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Username    jonrkarr
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42 projects

biosimulators-bionetgen

Last released

BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.

biosimulators-utils

Last released

Command-line program and library for reading, writing, validating and executing modeling projects (COMBINE/OMEX archives with SED-ML files).

kisao

Last released

Utilities for working with the Kinetic Simulation Algorithm Ontology (KiSAO)

biosimulators-pysces

Last released

BioSimulators-compliant command-line interface to the PySCeS simulation program <http://pysces.sourceforge.net/>.

biosimulators-test-suite

Last released

Tools for validating that biosimulation tools are consistent with the BioSimulators standards

biosimulators-amici

Last released

BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>.

biosimulators-boolnet

Last released

BioSimulators-compliant command-line interface to the BoolNet simulation program.

biosimulators-cobrapy

Last released

BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.

biosimulators-cbmpy

Last released

BioSimulators-compliant command-line interface to the CBMPy simulation program <http://cbmpy.sourceforge.net/>.

biosimulators-ginsim

Last released

BioSimulators-compliant command-line interface to the GINsim simulation program.

biosimulators-copasi

Last released

BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

biosimulators-tellurium

Last released

BioSimulators-compliant command-line interface to the tellurium simulation program <http://tellurium.analogmachine.org>.

biosimulators-pyneuroml

Last released

BioSimulators-compliant command-line interface to the jNeuroML/pyNeuroML, NEURON, and NetPyNe simulation programs.

biosimulators-opencor

Last released

BioSimulators-compliant command-line interface to the OpenCOR simulation program.

biosimulators-masspy

Last released

BioSimulators-compliant command-line interface to the MASSpy simulation program.

biosimulators-xpp

Last released

BioSimulators-compliant command-line interface to the XPP simulation program.

biosimulators-gillespy2

Last released

BioSimulators-compliant command-line interface to the GillesPy2 simulation program.

biosimulators-libsbmlsim

Last released

BioSimulators-compliant command-line interface to LibSBMLsim <http://fun.bio.keio.ac.jp/software/libsbmlsim/>.

vcell-cli-utils

Last released

Python utility package for VCell CLI Java App

conv-opt

Last released

High-level Python package for solving linear and quadratic optimization problems using multiple solvers

de-sim

Last released

object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems

wc-utils

Last released

Utilities for whole-cell modeling

obj-tables

Last released

Tools for creating and reusing high-quality spreadsheets

gdoc-down

Last released

Download Google documents to files

bcforms

Last released

Toolkit for concretely describing macromolecular complexes

bpforms

Last released

Unambiguous representation of modified DNA, RNA, and proteins

datanator-query-python

Last released

A package to query and format the data in the integrated Datanator database

wc-onto

Last released

Ontology for whole-cell modeling

pkg-utils

Last released

Utilities for linking setuptools with version metadata, README files, requirements files, and restoring overridden entry points

unitth

Last released

Python interface for UnitTH unit test history report generator

nose2unitth

Last released

Convert nose-style test reports to UnitTH-style test reports

wc-sandbox

Last released

Jupyter playground for whole-cell modeling

wc-cli

Last released

Whole-cell models and whole-cell modeling tools

h1-hesc

Last released

Whole-cell model of H1 human embryonic stem cells (hESCs)

wc-env-manager

Last released

Tools for managing computing environments for whole-cell modeling

karr-lab-build-utils

Last released

Karr Lab build utilities

wc-test

Last released

Methods for testing whole-cell knowledge bases and models

wc-sim

Last released

Sequential whole-cell model simulator

wc-rules

Last released

Language for describing whole-cell models

wc-model-gen

Last released

Framework for systematically and scalably designing whole-cell models from large datasets such as `wc_kb`

test-history-server

Last released

Unit test history server

wc-lang

Last released

Language for describing whole-cell models

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