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53 search results found

Cobrapy ⭐ 414

COBRApy is a package for constraint-based modeling of metabolic networks.

Pypesto ⭐ 183

python Parameter EStimation TOolbox

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Python framework for Systems Biology modeling

Advanced Multilanguage Interface to CVODES and IDAS

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

Yeast Gem ⭐ 80

The consensus GEM for Saccharomyces cerevisiae

Python package to study microbial communities using metabolic modeling.

Ecell4_base ⭐ 61

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

Toolbox for including enzyme constraints on a genome-scale model.

A python library for metabolic networks sampling and analysis

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

Straindesign ⭐ 27

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

A Python Framework for Modeling and Analysis of Signaling Systems

Benchmark Models Petab ⭐ 23

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

Pybiopax ⭐ 19

PyBioPAX: A python implementation of the BioPAX object model

Colomoto Docker ⭐ 18

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Drug2ways ⭐ 18

A Python package for drug discovery by analyzing causal paths on multiscale networks

Enzyme-constrained genome-scale models in python

Patient-Specific Modeling in Python

Libpetab Python ⭐ 14

Python package for working with PEtab files

Biosimulators ⭐ 13

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

CBMPy is a Python based platform for constraint based modelling and analysis.

Biojupies Plugins ⭐ 13

User-submitted RNA-seq data analysis tools for BioJupies.

Datanator ⭐ 11

Toolkit for discovering and aggregating data for whole-cell modeling

Indra_db ⭐ 11

A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.

Ecosystem of Machine-maintained Models with Automated Analysis

Pathway Forte ⭐ 10

A Python package for benchmarking pathway database with functional enrichment and classification methods

Py4lifesci ⭐ 9

Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

Intro_to_wc_modeling ⭐ 9

Whole-cell modeling tutorials

Galibrate ⭐ 8

Parameter estimation and model calibration using Genetic Algorithm optimization in Python.

SPARCED model creation and simulation package.

Biosimulators_test_suite ⭐ 7

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

MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.

Language for describing whole-cell models as reaction networks

Intro_to_param_estim ⭐ 7

Parameter estimation of ODE models describing biological processes

Advancesyntoolkit ⭐ 7

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

PEtab visualization tool

Codes and data for the paper entitled "Learning representations to predict intermolecular interactions on large-scale heterogeneous molecular association network"

Rule-based modeling for whole-cell models.

Distributed simulations and analysis of synchronous Boolean networks

Petab_test_suite ⭐ 5

PEtab test suite

MultiModal Classifier Hierarchy (MMoCHi)

Wc_model_gen ⭐ 5

Framework for systematically and scalably designing whole-cell models from large datasets

mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models

Physiofit ⭐ 5

Estimation of extracellular fluxes and growth rate

FLYCOP (FLexible sYnthetic Consortium OPtimization)

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

Sbml2julia ⭐ 5

A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.

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