draeger-lab / SBSCL

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

https://draeger-lab.github.io/SBSCL/

draeger-lab/SBSCL Issues

Errors are detected when running some SBMLTestSuite case.
Updated 7 months ago8
download_bigg_models.sh throws ERROR 404
Updated a year ago2
Exchangable solvers
Updated a year ago
Support pure Java solver for constraint-based modeling
Updated a year ago
Update the project's website
Updated 2 years ago
Improve the curation level on BioSimulators
Updated 2 years ago1
Update Maven dependency documentation (version 2.0)
Closed 3 years ago1
SBML TestSuite semantic/01592 takes 15-25 minutes to run
Updated 3 years ago10
Upload SBSCL to mvnrepository
Closed 3 years ago3
SBML Version Support Documentation
Closed 4 years ago4
Refactor FERN classes to use SBSCL classes
Updated 4 years ago1
Terminology, Power and Oppressive Language in Computer Science
Closed 4 years ago2
SBML L3V2 tests failing with no identified reason yet
Closed 4 years ago1
Simulation of SBML models with changing compartment size
Closed 4 years ago4
Update the SBMLTestSuite Runner for L3V2
Closed 4 years ago4
SBML TestSuite failing test semantic/01488/01488 `java.lang.ArithmeticException: arcsech(0) undefined`
Closed 4 years ago4
Simulation of models with reaction without reactants and products
Closed 4 years ago
Add support for rateOf csymbol
Closed 4 years ago12
FBA tests fail on parallel testing
Closed 4 years ago2
Add functions in ASTNodeInterpreter class for calculating node values of SBML L3V2 models
Closed 4 years ago1
Support for FBA FROG analysis
Updated 4 years ago
Add delay property to the rateOf function
Updated 4 years ago1
Misinterpretation of function variables with parameters
Updated 4 years ago
Event triggers before the mentioned condition
Updated 4 years ago4
Some comp tests are failing due to JSBML flattening
Updated 4 years ago4
Update to JSBML 1.5
Closed 4 years ago
Build icon in README links to incorrect page
Closed 4 years ago2
Travis tests are currently failing
Closed 4 years ago8
Example OMEX file contains wrong model file name
Closed 5 years ago
Update uni-rostock maven dependencies
Closed 6 years ago4
Comp example file missing
Closed 6 years ago3
Deleting the dist folder
Closed 6 years ago2
Run SBSCL against the SBML test suite in CI
Closed 6 years ago1
Implement comp support
Closed 6 years ago
SED-ML FileResolver is broken
Closed 6 years ago2
Postprocessing function for SED-ML files not working any more
Closed 6 years ago2
Remove repeated-stochastic-runs test
Closed 6 years ago1
Remove repeated-steady-scan-oscli test
Closed 6 years ago10
No output generated for osci-nested-pulse sedml example
Closed 6 years ago1
Move the assembly file to the source folder
Closed 6 years ago3
Number of points in SED-ML simulations incorrect
Closed 6 years ago1
SBSCL expect one of the Output elements to be a time symbol
Closed 6 years ago6
Example SEDML L1V2 files have errors
Closed 6 years ago3
Update index.html and wiki
Closed 6 years ago3
Remove 3rd party libs from src/lib folder
Closed 6 years ago3
Remove org.simulator.examples folder
Closed 6 years ago2
Cannot reach steadyState for repeated-steady-scan-oscli test
Closed 6 years ago7
Incorrect output curve for repressilator output #3
Closed 6 years ago4
Incorrect graphical output for some sedml tests
Closed 6 years ago11
Remove old javadocs
Closed 6 years ago3