sbmlteam / jsbml

JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

https://sbml.org/software/jsbml/

sbmlteam/jsbml Issues

Unary operator precedence ignored by ASTNode parser.
Updated 7 months ago6
Found the bug in ASTNode.toFomula()
Updated 8 months ago5
NullPointerException in ASTNode
Updated 8 months ago
No property change happens when a value is explicitly set to NaN that was undefined before
Updated 2 years ago
Add checks if a model element already exists before adding it to avoid clashes in ModelBuilder
Updated 2 years ago
Cloning of GeneProduct may create invalid SBML because of missing required attribute `label`
Updated 2 years ago
Improve flattening by testing and merging an existing fork
Updated 2 years ago1
Removing objectives from a model is not sensitive for removal of the active objective
Updated 2 years ago
Error reading file
Closed 2 years ago
Deriving a unit for a lambda expression may cause an out of bounds exception
Updated 2 years ago
Make offline validation the default
Updated 2 years ago
Issue when parsing math formula
Closed 2 years ago9
no update on maven
Closed 2 years ago13
java.lang.NoClassDefFoundError: org/apache/logging/log4j/util/ReflectionUtil
Closed 2 years ago3
Spatial: nearestneighbor should be nearestNeighbor
Closed 3 years ago1
hardcoded version of internal dependency
Closed 3 years ago5
Stable version link in Readme.md file is not correct
Closed 3 years ago
Exceptions thrown depending on the log level
Closed 4 years ago4
Errors in comp flattening routine (cannot register compartment, cannot register parameter)
Updated 4 years ago5
order of authors is not correct
Updated 4 years ago1
The test if a plugin is loaded returns true when JSBML has a parser loaded
Updated 4 years ago6
suggestion for all libraries: implement a logging facade instead of the logger
Updated 4 years ago5
Add a method to quickly check if an SBase has a certain extension
Closed 4 years ago
Building javadoc fails (at least on macOS)
Closed 4 years ago2
Logo images are broken in Javadoc output
Closed 4 years ago
XMLNode.convertStringToXMLNode is not thread safe
Closed 4 years ago3
Add a method to strip unused namespaces for packages not being used
Closed 4 years ago7
Parsing mod
Closed 4 years ago3
comp flattening
Closed 5 years ago
processUnknownAttribute() needing to be called explicitly in SpatialParser
Closed 5 years ago
setting notes that is invalid xml throws com.ctc.wstx.exc.WstxUnexpectedCharException: Unexpected character '<'
Updated 5 years ago
EmptyStackException
Closed 5 years ago8
export of listOfSpeciesFeatures
Closed 5 years ago1
parsing sbml with multi package
Closed 5 years ago2
Incorrect error message setting id
Closed 6 years ago2
log4j.properties
Closed 6 years ago1
Problems converting ASTNode2 to ASTNode with FormulaParserLL3
Closed 6 years ago4
ParseException when reading formula
Closed 6 years ago2
SBML error 20103, 20101, 20102 when using offline validator
Closed 6 years ago3
correct OverdeterminationValidator for L3V2
Updated 6 years ago
setSBOTerm with null value throws NPE
Closed 6 years ago1
wrong interpolationType used for spatial extension
Closed 6 years ago1
Strip a package from an SBML file
Closed 6 years ago3
Add a function for the conversion of ASTNodes to GPRs
Closed 6 years ago7
Notes format
Closed 7 years ago1
Pivotal tracker in README.md links to wrong project
Closed 7 years ago2
Arrays validation should check for dimensions of parent objects
Updated 7 years ago
Arrays Validation Rule 20116
Updated 7 years ago
NPE when parsing MODEL1603150000 from BioModels' non-curated branch
Closed 7 years ago3
Maven deploy/release to OSSRH and Central
Closed 8 years ago18