This is a list of recent software packages developed in our group, sometimes in collaboration with other external researchers. Click on the figures to access details, documentation and download links.
Questions and/or reporting of issues should be directed to the main developer of each package.
Older packages (SSmGO, DOTcvpSB, CRNreals, SensSB, GLOBALm, MITS, ACOmi) have been removed since they are no longer supported. However, email us is you would like to check their status.
In addition to these packages, in many papers we also provide the software necessary for computational reproducibility. These codes are not listed here (since they are not considered standalone packages) but can be found in the Publications section.
Finally, we have collaborated in other software initiatives, including:
STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition): a MATLAB toolbox that analyses the local structural identifiability, observability, and invertibility of (possibly nonlinear) dynamic models of ordinary differential equations (ODEs).
PEtab: a data format for specifying parameter estimation problems in systems biology
saCMM: self-adaptive Cooperative Multimethod library (parallel global optimization code)
saCeSS2: global mixed-integer optimization library for high-performance computing infrastructures
asynPDE: MPI asynchronous Parallel Differential Evolution