Alternatives and similar repositories for nfsim

Users that are interested in nfsim are comparing it to the libraries listed below

• amirpandi / METIS
  METIS: A versatile active learning workflow for optimization of genetic and metabolic networks
  ☆33Updated 3 years ago
• RuleWorld / bionetgen
  Rule-based modeling framework
  ☆65Updated 7 months ago
• pstjohn / dFBA
  Dynamic Flux Balance analysis in Python
  ☆11Updated 9 years ago
• hetio / xswap
  Python library (C++ backend) for degree-preserving network randomization
  ☆14Updated 6 years ago
• ZhangGroup-MITChemistry / DRAGON
  ☆12Updated 2 years ago
• KarrLab / intro_to_wc_modeling
  Whole-cell modeling tutorials
  ☆16Updated 5 years ago
• msneddon / nfsim
  A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
  ☆19Updated last year
• PhysiBoSS / PhysiBoSS
  PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
  ☆30Updated this week
• CovertLab / wcEcoli
  Whole Cell Model of E. coli
  ☆34Updated last week
• sbl-sdsc / mmtf-genomics
  Methods for mapping genomic data onto 3D protein structure.
  ☆28Updated 3 years ago
• SBRG / pymodulon
  Python package for analyzing and visualizing iModulons
  ☆14Updated 3 weeks ago
• mims-harvard / SPECTRA
  SPECTRA: Spectral framework for evaluation of biomedical AI models
  ☆41Updated 9 months ago
• allydunham / aa_subtypes
  Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape
  ☆11Updated 3 years ago
• BioJulia / BioGenerics.jl
  Generic methods, types and modules for the BioJulia ecosystem.
  ☆12Updated last year
• PDBeurope / PDBe_Programming
  PDBe Programming Interfaces information
  ☆14Updated 7 years ago
• SBRG / MASSpy
  ☆26Updated 3 years ago
• lifs-tools / awesome-lipidomics
  A collection of awesome lipidomics tools and resources
  ☆16Updated 3 years ago
• reactome / reactome2py
  python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.
  ☆34Updated last year
• tlubitz / parameter_balancing
  Software tool for metabolic modelling in Systems Biology
  ☆10Updated 5 years ago
• gmiaslab / mathiomica
  MathIOmica is a Mathematica package for omics data analyses
  ☆12Updated 2 years ago
• LoLab-MSM / pyvipr
  Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
  ☆27Updated 2 years ago
• MICommunity / ComplexViewer
  web based visualisation of molecular interaction data
  ☆12Updated 7 months ago
• lifs-tools / goslin
  Goslin is the Grammar on succinct lipid nomenclature.
  ☆12Updated last month
• biocircuits / bioscrape
  BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)
  ☆29Updated 9 months ago
• p-koo / deepomics
  deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis
  ☆22Updated 2 years ago
• SBRG / cobrame
  A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
  ☆35Updated 6 years ago
• phievo / phievo
  Software for in silico evolution - Paul François' group McGill University
  ☆10Updated 3 years ago
• MedChaabane / deepRAM
  End-to-end deep learning toolkit for predicting protein binding sites and motifs.
  ☆45Updated 6 years ago
• broadinstitute / g2papi
  Python Client Library for the G2P Portal API
  ☆15Updated 4 months ago
• normandavey / ProcessedAlphafold
  ☆31Updated 4 years ago