44 projects
kisao
Utilities for working with the Kinetic Simulation Algorithm Ontology (KiSAO)
biosimulators-utils
Command-line program and library for reading, writing, validating and executing modeling projects (COMBINE/OMEX archives with SED-ML files).
biosimulators-tellurium
BioSimulators-compliant command-line interface to the tellurium simulation program <http://tellurium.analogmachine.org>.
biosimulators-test-suite
Tools for validating that biosimulation tools are consistent with the BioSimulators standards
biosimulators-amici
BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>.
biosimulators-copasi
BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.
biosimulations-bigg
Command-line program for publishing the BiGG model repository to BioSimulations.
biosimulators-xpp
BioSimulators-compliant command-line interface to the XPP simulation program.
biosimulators-gillespy2
BioSimulators-compliant command-line interface to the GillesPy2 simulation program.
biosimulators-bionetgen
BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.
biosimulators-masspy
BioSimulators-compliant command-line interface to the MASSpy simulation program.
biosimulators-cbmpy
BioSimulators-compliant command-line interface to the CBMPy simulation program <http://cbmpy.sourceforge.net/>.
biosimulators-cobrapy
BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.
biosimulators-pyneuroml
BioSimulators-compliant command-line interface to the jNeuroML/pyNeuroML, NEURON, and NetPyNe simulation programs.
biosimulators-opencor
BioSimulators-compliant command-line interface to the OpenCOR simulation program.
biosimulators-boolnet
BioSimulators-compliant command-line interface to the BoolNet simulation program.
biosimulators-pysces
BioSimulators-compliant command-line interface to the PySCeS simulation program <http://pysces.sourceforge.net/>.
biosimulators-rbapy
BioSimulators-compliant command-line interface to the RBApy simulation program.
biosimulators-libsbmlsim
BioSimulators-compliant command-line interface to LibSBMLsim <http://fun.bio.keio.ac.jp/software/libsbmlsim/>.
biosimulators-ginsim
BioSimulators-compliant command-line interface to the GINsim simulation program.
vcell-cli-utils
Python utility package for VCell CLI Java App
conv-opt
High-level Python package for solving linear and quadratic optimization problems using multiple solvers
de-sim
object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems
wc-utils
Utilities for whole-cell modeling
obj-tables
Tools for creating and reusing high-quality spreadsheets
gdoc-down
Download Google documents to files
bcforms
Toolkit for concretely describing macromolecular complexes
bpforms
Unambiguous representation of modified DNA, RNA, and proteins
datanator-query-python
A package to query and format the data in the integrated Datanator database
wc-onto
Ontology for whole-cell modeling
pkg-utils
Utilities for linking setuptools with version metadata, README files, requirements files, and restoring overridden entry points
unitth
Python interface for UnitTH unit test history report generator
nose2unitth
Convert nose-style test reports to UnitTH-style test reports
wc-sandbox
Jupyter playground for whole-cell modeling
wc-cli
Whole-cell models and whole-cell modeling tools
h1-hesc
Whole-cell model of H1 human embryonic stem cells (hESCs)
wc-env-manager
Tools for managing computing environments for whole-cell modeling
karr-lab-build-utils
Karr Lab build utilities
wc-test
Methods for testing whole-cell knowledge bases and models
wc-sim
Sequential whole-cell model simulator
wc-rules
Language for describing whole-cell models
wc-model-gen
Framework for systematically and scalably designing whole-cell models from large datasets such as `wc_kb`
test-history-server
Unit test history server
wc-lang
Language for describing whole-cell models
