Activity for Tramy Nguyen
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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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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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- Implemented replacements for all species, com...
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- moved implementation for replacements on top ...
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- updated jsbml jar to use SBO terms: thermodyn...
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- Added support for creating multiple pathways ...
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- removed excess parameter for generating xrefs
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- Modified parsing of multiple pathways to so t...
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- generated new jsbml jar to use sbo terms for ...
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- implemented KineticLaw with LocalParameters o...
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- add validation to sbml document to only print...
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modified parsing of each pathway so it will cre...
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- Implemented CellularLocationVocabulary to rea...
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1. Implemented BioPAX2SBML conversion to suppor...
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- modified BioPAX2SBML converter to take in par...
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- Completed implementation for creating custom ...
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started method to add custom annotation for xref.
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- updated sbo terms for dna and rna region with...
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- Tested gene entity through both conversion.
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Import biopax files that will help test differe...
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Added the following changes for the SBML2BioPAX...
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Played around with SBML2BioPAX converter by add...
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- Modified how TemplateReaction should be parsed
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Restructured xref annotation for species, compa...
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- Added implementation for MIRIAM annotation fr...
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- Reimplemented TemplateReaction, GeneticIntera...
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Add missing javadoc fields
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Completed javadoc to all methods in BiopAX2SBML...
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- Accidentally added InteractionTests test case...
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- Started adding javadoc comments for BioPAX2SB...
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- Replaced used of .class.isAssignableFrom(enti...
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- Code wasn't ensuring that PhysicalEntities an...
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- Set up JUnit test cases for all physicalEntit...
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Version 2 of adding parsing to support zero or ...
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- Added parsing for multiple pathways in a biop...
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- added parser for PhysicalInteraction and sbo ...
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Added SBO terms for Biopax2SBML conversion by c...
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- Finished implementing method to set SBO value...
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- Forgot to check that when getting biopax id, ...
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The following changes were made:
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recommitting sbml2dot.sh with correct name with...
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- wrote methods to check for valid sbml id, val...
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recommiting a revert version 90 for sbml2dot.sh
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- Clean up duplicate code for creating compartm...
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Request for DNA Region and RNA Region SBO Term
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The following changes were made.
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Setup BioPax2SBML conversion. Currently, conver...
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First commit to sbfc-code source code to initia...
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