Alternatives and similar repositories for vivarium-core:

Users that are interested in vivarium-core are comparing it to the libraries listed below

• CovertLab / vEcoli
  Whole cell model of E. coli implemented with Vivarium
  ☆16Updated this week
• reactome / reactome2py
  python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.
  ☆31Updated last year
• RuleWorld / bionetgen
  Rule-based modeling framework
  ☆61Updated this week
• PhysiBoSS / PhysiBoSS
  PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
  ☆24Updated this week
• ginkgobioworks / edge
  Efficiently keep track of changes to genomes
  ☆38Updated 9 months ago
• pstjohn / dFBA
  Dynamic Flux Balance analysis in Python
  ☆11Updated 9 years ago
• broadinstitute / cell-health
  Predicting Cell Health with Morphological Profiles
  ☆36Updated 3 years ago
• virtualcell / vcell
  Virtual Cell Framework
  ☆80Updated this week
• CovertLab / WholeCellEcoliRelease
  Release of the whole cell E. coli model.
  ☆65Updated 4 months ago
• sbmlteam / python-libsbml
  Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.
  ☆22Updated 6 months ago
• sanderlab / CellBox
  CellBox: Interpretable Machine Learning for Perturbation Biology
  ☆53Updated last year
• theislab / deepflow
  This code contains the neural network implementation from the nature communication manuscript NCOMMS-16-25447A.
  ☆32Updated 7 years ago
• tissue-forge / tissue-forge
  Interactive, particle-based physics, chemistry and biology modeling and simulation environment
  ☆22Updated 3 months ago
• biomass-dev / biomass
  A Python Framework for Modeling and Analysis of Signaling Systems
  ☆29Updated 3 weeks ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆72Updated last year
• gyorilab / pybiopax
  PyBioPAX: A python implementation of the BioPAX object model
  ☆24Updated 11 months ago
• cellannotation / cell-annotation-schema
  General, open-standard schema for cell annotations
  ☆15Updated 3 weeks ago
• MathCancer / PhysiCell
  PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch.…
  ☆158Updated 2 months ago
• AllenCell / cvapipe_analysis
  Analysis of data produced by cvapipe for the variance paper
  ☆23Updated 4 months ago
• obophenotype / cell-ontology
  An ontology of cell types
  ☆168Updated last week
• 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
• copasi / COPASI
  COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
  ☆105Updated 3 weeks ago
• idekerlab / DCell
  DCell browser and gene deletion simulator
  ☆123Updated 2 years ago
• matthiaskoenig / dfba
  Encoding Dynamic Flux Balance Analysis in SBML
  ☆11Updated 4 years ago
• burtonrj / CytoPy
  A data-centric flow/mass cytometry automated analysis framework
  ☆39Updated 3 months ago
• Luthey-Schulten-Lab / Lattice_Microbes
  ☆31Updated 3 years ago
• piximi / application_archived
  A web application for classifying objects
  ☆29Updated 3 years ago
• erolkavvas / metabolic-allele-classifiers
  A flux balance analysis machine learning classifier for microbial GWAS
  ☆14Updated 5 years ago
• KarrLab / intro_to_wc_modeling
  Whole-cell modeling tutorials
  ☆16Updated 4 years ago
• ialbert / booleannet
  Boolean Network Modeling
  ☆40Updated 5 years ago