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33 search results found

Cobrapy ⭐ 414

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

Awesome Biology ⭐ 313

Curated (meta)list of resources for Biology.

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.

Pandora ⭐ 127

PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻

Biojupies ⭐ 94

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

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

Pathway Mapper ⭐ 52

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

A web application to visualize and edit pathway models

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!

Sbgnviz.js ⭐ 33

A web based visualization tool for process description maps in SBGN

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

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

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Drug2ways ⭐ 18

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

Harmonizing pathway databases using Biological Expression Language (BEL)

PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.

Chise.js ⭐ 14

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

Biojupies Plugins ⭐ 13

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

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

Pathway Forte ⭐ 10

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

Randomwalkrestartmh ⭐ 10

A package to perform Random Walk with Restart on different types of networks

Autopacmen ⭐ 10

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

Py4lifesci ⭐ 9

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

Julia Theosysbio ⭐ 8

Advancesyntoolkit ⭐ 7

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

A web application for exploring, analyzing, and curating pathway databases

SyBLaRS: Systems Biology Layout & Rendering Service

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

Results of the evaluation of pathway databases using TCGA datasets

Cd2sbgnml ⭐ 5

Translation between CellDesigner-flavoured SBML and SBGN-ML

Distributed simulations and analysis of synchronous Boolean networks

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