Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

pypi.org "systems-biology" keyword

biomass 0.13.0
A Python Framework for Modeling and Analysis of Signaling Systems
30 versions - Latest release: 2 months ago - 1 dependent package - 3 dependent repositories - 139 downloads last month - 24 stars on GitHub - 1 maintainer
autopacmen-paulocracy 0.6.2
The AutoPACMEN package
9 versions - Latest release: 11 months ago - 53 downloads last month - 11 stars on GitHub - 1 maintainer
Top 6.3% on pypi.org
indra 1.22.0
Integrated Network and Dynamical Reasoning Assembler
28 versions - Latest release: almost 2 years ago - 4 dependent packages - 10 dependent repositories - 819 downloads last month - 163 stars on GitHub - 1 maintainer
biosimulators-cbmpy 0.1.15
BioSimulators-compliant command-line interface to the CBMPy simulation program <http://cbmpy.sour...
16 versions - Latest release: over 2 years ago - 3 dependent repositories - 93 downloads last month - 0 stars on GitHub - 2 maintainers
bel2scm 0.0.4
A package for creating causal graphs in pyro
4 versions - Latest release: about 4 years ago - 19 downloads last month - 10 stars on GitHub - 1 maintainer
netmedpy
NetMedPy evaluates network localization (statistical analysis of the largest connected component/...
2 versions - 236 downloads last month - 0 stars on GitHub - 1 maintainer
diffupath 0.0.3
Compute diffusion scores over networks from biological databases
3 versions - Latest release: about 4 years ago - 1 dependent repositories - 14 downloads last month - 6 stars on GitHub - 1 maintainer
pybel-cx 0.1.3
A PyBEL extension for interconversion with CX
6 versions - Latest release: over 4 years ago - 1 dependent repositories - 21 downloads last month - 0 stars on GitHub - 1 maintainer
geckopy 2.0.2
Methods for using the GECKO model with cobrapy
11 versions - Latest release: over 3 years ago - 1 dependent repositories - 82 downloads last month - 63 stars on GitHub - 2 maintainers
galibrate 0.4.2
Python toolkit for continuous Genetic Algorithm optimization.
3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 6 downloads last month - 8 stars on GitHub - 1 maintainer
biobalm 0.2.0
Boolean Attractor Landscape Mapper
3 versions - Latest release: about 2 months ago - 37 downloads last month - 2 stars on GitHub - 1 maintainer
sbml2hyb 1.0.3
sbml2hyb is a Pyton tool for SBML compatible hybrid modelling.
4 versions - Latest release: over 1 year ago - 17 downloads last month - 4 stars on GitHub - 1 maintainer
gleipnir-ns 0.25.0
Python toolkit for Nested Sampling.
1 version - Latest release: almost 5 years ago - 1 dependent repositories - 7 downloads last month - 2 stars on GitHub - 1 maintainer
corda 0.5.1
Genome-scale model construction with CORDA
15 versions - Latest release: over 1 year ago - 1 dependent package - 2 dependent repositories - 157 downloads last month - 21 stars on GitHub - 1 maintainer
biosimulators-cobrapy 0.1.23
BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencob...
24 versions - Latest release: over 2 years ago - 3 dependent repositories - 223 downloads last month - 2 stars on GitHub - 2 maintainers
emmaa 1.17.0
Ecosystem of Machine-maintained Models with Automated Analysis
15 versions - Latest release: almost 3 years ago - 1 dependent repositories - 45 downloads last month - 10 stars on GitHub - 1 maintainer
pyrthomas 0.0.10
Python implementation for René Thomas's Framework
6 versions - Latest release: almost 3 years ago - 1 dependent repositories - 14 downloads last month - 0 stars on GitHub - 1 maintainer
biosimulators-boolnet 0.1.18
BioSimulators-compliant command-line interface to the BoolNet simulation program.
19 versions - Latest release: over 2 years ago - 2 dependent repositories - 104 downloads last month - 0 stars on GitHub - 2 maintainers
rbatools 1.0.3
Programming interface to resource allocation modelling with the Resource Balance Analysis (RBA) m...
5 versions - Latest release: about 1 year ago - 1 dependent repositories - 42 downloads last month - 2 stars on GitHub - 1 maintainer
molclustpy 0.1.0
A Python package to analyze multivalent biomolecular clustering.
5 versions - Latest release: about 1 year ago - 7 downloads last month - 0 stars on GitHub - 1 maintainer
petabvis 0.0.2
Interactive visualization of PEtab problems
2 versions - Latest release: over 3 years ago - 1 dependent repositories - 22 downloads last month - 7 stars on GitHub - 2 maintainers
commmodelpy 0.0.3
The commmodelpy package
2 versions - Latest release: almost 3 years ago - 21 downloads last month - 3 stars on GitHub - 1 maintainer
bio2bel-entrez 0.2.2
A package for parsing and storing Entrez Gene
12 versions - Latest release: over 4 years ago - 65 downloads last month - 0 stars on GitHub - 1 maintainer
bio2bel-wikipathways 0.2.3
A package for converting Wikipathways to BEL
27 versions - Latest release: about 5 years ago - 104 downloads last month - 3 stars on GitHub - 2 maintainers
biosimulators-bionetgen 0.1.20
BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bione...
21 versions - Latest release: over 2 years ago - 3 dependent repositories - 68 downloads last month - 1 stars on GitHub - 3 maintainers
Top 9.7% on pypi.org
sme 1.6.0
Spatial Model Editor python bindings
22 versions - Latest release: 2 months ago - 1 dependent package - 2 dependent repositories - 918 downloads last month - 14 stars on GitHub - 2 maintainers
biosimulators-gillespy2 0.1.37
BioSimulators-compliant command-line interface to the GillesPy2 simulation program.
31 versions - Latest release: over 2 years ago - 3 dependent repositories - 465 downloads last month - 1 stars on GitHub - 2 maintainers
bio2bel-drugbank 0.1.1
A package for converting DrugBank to BEL
4 versions - Latest release: over 5 years ago - 1 dependent repositories - 31 downloads last month - 9 stars on GitHub - 1 maintainer
Top 2.2% on pypi.org
cobra 0.29.0
COBRApy is a package for constraint-based modeling of metabolic networks.
99 versions - Latest release: 7 months ago - 56 dependent packages - 240 dependent repositories - 7.99 thousand downloads last month - 444 stars on GitHub - 5 maintainers
cobra-utils 0.3.1
TBD
8 versions - Latest release: over 4 years ago - 1 dependent repositories - 68 downloads last month - 442 stars on GitHub - 1 maintainer
pamodelpy 0.0.2
Python framework for building and analysing protein allocation models
22 versions - Latest release: 10 months ago - 118 downloads last month - 444 stars on GitHub - 1 maintainer
mergem 1.1.0
mergem is a python package and command-line tool for merging, comparing, and translating genome-s...
31 versions - Latest release: 3 months ago - 1 dependent repositories - 200 downloads last month - 5 stars on GitHub - 2 maintainers
biosimulations-modeldb 0.0.4
Command-line program for publishing the ModelDB model repository to BioSimulations.
3 versions - Latest release: over 2 years ago - 11 downloads last month - 0 stars on GitHub - 1 maintainer
datanator-query 0.1
A python API to for querying datanator DB server
1 version - Latest release: almost 5 years ago - 1 dependent repositories - 13 downloads last month - 1 maintainer
biosimulators-masspy 0.0.9
BioSimulators-compliant command-line interface to the MASSpy simulation program.
9 versions - Latest release: over 2 years ago - 2 dependent repositories - 55 downloads last month - 1 stars on GitHub - 2 maintainers
crazydoc 0.1.6
Read genetic sequences from stylized docx files
6 versions - Latest release: about 1 year ago - 1 dependent package - 1 dependent repositories - 3 thousand downloads last month - 31 stars on GitHub - 1 maintainer
metevolsim 1.0.0
MetEvolSim (Metabolome Evolution Simulator) Python Package
29 versions - Latest release: 9 months ago - 1 dependent repositories - 138 downloads last month - 4 stars on GitHub - 1 maintainer
biosimulators-rbapy 0.0.4
BioSimulators-compliant command-line interface to the RBApy simulation program.
4 versions - Latest release: over 2 years ago - 3 dependent repositories - 30 downloads last month - 0 stars on GitHub - 2 maintainers
straindesign 1.4.1
Computational strain design package for the COBRApy framework
20 versions - Latest release: about 2 years ago - 1 dependent repositories - 338 downloads last month - 32 stars on GitHub - 1 maintainer
rebop 0.6.1
A fast stochastic simulator for chemical reaction networks
2 versions - Latest release: 8 months ago - 17 downloads last month - 42 stars on GitHub - 1 maintainer
pydyno 0.1.2
Dynamic analysis of systems biology models
2 versions - Latest release: about 3 years ago - 1 dependent repositories - 19 downloads last month - 8 stars on GitHub - 1 maintainer
Top 7.3% on pypi.org
pypesto 0.5.1
python-based Parameter EStimation TOolbox
42 versions - Latest release: about 2 months ago - 2 dependent packages - 3 dependent repositories - 344 downloads last month - 180 stars on GitHub - 3 maintainers
colomoto-docker 7.0.2
Helper script to run docker image colomoto/colomoto-docker
37 versions - Latest release: about 5 years ago - 1 dependent repositories - 278 downloads last month - 0 stars on GitHub - 1 maintainer
wc-rules 0.0.1
Language for describing whole-cell models
1 version - Latest release: 10 months ago - 1 dependent repositories - 9 stars on GitHub - 2 maintainers
biomodels-qc 0.0.1
Tools for quality controlling the BioModels database
1 version - Latest release: about 2 years ago - 1 dependent repositories - 17 downloads last month - 0 stars on GitHub - 1 maintainer
ggshu 0.1.0
Grammar of Graphics for shu.
1 version - Latest release: 8 months ago - 7 downloads last month - 37 stars on GitHub - 1 maintainer
bio2bel-go 0.0.1
A package for converting GO to BEL
1 version - Latest release: over 5 years ago - 1 dependent repositories - 20 downloads last month - 1 stars on GitHub - 1 maintainer
pathway-forte 0.0.2
A Python package for comparing the effect of pathway database choice in functional enrichment and...
2 versions - Latest release: about 5 years ago - 1 dependent repositories - 12 downloads last month - 13 stars on GitHub - 1 maintainer
wc-onto 0.0.2
Ontology for whole-cell modeling
1 version - Latest release: about 4 years ago - 1 dependent repositories - 29 downloads last month - 1 stars on GitHub - 2 maintainers
wc-model-gen 0.0.1
Framework for systematically and scalably designing whole-cell models from large datasets such as...
1 version - Latest release: 10 months ago - 1 dependent repositories - 5 stars on GitHub - 2 maintainers
bel-commons 0.3.1
A web application exposing core PyBEL functionalities
2 versions - Latest release: about 4 years ago - 1 dependent repositories - 22 downloads last month - 4 stars on GitHub - 1 maintainer
boolsi 1.0.4
BoolSi is a tool for distributed simulations and analysis of Boolean networks
8 versions - Latest release: almost 4 years ago - 1 dependent repositories - 49 downloads last month - 6 stars on GitHub - 1 maintainer
pyvipr 1.0.7
Widget to visualize PySB models in Jupyter Notebook
26 versions - Latest release: about 2 years ago - 2 dependent repositories - 117 downloads last month - 27 stars on GitHub - 1 maintainer
ecell4-base 2.1.0
A software platform for modeling, simulation and analysis of complex, heterogeneous and multi-sca...
13 versions - Latest release: about 3 years ago - 1 dependent repositories - 27 downloads last month - 62 stars on GitHub - 1 maintainer
pybel-tools 0.9.1
A cool pool of tools for BEL
41 versions - Latest release: over 3 years ago - 1 dependent repositories - 176 downloads last month - 5 stars on GitHub - 2 maintainers
Top 4.2% on pypi.org
pysb 1.16.0
Python Systems Biology modeling framework
35 versions - Latest release: 4 months ago - 5 dependent packages - 23 dependent repositories - 1.56 thousand downloads last month - 160 stars on GitHub - 2 maintainers
spycone 0.2.0
A splicing-aware time course network enricher
17 versions - Latest release: 9 months ago - 1 dependent repositories - 87 downloads last month - 7 stars on GitHub - 1 maintainer
Top 4.6% on pypi.org
pybel 0.15.5
Parsing, validation, compilation, and data exchange of Biological Expression Language (BEL)
92 versions - Latest release: over 2 years ago - 6 dependent packages - 18 dependent repositories - 2.26 thousand downloads last month - 130 stars on GitHub - 2 maintainers
wc-lang 0.0.1
Language for describing whole-cell models
1 version - Latest release: 10 months ago - 1 dependent repositories - 8 stars on GitHub - 2 maintainers
biosimulations-bigg 0.0.5
Command-line program for publishing the BiGG model repository to BioSimulations.
5 versions - Latest release: over 2 years ago - 1 dependent repositories - 37 downloads last month - 1 stars on GitHub - 2 maintainers
biosimulators-amici 0.1.24
BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.co...
29 versions - Latest release: 12 months ago - 2 dependent repositories - 197 downloads last month - 2 stars on GitHub - 2 maintainers
bio2bel-interpro 0.2.1
A package for converting InterPro to BEL
3 versions - Latest release: about 5 years ago - 1 dependent repositories - 39 downloads last month - 0 stars on GitHub - 1 maintainer
physiofit 3.3.6
Calculate extracellular fluxes from metabolite concentrations and biomass data
30 versions - Latest release: 2 months ago - 3 dependent repositories - 199 downloads last month - 6 stars on GitHub - 2 maintainers
toymaker 0.2.5
This library is designed to facilitate research of stochasticity effects in genetic circuits
6 versions - Latest release: 11 months ago - 27 downloads last month - 2 stars on GitHub - 1 maintainer
sbml2julia 0.1.1
Optimization tool based on ODE discretisation.
2 versions - Latest release: over 3 years ago - 1 dependent repositories - 18 downloads last month - 5 stars on GitHub - 1 maintainer
bio2bel-hmdd 0.0.2
A package for converting the Human microRNA Disease Database (HMDD) to BEL.
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 15 downloads last month - 0 stars on GitHub - 1 maintainer
ymap 2.0.8
An automated method to map yeast variants to protein modifications and functional regions
11 versions - Latest release: over 7 years ago - 1 dependent repositories - 108 downloads last month - 5 stars on GitHub - 1 maintainer
ssbio 0.9.9
Tools to enable structural systems biology
20 versions - Latest release: over 6 years ago - 3 dependent repositories - 96 downloads last month - 101 stars on GitHub - 1 maintainer
stochpy 1.1.2
StochPy (Stochastic modeling in Python) provides several stochastic simulation algorithms to simu...
13 versions - Latest release: over 10 years ago - 1 dependent repositories - 204 downloads last month - 39 stars on GitHub - 2 maintainers
biosimulators-libsbmlsim 0.0.6
BioSimulators-compliant command-line interface to LibSBMLsim <http://fun.bio.keio.ac.jp/software/...
6 versions - Latest release: over 2 years ago - 3 dependent repositories - 64 downloads last month - 0 stars on GitHub - 2 maintainers
micom 0.35.0
Microbial community modeling based on cobrapy.
106 versions - Latest release: about 2 months ago - 1 dependent package - 1 dependent repositories - 1.47 thousand downloads last month - 77 stars on GitHub - 1 maintainer
mmodes 0.2.6
Metabolic Models based Ordinary Differential Equations Simulation
7 versions - Latest release: almost 4 years ago - 1 dependent repositories - 81 downloads last month - 1 maintainer
biosimulators-utils 0.1.187
Command-line program and library for reading, writing, validating and executing modeling projects...
179 versions - Latest release: 4 months ago - 4 dependent packages - 4 dependent repositories - 3.74 thousand downloads last month - 5 stars on GitHub - 2 maintainers
dysregnet 0.1.0
DysRegNet
6 versions - Latest release: about 2 months ago - 1 dependent repositories - 123 downloads last month - 2 stars on GitHub - 1 maintainer
pasmopy 0.5.0
Patient-Specific Modeling in Python
20 versions - Latest release: about 1 year ago - 1 dependent repositories - 210 downloads last month - 16 stars on GitHub - 1 maintainer
biosimulators-test-suite 0.1.88
Tools for validating that biosimulation tools are consistent with the BioSimulators standards
88 versions - Latest release: 11 months ago - 1 dependent repositories - 575 downloads last month - 7 stars on GitHub - 2 maintainers
biosimulators-tellurium 0.1.42
BioSimulators-compliant command-line interface to the tellurium simulation program <http://tellur...
39 versions - Latest release: 10 months ago - 3 dependent repositories - 212 downloads last month - 1 stars on GitHub - 2 maintainers
diffupy 0.0.5
Compute diffusion scores over networks
5 versions - Latest release: about 4 years ago - 1 dependent repositories - 30 downloads last month - 7 stars on GitHub - 1 maintainer
biosimulators-copasi 0.1.35
BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.
35 versions - Latest release: about 2 years ago - 2 dependent repositories - 330 downloads last month - 2 stars on GitHub - 2 maintainers
drug2ways 0.0.12
Reasoning over polar paths in biological networks for drug discovery applications
12 versions - Latest release: almost 2 years ago - 2 dependent repositories - 69 downloads last month - 26 stars on GitHub - 1 maintainer
pathme 0.1.13
Harmonizing pathway databases using Biological Expression Language (BEL)
23 versions - Latest release: about 4 years ago - 1 dependent repositories - 105 downloads last month - 17 stars on GitHub - 1 maintainer
kisao 2.15.3
Utilities for working with the Kinetic Simulation Algorithm Ontology (KiSAO)
21 versions - Latest release: about 3 years ago - 5 dependent packages - 20 dependent repositories - 2.33 thousand downloads last month - 9 stars on GitHub - 2 maintainers
Top 6.8% on pypi.org
petab 0.2.9
Parameter estimation tabular data
58 versions - Latest release: 3 months ago - 7 dependent packages - 14 dependent repositories - 5.64 thousand downloads last month - 14 stars on GitHub - 2 maintainers
pycotools 1.0.10
A python toolbox for COPASI
106 versions - Latest release: almost 5 years ago - 4 dependent repositories - 477 downloads last month - 7 stars on GitHub - 1 maintainer
compath 0.1.3
A web application for exploring and comparing the overlaps across pathway resources
8 versions - Latest release: over 3 years ago - 1 dependent repositories - 69 downloads last month - 11 stars on GitHub - 2 maintainers
bio2bel-kegg 0.3.0
A package for converting KEGG gene sets into BEL
22 versions - Latest release: over 3 years ago - 1 dependent repositories - 213 downloads last month - 13 stars on GitHub - 2 maintainers
pymgpipe 0.16.10
Community level microbiome metabolic modeling in Python
5 versions - Latest release: 11 months ago - 42 downloads last month - 6 stars on GitHub - 1 maintainer
django-disbi 0.0.2
A Django app framework for managing and integrating systems biology data.
1 version - Latest release: over 7 years ago - 1 dependent repositories - 10 downloads last month - 3 stars on GitHub - 1 maintainer
hemekg 0.0.1
Mechanistic knowledge about heme and hemolytic disorders in Biological Expression Language with P...
1 version - Latest release: over 3 years ago - 1 dependent repositories - 13 downloads last month - 3 stars on GitHub - 1 maintainer
efmlrs 2.3.6
Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that...
17 versions - Latest release: almost 3 years ago - 1 dependent repositories - 155 downloads last month - 3 stars on GitHub - 1 maintainer
couzinswarm 0.0.3
Simulating fish swarming behavior with the model by Iain Couzin et al.
3 versions - Latest release: about 5 years ago - 1 dependent repositories - 8 downloads last month - 6 stars on GitHub - 1 maintainer
Top 8.4% on pypi.org
cbmpy 0.8.8
CBMPy: https://systemsbioinformatics.github.io/cbmpy/ is a platform for constraint based modellin...
20 versions - Latest release: 7 months ago - 1 dependent package - 7 dependent repositories - 331 downloads last month - 16 stars on GitHub - 1 maintainer
biosimulators-opencor 0.0.13
BioSimulators-compliant command-line interface to the OpenCOR simulation program.
12 versions - Latest release: over 2 years ago - 1 dependent repositories - 112 downloads last month - 1 stars on GitHub - 2 maintainers
biosimulators-pysces 0.1.25
BioSimulators-compliant command-line interface to the PySCeS simulation program <http://pysces.so...
29 versions - Latest release: over 2 years ago - 2 dependent repositories - 305 downloads last month - 1 stars on GitHub - 2 maintainers
bio2bel-expasy 0.2.0
A package for parsing and storing the ExPASy Enzyme Database
2 versions - Latest release: over 5 years ago - 13 downloads last month - 0 stars on GitHub - 1 maintainer
benchmark-models-petab 0.0.0a1 removed
A collection of models with experimental data in the PEtab format
1 version - Latest release: almost 2 years ago - 19 stars on GitHub
Top 8.9% on pypi.org
pybiopax 0.1.5
A Python implementation of the BioPAX object model, and parts of PaxTools.
12 versions - Latest release: about 1 month ago - 1 dependent package - 6 dependent repositories - 937 downloads last month - 21 stars on GitHub - 1 maintainer
Related Keywords
computational-biology 28 bioinformatics 26 sbml 25 python 25 simulation 21 modeling 19 sed-ml 18 systems biology 18 Systems Biology 17 biology 17 biosimulators 16 Networks Biology 15 biological-expression-language 15 metabolism 13 networks-biology 13 systems 12 combine 12 computational biology 12 metabolic-models 11 omex 11 SED-ML 11 Biological Expression Language 11 BioSimulators 11 BEL 10 COMBINE 10 SBML 10 OMEX 9 biochemistry 9 biochemical-networks 9 parameter-estimation 8 numerical simulation 8 sbml-model 7 docker 7 combine-archive 7 metabolic-network 7 flux 6 omex-metadata 6 pathways 6 cobrapy 6 cobra 6 numerical-simulation 5 optimization 5 dynamical-modeling 5 whole-cell-modeling 5 cell-biology 5 constraint-based-modeling 4 kinetic-modeling 4 flux-balance-analysis 4 strain-engineering 4 kinetic model 4 mathematical model 4 mathematical-model 4 whole-cell 4 mathematical-modeling 4 copasi 4 pysb 4 pathway-analysis 3 mathematical modeling 3 modelling 3 stochastic-simulation-algorithm 3 data-integration 3 terminology 3 visualization 3 petab 3 rule-based-modeling 3 networks 3 bionetgen 3 ontology 3 model 3 fba 3 systems-biology-simulation 3 synthetic-biology 3 hacktoberfest 3 proteins 3 sbml-simulation 3 cell-design 3 ode 3 network-analysis 3 microbiome 2 metabolic-reconstruction 2 cancer 2 console-application 2 genome-scale-models 2 biotechnology 2 cell biology 2 mathematical-modelling 2 BioNetGen 2 gillespie-algorithm 2 tellurium 2 transcriptomics 2 pybel 2 kinetic-model 2 stochastic 2 jupyter-notebook 2 computational 2 Gene Ontology 2 Pathway Databases 2 protein-domains 2 protein-families 2 kisao 2