SBSCL
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draeger-lab
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 Languag...
I'd love to use sbscl.v.2.1, so I wrote the wrapper class for SBMLTestSuite using `org.testsuite.SBMLTestSuiteRunnerWrapper`. But in some SBMLTestSuite cases, the same error has been detected. Specifically, the case numbers...
Hi, I tried to download bigg_models following the instructions in [INSTALL.md](https://github.com/draeger-lab/SBSCL/blob/master/INSTALL.md), but the Dropbox link seems to be invalid. Any help? ```bash % bash ./src/test/scripts/download_bigg_models.sh --2023-07-08 00:45:42-- https://www.dropbox.com/sh/ye05djxrpxy37da/AAAPwL27xQ97mHGoLmCxhI-4a/v1.6/models.tgz Resolving www.dropbox.com...
At the moment, a default solver (GLPK) is used as the backend for flux balance analysis. It should be possible to make this exchangable. Implement support for multiple solvers.
On some platforms, it might be difficult to run the Java Native Interface (JNI) needed for SCPsolver. Consider adding support for pure Java implementations, such as * https://www.ojalgo.org/code-examples/ * https://advancedweb.hu/running-lp-and-ip-optimisation-from-java/
The project's [website](https://draeger-lab.github.io/SBSCL/) does not properly describe the software anymore and needs to be updated: * The landing page does not mention constraint-based modeling (flux balance analysis) * CellML is...
The website biosimulators.org collects various simulation engine and stand-alone tools for simulation in systems biology. SBSCL is among them but currently with suboptimal curation level indication. The curation level is...
The test takes much too long to run. This creates a ton of problems. E.g. very long travis runtimes and also very long runtimes for the local tests. Tests should...
@draeger, @matthiaskoenig, @zakharc, @shalinshah1993 **This issue is created for discussion of making FERN use the classes from SBSCL for interpreting and processing the models to perform the stochastic simulation.** Here's...
SBSCL has a working FBA model solver. As part of the recent HARMONY we developed basic FROG guidelines. See also https://github.com/matthiaskoenig/fbc_curation/. SBSCL should support the generation of these files for...
Currently, whenever the rateOf is defined inside the delay tag for any of the SBML model then it does not take that delay into account and just provides the rateOf...
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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 Languag...