biosimulators/Biosimulators_COPASI

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 10.8 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 3

biosimulators/bio-check 📦

A microservices-based data service leveraging Kubernetes for efficient orchestration of bio-chemical simulation comparisons.

Language: Python - Size: 261 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 1

biosimulators/SimpleProcessBigraphRuntime

A simple project demonstrating how to take a process bigraph input file, and run simulations / workflows utilizing a simple registry

Size: 93.8 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

biosimulators/compose-server

This repo is intended to replace both the bio-check and bio-compose-server repos. The aforementioned repos will be archived.

Language: Python - Size: 6.49 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_pyNeuroML

pyNeuroML simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.38 MB - Last synced at: 30 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

biosimulators/Biosimulators_OpenCOR

OpenCOR simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 1.76 MB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

biosimulators/bio-compose-server Fork of biosimulators/bio-check

Backend for BioCompose: a microservices-based data service leveraging Kubernetes for efficient orchestration of bio-chemical simulation comparisons.

Language: Python - Size: 261 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

biosimulators/bsvs

A high-level Python client for the Biological Simulation Verification Service REST API.

Language: Python - Size: 0 Bytes - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

biosimulators/bio-compose

Create, execute, and introspect reproducible composite simulations of dynamic biological systems.

Language: Jupyter Notebook - Size: 31 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_test_suite

Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators

Language: Python - Size: 56 MB - Last synced at: 29 days ago - Pushed at: 8 months ago - Stars: 7 - Forks: 2

biosimulators/Biosimulators_MASSpy

MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 3.64 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

biosimulators/Biosimulators_PySCeS

PySCeS biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 3.29 MB - Last synced at: about 21 hours ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

biosimulators/Biosimulators_tellurium

tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 4.4 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 2 - Forks: 2

biosimulators/Biosimulators_utils

Utilities for building standardized command-line interfaces for biosimulation software packages

Language: Python - Size: 14.4 MB - Last synced at: 29 days ago - Pushed at: 2 months ago - Stars: 4 - Forks: 6

biosimulators/Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface

Language: Python - Size: 696 KB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 13 - Forks: 0

biosimulators/Biosimulators_smoldyn

Smoldyn biochemical network stochastic simulation program via BioSimulators-compliant python interface.

Language: Python - Size: 1.65 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_AMICI

AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.5 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1

biosimulators/Biosimulators_simularium

Converting Biosimulators spatial simulation outputs into a Simularium-compliant format.

Language: Jupyter Notebook - Size: 184 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

biosimulators/OMEX-archive-editor

Language: Jupyter Notebook - Size: 4.61 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

biosimulators/biosimulator-processes Fork of vivarium-collective/biosimulator-processes 📦

Core implementations of simulator processes using the process-bigraph Process API

Language: Jupyter Notebook - Size: 19.7 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

biosimulators/Smoldyn Fork of ssandrews/Smoldyn

Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions

Size: 382 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

biosimulators/xvfb-action Fork of GabrielBB/xvfb-action

Fork of GabrielBB/xvfb-action

Language: JavaScript - Size: 923 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

biosimulators/sphinx-pretty-searchresults Fork of sphinx-contrib/sphinx-pretty-searchresults

Fork of "Sphinx: pretty search results" adding a necessary os import statement

Language: Python - Size: 31.3 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_tutorials

Tutorials for BioSimulators

Language: Jupyter Notebook - Size: 1.71 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

biosimulators/Biosimulators_COBRApy

COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.26 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

biosimulators/Biosimulators_GillesPy2

GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.4 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

biosimulators/.github

Profile for the BioSimulators organization

Size: 4.88 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_BoolNet

BoolNet biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.06 MB - Last synced at: 28 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_XPP

XPP mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 1.82 MB - Last synced at: 30 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

biosimulators/Biosimulators_RBApy

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.18 MB - Last synced at: about 20 hours ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_LibSBMLSim Fork of libsbmlsim/libsbmlsim

LibSBMLSim mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

Language: C - Size: 33.7 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_GINsim

GINsim biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 1.76 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_CBMPy

CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.08 MB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_iBioSim Fork of MyersResearchGroup/Biosimulators_iBioSim

CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 49.1 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_BioNetGen Fork of ASinanSaglam/BNG_BioSimDocker

BioNetGen biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.21 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

biosimulators/Biosimulators_simulator_template

Template for a repository for building a BioSimulators-compliant command-line interface and Dockerfile for a biosimulation program

Language: Python - Size: 348 KB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 3

biosimulators/biosimulators.github.io

Summary of the technical documentation for BioSimulators

Language: Python - Size: 1.92 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

biosimulators/edamontology Fork of edamontology/edamontology

EDAM is an ontology of bioscientific data analysis and data management.

Language: Shell - Size: 17.4 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

biosimulators/RBApy Fork of SysBioInra/RBApy

Python package for creating, calibrating and simulating RBA models

Language: Python - Size: 52.4 MB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0