Activity for Systems Biology Format Converter
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Nilay Yönet created ticket #27
SBML2SBML V3L1
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Tung Nguyen committed [r757] on Code
improved the methods of the Converter class
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reimplemented SBML2SBML.convert method using jsbml library
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this static block muted org.sbfc.converter.sbml2sbml.* so the converter throws exception
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Anonymous created ticket #26
conversion SBML2 to SBML3
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Updated the newly changed package name
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Make sure the package name lower case
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Corrected the way to get the sys env var
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Changed the SMTP mail server host
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Upgraded the look and feel by using EBI Visual Framework V.1.3
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Replaced the email address with the session identifier
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Treated the file name in case of dowloading models from BioModels
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Updated the mail SMTP host
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Directed Tomcat creating the temporary files in the java.io.tmpdir directory
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Matthias König created ticket #25
SBML2SBGN not available in the webinterface
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Lucian Smith created ticket #24
'mi' and 'mim' annotations not converted
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Jonathan Karr created ticket #23
Conversion of SBML to PDF sometimes fails with no error
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Conversion of SBML to SVG sometimes fails with no error
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Anonymous created ticket #21
Convert of SBML to PNG sometimes fails with no error
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Conversion of SBML to Octave often generates empty files with no error
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SBML URN conversion creates invalid SBML when the layout package is used
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Anonymous created ticket #13
Raise warning when trying to convert non-kinetic SBML models to other ODE formats
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sbfConverter.sh contains paths specific to the developer
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sbfConverter.sh cannot handle spaces in filenames
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Converter generates invalid XPP for some models
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Anonymous created ticket #15
SBML2SBML ACSN
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Nicolas Rodriguez committed [r745]
Updated libsbml jar file and scripts + updated jsbml jar file to the latest version
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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.
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Ana Nascimento created ticket #14
SBML2SBML
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Anonymous created ticket #13
SBML2SBML
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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.
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Anonymous created ticket #12
SBML2SBML conversion
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updated jar file
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added support for more SBML level and version
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Fixed the sbfc online script
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Added conversion to SBML L3V2 + Modified SBML to Biopax to use the latest version only. Removed biopax L2 conversion.
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Updated sbml to biopax converter name.
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Renamed the biopax converters in preparation for the removal of the old and deprecated ones.
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Missing # comment
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Conversion to SBML L3 results in SBML L2
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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.
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updated jar file
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Improved the display of SBML2SBML conversion errors.
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Conversion to SBML L3 results in SBML L2
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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 <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model. Reference: L2V1 Section 4.9.5 The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species...
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Anonymous created ticket #11
Conversion to SBML L3 results in SBML L2
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SBML -> Matlab: Initial conditions incorrect for amount species
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Tramy Nguyen created ticket #12
Expand Testing for SBML to/from BioPAX
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Support SBML Group Annotation
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Lost Stoichiometry in SBMLtoBioPAX
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Request MIRIAM Qualifiers for SBML Custom Annotations
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Custom Annotation in BioPAX to SBML
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Converting SBML with Multiple Levels of Hierarchy
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updated jar file.
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removed wrong/unused imports.
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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.
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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.
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replace a forgotten usage of Modulation so that the conversion of modifier works properly in all the cases.
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corrected linux scripts to include the paxtools jar. Put back the creation of BioPAX EntityReferences that will old the annotations
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updated paxtools version in the pom file as well.
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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.
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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.
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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.
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Using the converter names in the GUI now.
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updated identifiers.org registry xml. Added javadoc to ConversionException.
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updated jsbml jar.
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removed the call to bsub in the shell script as it was not necessary
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changed the method used to check the size of a file
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changed the method used to check the size of a file
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improvements on the way we load files and how we extract the model from the request.
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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.
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Updated build.xml to be able to deploy apps to tomcat 8 + updated copyright to include Babraham.
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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.
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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.
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Started to improve the SBFC web service client.
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Mihai Glonț committed [r714]
Fix stale groupId for registry-lib in pom.xml
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Add Maven integration.
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Ignore Maven and IntelliJ artefacts.
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fixed type casting error when converting comp submodels to biopax
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adding the two files needed to use SBML2BioPAX_Arman.
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added a new SBML2Biopax converter so that we can use both Arman2014 and Tramy2016 converters.
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small update to the miriam export file.
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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.
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Stopping the SBML2SBML conversion if libsbml was not successfull
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Anonymous created ticket #6
Octave Module's Resulting Code Structure split
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octave file generation is missing the constant fluxes
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updated the jsbml jar file to use 1.2 + correct...
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Anonymous created ticket #8
matlab - octave converter - csymbol time should be called 't'
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implemented custom annotation for biopax commen...
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Implemented custom annotation for BioPAX availa...
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implemented custom annotation for all BioPAX An...
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Included SBML2BioPAX converter to parse multipl...
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Made the following changes:
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- generated new jar file for sbfc-1.3.7.jar
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Added javadoc to majority of the methods in Bio...
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- modified parsing of reaction in SBML2BioPAX t...
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- added owl files to test all biopax entities a...
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- expanded support for replacements and replace...
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- implemented version 2 for modification of sbm...
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- Added GeneticToggleSwitch sbml model with 2 l...
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