no major problems are encountered we will tweet and send an email announcement about it next week. Thanks, Nico |
|
From: Martijn v. I. <mva...@gm...> - 2015-06-29 16:10:59
|
Yes, no objection here. regards, Martijn On 29/06/15 16:31, Martina Summer-Kutmon wrote: > Fine by me! > > Best regards, > Tina > > On Mon, Jun 29, 2015 at 5:22 PM, Nicolas Rodriguez <rod...@eb... > <mailto:rod...@eb...>> wrote: > > Hello all, > > We are thinking about the current licensing of the SBFC framework > and associated converters. > At the moment, most files in the trunk have a GPL header that > point to a non existing AUTHORS file for the > copyright. On the OSGi branch the new files have not license > information at all. > > We are proposing to switch everything to LGPL (probably version > 2.1 similar to what JSBML and libSBML are using) or at least the > framework then individual converters > can have different licenses. > > Please, let us know as soon as possible if you have anything > against this. > > The reasons for the change are two fold. First we are trying to > polish everything in order to try to publish a paper at the end > and we thought LGPL is > better, easier to know what you are allowed to do or not. > Secondly, we are trying to find some more money as part of a new > NIH grant and in general > they prefer LGPL. > > Thanks, > Nico > > > > > -- > /----------------------------------------------- > Martina Summer-Kutmon, PhD > email: mk...@gm... <mailto:mk...@gm...> > skype: mkutmon/ > > > ------------------------------------------------------------------------------ > Monitor 25 network devices or servers for free with OpManager! > OpManager is web-based network management software that monitors > network devices and physical & virtual servers, alerts via email & sms > for fault. Monitor 25 devices for free with no restriction. Download now > http://ad.doubleclick.net/ddm/clk/292181274;119417398;o > > > _______________________________________________ > Sbfc-devel mailing list > Sbf...@li... > https://lists.sourceforge.net/lists/listinfo/sbfc-devel |
|
From: Martina Summer-K. <mk...@gm...> - 2015-06-29 15:31:48
|
Fine by me! Best regards, Tina On Mon, Jun 29, 2015 at 5:22 PM, Nicolas Rodriguez <rod...@eb...> wrote: > Hello all, > > We are thinking about the current licensing of the SBFC framework and > associated converters. > At the moment, most files in the trunk have a GPL header that point to a > non existing AUTHORS file for the > copyright. On the OSGi branch the new files have not license information > at all. > > We are proposing to switch everything to LGPL (probably version 2.1 > similar to what JSBML and libSBML are using) or at least the framework then > individual converters > can have different licenses. > > Please, let us know as soon as possible if you have anything against this. > > The reasons for the change are two fold. First we are trying to polish > everything in order to try to publish a paper at the end and we thought > LGPL is > better, easier to know what you are allowed to do or not. Secondly, we are > trying to find some more money as part of a new NIH grant and in general > they prefer LGPL. > > Thanks, > Nico > > -- *-----------------------------------------------Martina Summer-Kutmon, PhDemail: mk...@gm... <mk...@gm...>skype: mkutmon* |
|
From: Nicolas R. <rod...@eb...> - 2015-06-29 15:23:17
|
Hello all, We are thinking about the current licensing of the SBFC framework and associated converters. At the moment, most files in the trunk have a GPL header that point to a non existing AUTHORS file for the copyright. On the OSGi branch the new files have not license information at all. We are proposing to switch everything to LGPL (probably version 2.1 similar to what JSBML and libSBML are using) or at least the framework then individual converters can have different licenses. Please, let us know as soon as possible if you have anything against this. The reasons for the change are two fold. First we are trying to polish everything in order to try to publish a paper at the end and we thought LGPL is better, easier to know what you are allowed to do or not. Secondly, we are trying to find some more money as part of a new NIH grant and in general they prefer LGPL. Thanks, Nico |
|
From: Nicolas Le N. <n.l...@gm...> - 2015-05-19 09:45:04
|
On 19/05/15 10:41, Nicolas Rodriguez wrote: > I have started to add some README files on sourceforge to explain a bit what the different folders and files are about. > I still need to work on the content but you can see an example there: > > https://sourceforge.net/p/sbfc/code Excellent. > I found it nice in SBML/JSBML to have an ascii art at the end of the README so I have selected > two that I like. Any preferences? Would you like a different one or none at all ? The 3D is very nice I think. > Now about the logo. It would be nice to have a logo at least to display on the main page at http://sbfc.sourceforge.net/. > (more images or graph in the text as well) > > I was thinking of doing something very simple using SBFC with the COMBINE colors ? Any thoughts ? Yep. I must still have the original files from the COMBINE logo, so we can use the exact same colours and fonts. -- Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere n.l...@gm..., http://orcid.org/0000-0002-6309-7327 http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/ |
|
From: Nicolas R. <rod...@eb...> - 2015-05-19 09:41:37
|
Hi, I have started to add some README files on sourceforge to explain a bit what the different folders and files are about. I still need to work on the content but you can see an example there: https://sourceforge.net/p/sbfc/code I found it nice in SBML/JSBML to have an ascii art at the end of the README so I have selected two that I like. Any preferences? Would you like a different one or none at all ? Now about the logo. It would be nice to have a logo at least to display on the main page at http://sbfc.sourceforge.net/. (more images or graph in the text as well) I was thinking of doing something very simple using SBFC with the COMBINE colors ? Any thoughts ? Thanks, Nico |
|
From: Nicolas R. <rod...@eb...> - 2013-05-01 10:12:31
|
Hi, The SBFC project was upgraded automatically. Anybody having checkout of the code need to change them to point to the new repository. Don't hesitate to contact sbf...@li... if you have any problems. cheers, Nico For more detailed instructions on migrating to your new repo, please see http://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/#how-do-i-change-svn-to-point-to-the-new-repo -------- Original Message -------- Subject: SourceForge Project Upgrade - Code Repo Complete Date: Tue, 30 Apr 2013 17:29:44 +0000 From: SourceForge.net <nor...@in...> Reply-To: no...@in... To: no...@in... Your code repository in upgraded project sbfc is now ready for use. Old repository url: http://sbfc.svn.sourceforge.net/svnroot/sbfc New repository checkout command: svn checkout --username=niko-rodrigue svn+ssh://nik...@sv.../p/sbfc/code/ sbfc-code You should do a checkout using the new repository location. The old repository is read-only now. For more detailed instructions on migrating to your new repo, please see https://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/ -- SourceForge.net has sent this mailing to you as a registered user of the SourceForge.net site to convey important information regarding your SourceForge.net account or your use of SourceForge.net services. If you have concerns about this mailing please contact our Support team per: http://sourceforge.net/support |
|
From: Martijn v. I. <mva...@gm...> - 2012-07-03 12:41:52
|
Allright, I've committed the code.
I'm not sure what other changes need to be done to the framework. At
least I do not get any compilation errors in eclipse.
--
Martijn
On 27/06/12 10:53, Nicolas Rodriguez wrote:
>
> Hi Martjin,
>
> Yes, that sound quite good, please commit.
>
> I think there are some changes to do in the framework as well that are
> missing in the patch but we
> can do that later.
>
> Cheers,
> Nico
>
>
> On 25/06/12 11:35, Martijn van Iersel wrote:
>> As mentioned before, I propose to change the isCorrectType API, so
>> that you can use isCorrectType() before completely loading a model.
>>
>> Furthermore, I propose to change getFileType() to return an array of
>> Strings and rename it to getExtensions(). This way, a GeneralModel
>> could declare itself to read files of more than one extension. The
>> first String of the array would indicate the preferred extension. This
>> is a system that we've used successfully in PathVisio for a while now.
>>
>> For example:
>>
>> SBMLmodel reads ".xml", ".sbml"
>> SBGNmodel reads ".sbgn", ".xml"
>> GPMLmodel reads ".gpml", ".xml"
>>
>> With the combination, the appropriate converter could be easily
>> selected based on file type extension, even with ambiguous extensions.
>> Assuming input and output are the chosen File objects, one could pick
>> the correct converter with code like this:
>>
>> String inFname = input.getAbsolutePath();
>> String outFname = output.getAbsolutePath();
>>
>> GeneralConverter matchingConverter = null;
>> for (GeneralConverter c : converters)
>> {
>> // linear search, stop on first match
>> GeneralModel model = c.getInputModel();
>> boolean extensionMatch = false;
>> for (String ext : model.getExtensions())
>> if (inFname.endsWith(ext))
>> {
>> extensionMatch = true;
>> break;
>> }
>> if (extensionMatch &&
>> model.isCorrectType(input) &&
>> outFname.endsWith(c.getResultExtension()))
>> {
>> matchingConverter = c;
>> break;
>> }
>> }
>>
>>
>> I've attached patches for the changes I propose. I can commit these
>> patches if all agree.
>>
>>
>> --
>> Martijn
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats.http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>
>>
>> _______________________________________________
>> Sbfc-devel mailing list
>> Sbf...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbfc-devel
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Sbfc-devel mailing list
> Sbf...@li...
> https://lists.sourceforge.net/lists/listinfo/sbfc-devel
>
|
|
From: Nicolas R. <rod...@eb...> - 2012-06-27 09:53:14
|
Hi Martjin,
Yes, that sound quite good, please commit.
I think there are some changes to do in the framework as well that are
missing in the patch but we
can do that later.
Cheers,
Nico
On 25/06/12 11:35, Martijn van Iersel wrote:
> As mentioned before, I propose to change the isCorrectType API, so
> that you can use isCorrectType() before completely loading a model.
>
> Furthermore, I propose to change getFileType() to return an array of
> Strings and rename it to getExtensions(). This way, a GeneralModel
> could declare itself to read files of more than one extension. The
> first String of the array would indicate the preferred extension. This
> is a system that we've used successfully in PathVisio for a while now.
>
> For example:
>
> SBMLmodel reads ".xml", ".sbml"
> SBGNmodel reads ".sbgn", ".xml"
> GPMLmodel reads ".gpml", ".xml"
>
> With the combination, the appropriate converter could be easily
> selected based on file type extension, even with ambiguous extensions.
> Assuming input and output are the chosen File objects, one could pick
> the correct converter with code like this:
>
> String inFname = input.getAbsolutePath();
> String outFname = output.getAbsolutePath();
>
> GeneralConverter matchingConverter = null;
> for (GeneralConverter c : converters)
> {
> // linear search, stop on first match
> GeneralModel model = c.getInputModel();
> boolean extensionMatch = false;
> for (String ext : model.getExtensions())
> if (inFname.endsWith(ext))
> {
> extensionMatch = true;
> break;
> }
> if (extensionMatch &&
> model.isCorrectType(input) &&
> outFname.endsWith(c.getResultExtension()))
> {
> matchingConverter = c;
> break;
> }
> }
>
>
> I've attached patches for the changes I propose. I can commit these
> patches if all agree.
>
>
> --
> Martijn
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Sbfc-devel mailing list
> Sbf...@li...
> https://lists.sourceforge.net/lists/listinfo/sbfc-devel
|
|
From: Martijn v. I. <mva...@gm...> - 2012-06-25 10:35:19
|
As mentioned before, I propose to change the isCorrectType API, so that
you can use isCorrectType() before completely loading a model.
Furthermore, I propose to change getFileType() to return an array of
Strings and rename it to getExtensions(). This way, a GeneralModel could
declare itself to read files of more than one extension. The first
String of the array would indicate the preferred extension. This is a
system that we've used successfully in PathVisio for a while now.
For example:
SBMLmodel reads ".xml", ".sbml"
SBGNmodel reads ".sbgn", ".xml"
GPMLmodel reads ".gpml", ".xml"
With the combination, the appropriate converter could be easily selected
based on file type extension, even with ambiguous extensions. Assuming
input and output are the chosen File objects, one could pick the correct
converter with code like this:
String inFname = input.getAbsolutePath();
String outFname = output.getAbsolutePath();
GeneralConverter matchingConverter = null;
for (GeneralConverter c : converters)
{
// linear search, stop on first match
GeneralModel model = c.getInputModel();
boolean extensionMatch = false;
for (String ext : model.getExtensions())
if (inFname.endsWith(ext))
{
extensionMatch = true;
break;
}
if (extensionMatch &&
model.isCorrectType(input) &&
outFname.endsWith(c.getResultExtension()))
{
matchingConverter = c;
break;
}
}
I've attached patches for the changes I propose. I can commit these
patches if all agree.
--
Martijn
|
