Andreas Dräger
Andreas Dräger
The test `isSetPlugin` on `AbstractSBase` should return `true` if the `SBase` has a child with the given namespace. In the current implementation, however, it returns `true` if JSBML has (at...
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...
In input files, reactions are usually given in millimole per gram dry weight per hour (mmol / gDW / h). The given unit needs to be decomposed into its parts:...
Suggested enhancement by @tpfau: Look over all present annotations and map every annotation that can be mapped to BiGG. For instance, if there is a KEGG compound annotation that compound...
@Midnighter requests at https://github.com/SBRG/bigg_models/issues/368: Many models in BiGG are currently annotated with a taxonomic identifier and a reference to the model itself, for example, as shown below. ```xml ``` On...
Recently, the dependency to JDOM was updated because of a potential security issue. Unfortunately, libSBGN still relies on the older library. Consequently, the main repository is currently unable to produce...