Expand Testing for SBML to/from BioPAX
Support SBML Group Annotation
Lost Stoichiometry in SBMLtoBioPAX
Request MIRIAM Qualifiers for SBML Custom Annotations
Custom Annotation in BioPAX to SBML
Converting SBML with Multiple Levels of Hierarchy
implemented custom annotation for biopax commen...
Implemented custom annotation for BioPAX availa...
implemented custom annotation for all BioPAX An...
Included SBML2BioPAX converter to parse multipl...
Made the following changes:
- generated new jar file for sbfc-1.3.7.jar
Added javadoc to majority of the methods in Bio...
- modified parsing of reaction in SBML2BioPAX t...
- added owl files to test all biopax entities a...
- expanded support for replacements and replace...
- implemented version 2 for modification of sbm...
- Added GeneticToggleSwitch sbml model with 2 l...
- Implemented replacements for all species, com...
- moved implementation for replacements on top ...
- updated jsbml jar to use SBO terms: thermodyn...
- Added support for creating multiple pathways ...
- removed excess parameter for generating xrefs
- Modified parsing of multiple pathways to so t...
- generated new jsbml jar to use sbo terms for ...
- implemented KineticLaw with LocalParameters o...
- add validation to sbml document to only print...
modified parsing of each pathway so it will cre...
- Implemented CellularLocationVocabulary to rea...
1. Implemented BioPAX2SBML conversion to suppor...
- modified BioPAX2SBML converter to take in par...
- Completed implementation for creating custom ...
started method to add custom annotation for xref.
- updated sbo terms for dna and rna region with...
- Tested gene entity through both conversion.
Import biopax files that will help test differe...
Added the following changes for the SBML2BioPAX...
Played around with SBML2BioPAX converter by add...
- Modified how TemplateReaction should be parsed
Restructured xref annotation for species, compa...
- Added implementation for MIRIAM annotation fr...
- Reimplemented TemplateReaction, GeneticIntera...
Add missing javadoc fields
Completed javadoc to all methods in BiopAX2SBML...
- Accidentally added InteractionTests test case...
- Started adding javadoc comments for BioPAX2SB...
- Replaced used of .class.isAssignableFrom(enti...
- Code wasn't ensuring that PhysicalEntities an...
- Set up JUnit test cases for all physicalEntit...
Version 2 of adding parsing to support zero or ...
- Added parsing for multiple pathways in a biop...
- added parser for PhysicalInteraction and sbo ...
Added SBO terms for Biopax2SBML conversion by c...
- Finished implementing method to set SBO value...
- Forgot to check that when getting biopax id, ...
The following changes were made:
recommitting sbml2dot.sh with correct name with...
- wrote methods to check for valid sbml id, val...
recommiting a revert version 90 for sbml2dot.sh
- Clean up duplicate code for creating compartm...
Request for DNA Region and RNA Region SBO Term
The following changes were made.
Setup BioPax2SBML conversion. Currently, conver...
First commit to sbfc-code source code to initia...