systems-biology 开源项目推荐（792 个）

opencobra /cobrapy

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

SciML /Catalyst.jl

化学反应网络与系统生物学接口，用于科学机器学习（SciML）。高性能、GPU并行化和开源软件中的O（1）求解器。

raivivek /awesome-biology

Curated (meta)list of resources for Biology.

ICB-DCM /pyPESTO

python Parameter EStimation TOolbox

franciscozorrilla /metaGEM

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

gyorilab /indra

INDRA（集成网络与动态推理汇编器）是一个自动化模型汇编系统，与 NLP 系统和数据库对接以收集知识，并通过汇编过程生成因果图和动态模型。

saeyslab /multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

pysb /pysb

Python framework for Systems Biology modeling

micom-dev /micom

Python package to study microbial communities using metabolic modeling.

genular /pandora

PANDORA 💻

pybel /pybel

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

SysBioChalmers /yeast-GEM

The consensus GEM for Saccharomyces cerevisiae

SysBioChalmers /RAVEN

用于基因组规模模型重建、整理和分析的 RAVEN 工具箱。此仓库包含 RAVEN 2.x；RAVEN 3 在 CompMetEng/RAVEN 中开发。

copasi /COPASI

COPASI 是一款用于生化网络及其动力学模拟与分析的软件应用。

florianhartig /BayesianTools

General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

Rockman6 /CellSim

Physics-first, uncertainty-honest in-silico cell and drug-response simulator (Python). Validated docking/ADMET input layer (Vina, OpenFF, xTB), cell-level PK/PD modules, and a cell/colony engine under construction toward a validated interactive dish.

MaayanLab /biojupies

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

SBRG /ssbio

A Python framework for structural systems biology

seek4science /seek

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

SysBioChalmers /GECKO

Toolbox for including enzyme constraints on a genome-scale model. This repository holds GECKO 3.x; GECKO 4 is developed in CompMetEng/GECKO.