Activity for Systems Biology Format Converter

Nilay Yönet created ticket #27

Nilay Yönet — Wed, 24 Jan 2024 19:09:07 -0000

SBML2SBML V3L1

Tung Nguyen committed [r757] on Code

Tung Nguyen — Mon, 06 Nov 2023 10:54:45 -0000

improved the methods of the Converter class

Tung Nguyen committed [r756] on Code

Tung Nguyen — Mon, 06 Nov 2023 10:40:18 -0000

reimplemented SBML2SBML.convert method using jsbml library

Tung Nguyen committed [r755] on Code

Tung Nguyen — Mon, 06 Nov 2023 10:08:02 -0000

this static block muted org.sbfc.converter.sbml2sbml.* so the converter throws exception

Anonymous created ticket #26

Anonymous — Tue, 31 Oct 2023 10:21:47 -0000

conversion SBML2 to SBML3

Tung Nguyen committed [r754]

Tung Nguyen — Fri, 09 Sep 2022 22:16:39 -0000

Updated the newly changed package name

Tung Nguyen committed [r753]

Tung Nguyen — Fri, 09 Sep 2022 22:13:17 -0000

Make sure the package name lower case

Tung Nguyen committed [r752]

Tung Nguyen — Fri, 09 Sep 2022 21:12:04 -0000

Corrected the way to get the sys env var

Tung Nguyen committed [r751]

Tung Nguyen — Fri, 09 Sep 2022 20:40:12 -0000

Changed the SMTP mail server host

Tung Nguyen committed [r750]

Tung Nguyen — Fri, 09 Sep 2022 20:20:57 -0000

Upgraded the look and feel by using EBI Visual Framework V.1.3

Tung Nguyen committed [r749]

Tung Nguyen — Fri, 09 Sep 2022 15:32:38 -0000

Replaced the email address with the session identifier

Tung Nguyen committed [r748]

Tung Nguyen — Fri, 09 Sep 2022 15:24:59 -0000

Treated the file name in case of dowloading models from BioModels

Tung Nguyen committed [r747]

Tung Nguyen — Thu, 08 Sep 2022 17:58:18 -0000

Updated the mail SMTP host

Tung Nguyen committed [r746]

Tung Nguyen — Thu, 08 Sep 2022 13:47:34 -0000

Directed Tomcat creating the temporary files in the java.io.tmpdir directory

Matthias König created ticket #25

Matthias König — Wed, 17 Aug 2022 08:00:12 -0000

SBML2SBGN not available in the webinterface

Lucian Smith created ticket #24

Lucian Smith — Fri, 22 Apr 2022 18:08:58 -0000

'mi' and 'mim' annotations not converted

Jonathan Karr created ticket #23

Jonathan Karr — Sun, 06 Feb 2022 00:51:27 -0000

Conversion of SBML to PDF sometimes fails with no error

Jonathan Karr created ticket #22

Jonathan Karr — Sun, 06 Feb 2022 00:44:52 -0000

Conversion of SBML to SVG sometimes fails with no error

Anonymous created ticket #21

Anonymous — Sun, 06 Feb 2022 00:44:25 -0000

Convert of SBML to PNG sometimes fails with no error

Jonathan Karr created ticket #20

Jonathan Karr — Thu, 06 May 2021 04:29:35 -0000

Conversion of SBML to Octave often generates empty files with no error

Jonathan Karr created ticket #19

Jonathan Karr — Wed, 05 May 2021 04:41:58 -0000

SBML URN conversion creates invalid SBML when the layout package is used

Anonymous created ticket #13

Anonymous — Mon, 26 Apr 2021 23:03:17 -0000

Raise warning when trying to convert non-kinetic SBML models to other ODE formats

Jonathan Karr created ticket #18

Jonathan Karr — Mon, 26 Apr 2021 04:28:31 -0000

sbfConverter.sh contains paths specific to the developer

Jonathan Karr created ticket #17

Jonathan Karr — Mon, 26 Apr 2021 03:55:54 -0000

sbfConverter.sh cannot handle spaces in filenames

Jonathan Karr created ticket #16

Jonathan Karr — Fri, 23 Apr 2021 18:55:21 -0000

Converter generates invalid XPP for some models

Anonymous created ticket #15

Anonymous — Tue, 16 Feb 2021 12:17:39 -0000

SBML2SBML ACSN

Nicolas Rodriguez committed [r745]

Nicolas Rodriguez — Thu, 28 Jan 2021 15:53:39 -0000

Updated libsbml jar file and scripts + updated jsbml jar file to the latest version

Nicolas Rodriguez posted a comment on ticket #14

Nicolas Rodriguez — Wed, 18 Nov 2020 17:35:19 -0000

Hi Ana, I thought the online converter was fixed by somebody else but it seems that this problem is still there. For the standalone version, you need to have libSBML installed and properly configured so that the GUI display the SBML2SBML converters.

Ana Nascimento created ticket #14

Ana Nascimento — Tue, 17 Nov 2020 21:05:26 -0000

SBML2SBML

Anonymous created ticket #13

Anonymous — Tue, 27 Oct 2020 07:46:42 -0000

SBML2SBML

Nicolas Rodriguez posted a comment on ticket #12

Nicolas Rodriguez — Mon, 15 Jun 2020 15:21:52 -0000

Which version are you trying to run ? Is it a svn checkout ? Did you compile it yourself ? Which operating system do you use ? To have the sbml2sbml converters working, you need to have libsbml installed locally on the machine you are trying to run sbfc. You might need to adjust the path in the script so that the libsbml libraries are found.

Anonymous created ticket #12

Anonymous — Sat, 13 Jun 2020 17:29:00 -0000

SBML2SBML conversion

Nicolas Rodriguez committed [r744]

Nicolas Rodriguez — Thu, 12 Mar 2020 15:34:30 -0000

updated jar file

Nicolas Rodriguez committed [r743]

Nicolas Rodriguez — Thu, 12 Mar 2020 15:31:41 -0000

added support for more SBML level and version

Nicolas Rodriguez committed [r742]

Nicolas Rodriguez — Thu, 12 Mar 2020 15:09:52 -0000

Fixed the sbfc online script

Nicolas Rodriguez committed [r741]

Nicolas Rodriguez — Thu, 12 Mar 2020 13:43:52 -0000

Added conversion to SBML L3V2 + Modified SBML to Biopax to use the latest version only. Removed biopax L2 conversion.

Nicolas Rodriguez committed [r740]

Nicolas Rodriguez — Thu, 12 Mar 2020 12:53:04 -0000

Updated sbml to biopax converter name.

Nicolas Rodriguez committed [r739]

Nicolas Rodriguez — Thu, 12 Mar 2020 12:31:08 -0000

Renamed the biopax converters in preparation for the removal of the old and deprecated ones.

Nicolas Rodriguez modified ticket #4

Nicolas Rodriguez — Wed, 11 Mar 2020 11:36:40 -0000

Missing # comment

Nicolas Rodriguez modified ticket #11

Nicolas Rodriguez — Wed, 11 Mar 2020 10:20:55 -0000

Conversion to SBML L3 results in SBML L2

Nicolas Rodriguez posted a comment on ticket #11

Nicolas Rodriguez — Wed, 11 Mar 2020 10:20:55 -0000

I have now updated the converter on the web app so that it return an error and I have updated libsbml to the latest version in the same time. So next time you should have better result that will present the list of errors detected in your model.

Nicolas Rodriguez committed [r738]

Nicolas Rodriguez — Tue, 10 Mar 2020 15:10:08 -0000

updated jar file

Nicolas Rodriguez committed [r737]

Nicolas Rodriguez — Tue, 10 Mar 2020 15:03:19 -0000

Improved the display of SBML2SBML conversion errors.

Nicolas Rodriguez modified ticket #11

Nicolas Rodriguez — Tue, 10 Mar 2020 14:34:33 -0000

Conversion to SBML L3 results in SBML L2

Nicolas Rodriguez posted a comment on ticket #11

Nicolas Rodriguez — Tue, 10 Mar 2020 14:33:54 -0000

It is an old "feature" of the converter. If the convrsion fail, it does return the original model to the user, we need to change that so that it does fail and return the errors to the user directly. Here are the error detected for the model: line 50572: (21111 [Error]) The value of a 'species' attribute must be the identifier of an existing in the model. Reference: L2V1 Section 4.9.5 The in the with id 'biomass_bulk_c0' references species...

Anonymous created ticket #11

Anonymous — Wed, 26 Feb 2020 01:20:36 -0000

Conversion to SBML L3 results in SBML L2

Matthias König created ticket #10

Matthias König — Thu, 17 Oct 2019 09:24:24 -0000

SBML -> Matlab: Initial conditions incorrect for amount species

Tramy Nguyen created ticket #12

Tramy Nguyen — Thu, 11 Oct 2018 20:24:49 -0000

Expand Testing for SBML to/from BioPAX

Tramy Nguyen created ticket #11

Tramy Nguyen — Tue, 09 Oct 2018 19:49:13 -0000

Support SBML Group Annotation

Tramy Nguyen created ticket #10

Tramy Nguyen — Tue, 09 Oct 2018 18:30:36 -0000

Lost Stoichiometry in SBMLtoBioPAX

Tramy Nguyen created ticket #9

Tramy Nguyen — Tue, 09 Oct 2018 17:54:35 -0000

Request MIRIAM Qualifiers for SBML Custom Annotations

Tramy Nguyen created ticket #8

Tramy Nguyen — Tue, 09 Oct 2018 15:46:27 -0000

Custom Annotation in BioPAX to SBML

Tramy Nguyen created ticket #7

Tramy Nguyen — Tue, 09 Oct 2018 15:43:50 -0000

Converting SBML with Multiple Levels of Hierarchy

Nicolas Rodriguez committed [r736]

Nicolas Rodriguez — Wed, 20 Jun 2018 15:20:37 -0000

updated jar file.

Nicolas Rodriguez committed [r735]

Nicolas Rodriguez — Wed, 20 Jun 2018 15:17:53 -0000

removed wrong/unused imports.

Nicolas Rodriguez committed [r734]

Nicolas Rodriguez — Wed, 20 Jun 2018 14:00:36 -0000

Gene cannot be converted into PhysicalEntity. In few biomdels models we had the case where Gene were present in a Conversion that accept only PhysicalEntity. For the moment, I just removed the participant until we found a proper solution.

Nicolas Rodriguez committed [r733]

Nicolas Rodriguez — Wed, 20 Jun 2018 13:31:53 -0000

removed the creation of the BioPAX EntityReference from the annotations as it could be different than the sboTerm in some case, we will re-structure it to try to guess an SBOTerm from the annotations.

Nicolas Rodriguez committed [r732]

Nicolas Rodriguez — Wed, 20 Jun 2018 09:31:27 -0000

replace a forgotten usage of Modulation so that the conversion of modifier works properly in all the cases.

Nicolas Rodriguez committed [r731]

Nicolas Rodriguez — Fri, 25 May 2018 12:02:10 -0000

corrected linux scripts to include the paxtools jar. Put back the creation of BioPAX EntityReferences that will old the annotations

Nicolas Rodriguez committed [r730]

Nicolas Rodriguez — Thu, 24 May 2018 14:35:30 -0000

updated paxtools version in the pom file as well.

Nicolas Rodriguez committed [r729]

Nicolas Rodriguez — Thu, 24 May 2018 14:21:22 -0000

renamed the paxtools folder to remove the mention of the version and updated the scripts so that they use the new folder and are not dependent of a change in the paxtools version.

Nicolas Rodriguez committed [r728]

Nicolas Rodriguez — Thu, 24 May 2018 13:21:02 -0000

Upgraded to the latest paxtools, version 5.0.1. Fixed the problem with the creation of Control, we were creating Modulation by default but it can be used only for specific interaction, using Control by default fixed the problem.

Nicolas Rodriguez committed [r727]

Nicolas Rodriguez — Wed, 23 May 2018 16:46:11 -0000

Several fixes to the sbml2biopax converter. Added back the main biopax pathway that was removed probably when working on sbml comp support. Added a name to the pathways. Trying to fix the conversion of sbml modifiers into biopax control.

Nicolas Rodriguez committed [r726]

Nicolas Rodriguez — Wed, 23 May 2018 16:41:47 -0000

Using the converter names in the GUI now.

Nicolas Rodriguez committed [r725]

Nicolas Rodriguez — Wed, 23 May 2018 12:55:18 -0000

updated identifiers.org registry xml. Added javadoc to ConversionException.

Nicolas Rodriguez committed [r724]

Nicolas Rodriguez — Wed, 23 May 2018 12:50:29 -0000

updated jsbml jar.

Nicolas Rodriguez committed [r723]

Nicolas Rodriguez — Fri, 20 Apr 2018 14:15:22 -0000

removed the call to bsub in the shell script as it was not necessary

Nicolas Rodriguez committed [r722]

Nicolas Rodriguez — Fri, 20 Apr 2018 12:55:23 -0000

changed the method used to check the size of a file

Nicolas Rodriguez committed [r721]

Nicolas Rodriguez — Fri, 20 Apr 2018 12:54:40 -0000

changed the method used to check the size of a file

Nicolas Rodriguez committed [r720]

Nicolas Rodriguez — Fri, 20 Apr 2018 11:04:38 -0000

improvements on the way we load files and how we extract the model from the request.

Nicolas Rodriguez committed [r719]

Nicolas Rodriguez — Fri, 20 Apr 2018 11:02:11 -0000

Updated the SBFC web service client so that it does encode properly the model before sending it to the server. Also tried to do a better job at reading the file into memory and waiting for the job to be finished.

Nicolas Rodriguez committed [r718]

Nicolas Rodriguez — Fri, 13 Apr 2018 16:09:10 -0000

Updated build.xml to be able to deploy apps to tomcat 8 + updated copyright to include Babraham.

Nicolas Rodriguez committed [r717]

Nicolas Rodriguez — Fri, 13 Apr 2018 16:07:22 -0000

Attempt to set properly the encoding to UTF-8 everywhere. Adapted sligthly the code so that it can be run on a single desktop/laptop.

Nicolas Rodriguez committed [r716]

Nicolas Rodriguez — Wed, 28 Mar 2018 15:04:38 -0000

Added a timeout for the job status check and a check increase as well to not check too often when the job start to be long. Trying as well to make sure to properly read and send UTF-8 String.

Nicolas Rodriguez committed [r715]

Nicolas Rodriguez — Mon, 26 Mar 2018 15:32:00 -0000

Started to improve the SBFC web service client.

Mihai Glonț committed [r714]

Mihai Glonț — Fri, 23 Mar 2018 11:34:56 -0000

Fix stale groupId for registry-lib in pom.xml

Mihai Glonț committed [r713]

Mihai Glonț — Tue, 20 Mar 2018 11:35:44 -0000

Add Maven integration.

Mihai Glonț committed [r712]

Mihai Glonț — Tue, 20 Mar 2018 11:22:25 -0000

Ignore Maven and IntelliJ artefacts.

Mihai Glonț committed [r711]

Mihai Glonț — Mon, 19 Mar 2018 17:35:00 -0000

fixed type casting error when converting comp submodels to biopax

Nicolas Rodriguez committed [r710]

Nicolas Rodriguez — Tue, 30 Jan 2018 14:49:50 -0000

adding the two files needed to use SBML2BioPAX_Arman.

Nicolas Rodriguez committed [r709]

Nicolas Rodriguez — Thu, 30 Nov 2017 11:52:23 -0000

added a new SBML2Biopax converter so that we can use both Arman2014 and Tramy2016 converters.

Nicolas Rodriguez committed [r708]

Nicolas Rodriguez — Wed, 27 Sep 2017 09:51:04 -0000

small update to the miriam export file.

Nicolas Rodriguez committed [r707]

Nicolas Rodriguez — Tue, 29 Aug 2017 11:09:47 -0000

Fixes to the SBGNModel class so that it deal only with SBGN and properly. Added a hack to the GUI so that it does read correctly SBGNML files.

Nicolas Rodriguez committed [r706]

Nicolas Rodriguez — Fri, 04 Aug 2017 14:21:31 -0000

Stopping the SBML2SBML conversion if libsbml was not successfull

Anonymous created ticket #6

Anonymous — Wed, 19 Apr 2017 10:04:37 -0000

Octave Module's Resulting Code Structure split

Nicolas Rodriguez created ticket #9

Nicolas Rodriguez — Wed, 05 Apr 2017 09:49:58 -0000

octave file generation is missing the constant fluxes

Nicolas Rodriguez committed [r705]

Nicolas Rodriguez — Thu, 23 Feb 2017 12:53:43 -0000

updated the jsbml jar file to use 1.2 + correct...

Anonymous created ticket #8

Anonymous — Thu, 26 Jan 2017 15:29:29 -0000

matlab - octave converter - csymbol time should be called 't'

Tramy Nguyen committed [r704]

Tramy Nguyen — Tue, 03 Jan 2017 07:48:50 -0000

implemented custom annotation for biopax commen...

Tramy Nguyen committed [r703]

Tramy Nguyen — Tue, 03 Jan 2017 06:43:07 -0000

Implemented custom annotation for BioPAX availa...

Tramy Nguyen committed [r702]

Tramy Nguyen — Tue, 03 Jan 2017 05:54:25 -0000

implemented custom annotation for all BioPAX An...

Tramy Nguyen committed [r701]

Tramy Nguyen — Wed, 26 Oct 2016 19:33:40 -0000

Included SBML2BioPAX converter to parse multipl...

Tramy Nguyen committed [r700]

Tramy Nguyen — Mon, 24 Oct 2016 04:34:13 -0000

Made the following changes:

Tramy Nguyen committed [r699]

Tramy Nguyen — Fri, 19 Aug 2016 07:12:52 -0000

- generated new jar file for sbfc-1.3.7.jar

Tramy Nguyen committed [r698]

Tramy Nguyen — Thu, 18 Aug 2016 04:46:16 -0000

Added javadoc to majority of the methods in Bio...

Tramy Nguyen committed [r697]

Tramy Nguyen — Tue, 16 Aug 2016 16:17:09 -0000

- modified parsing of reaction in SBML2BioPAX t...

Tramy Nguyen committed [r696]

Tramy Nguyen — Tue, 16 Aug 2016 08:23:29 -0000

- added owl files to test all biopax entities a...

Tramy Nguyen committed [r695]

Tramy Nguyen — Mon, 15 Aug 2016 06:11:38 -0000

- expanded support for replacements and replace...

Tramy Nguyen committed [r694]

Tramy Nguyen — Fri, 12 Aug 2016 04:34:25 -0000

- implemented version 2 for modification of sbm...

Tramy Nguyen committed [r693]

Tramy Nguyen — Fri, 12 Aug 2016 04:33:25 -0000

- Added GeneticToggleSwitch sbml model with 2 l...