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Search results for systems biology
systems-biology
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131 search results found
Cobrapy
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414
COBRApy is a package for constraint-based modeling of metabolic networks.
Catalyst.jl
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402
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Awesome Biology
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313
Curated (meta)list of resources for Biology.
Pypesto
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183
python Parameter EStimation TOolbox
Metagem
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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
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154
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.
Pysb
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145
Python framework for Systems Biology modeling
Pandora
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127
PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻
Amici
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105
Advanced Multilanguage Interface to CVODES and IDAS
Bayesiantools
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103
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Ssbio
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96
A Python framework for structural systems biology
Biojupies
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94
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Pybel
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89
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
Raven
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87
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Copasi
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80
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Yeast Gem
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80
The consensus GEM for Saccharomyces cerevisiae
Micom
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73
Python package to study microbial communities using metabolic modeling.
Seek
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69
For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
Ecell4_base
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61
An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
Multinichenetr
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56
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
D2d
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55
a modeling environment tailored to parameter estimation in dynamical systems
Gecko
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54
Toolbox for including enzyme constraints on a genome-scale model.
Petab
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54
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Cellmltoolkit.jl
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53
CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
Pathway Mapper
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52
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Protti
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50
Picotti lab data analysis package.
Newt
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48
A web application to visualize and edit pathway models
Workshop_omics_integration
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43
Workshop in omics integration and systems biology
Momentclosure.jl
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41
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
Rebop
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38
Fast stochastic simulator for chemical reaction networks
Dingo
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36
A python library for metabolic networks sampling and analysis
Cnapy
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36
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!
Shiny Iatlas
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36
An interactive web portal for exploring immuno-oncology data
Sbmltoolkit.jl
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35
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Jsbml
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34
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
Sbgnviz.js
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33
A web based visualization tool for process description maps in SBGN
Libsbml
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31
LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
Cobrame
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29
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Smfsb
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29
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
Stochpy
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28
StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
Sbml.jl
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27
Julia interface to the Systems Biology Markup Language (SBML) library
Straindesign
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27
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Pyvipr
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25
Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
Benchmark Models Petab
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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
Modelpolisher
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23
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
Biomass
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23
A Python Framework for Modeling and Analysis of Signaling Systems
Isb_course_2022
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22
Materials and presentation for the 2022 ISB Microbiome course.
Sbml Test Suite
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21
The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.
Findr
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21
Fast Inference of Networks from Directed Regulations
Corda
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20
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Pybiopax
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19
PyBioPAX: A python implementation of the BioPAX object model
Parpe
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19
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
Decode
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19
A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions
Drug2ways
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18
A Python package for drug discovery by analyzing causal paths on multiscale networks
Colomoto Docker
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18
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Finitestateprojection.jl
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18
Finite State Projection algorithms for chemical reaction networks
Cobra.tutorials
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18
Repository of tutorials for The COBRA Toolbox
Pathme
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17
Harmonizing pathway databases using Biological Expression Language (BEL)
Doctoral Thesis
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17
Generation and Applications of Knowledge Graphs in Systems and Networks Biology
Delayssatoolkit.jl
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15
DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays
Pesto
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15
PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
Geckopy
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14
Enzyme-constrained genome-scale models in python
Chise.js
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14
A web application to visualize and edit the pathway models represented by SBGN Process Description Notation
Libpetab Python
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14
Python package for working with PEtab files
Escherconverter
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14
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
Pasmopy
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14
Patient-Specific Modeling in Python
Spatial Model Editor
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14
Spatial bio-chemical reaction model editor and simulator
Kroneckerbio
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13
KroneckerBio modelling toolbox for systems biology
Biosimulators
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13
Registry of containerized biosimulation tools that support a standard command-line interface
Biojupies Plugins
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13
User-submitted RNA-seq data analysis tools for BioJupies.
Cbmpy
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13
CBMPy is a Python based platform for constraint based modelling and analysis.
Likelihoodprofiler.jl
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12
LikelihoodProfiler is a Julia package for practical identifiability analysis and confidence intervals evaluation.
Datanator
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11
Toolkit for discovering and aggregating data for whole-cell modeling
Indra_db
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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.
Isb_course_2023
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10
Materials and presentation for the 2023 ISB Microbiome course.
Randomwalkrestartmh
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10
A package to perform Random Walk with Restart on different types of networks
Autopacmen
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10
Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
Emmaa
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10
Ecosystem of Machine-maintained Models with Automated Analysis
Pathway Forte
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10
A Python package for benchmarking pathway database with functional enrichment and classification methods
Libsbmlsim
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9
LibSBMLSim: A library for simulating SBML models
Pandora Backend
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9
Back-end interface for PANDORA https://github.com/genular/pandora
Sbtabeditor
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9
Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
Kisao
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9
Ontology of algorithms for analyzing biological models, their parameters, and their outputs
Py4lifesci
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9
Code repository for the book "Python for the Life Sciences" by Lancaster & Webster
Kegg
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9
A Bio2BEL package for integrating pathway-related information from KEGG in BEL
Intro_to_wc_modeling
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9
Whole-cell modeling tutorials
Sparced
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8
SPARCED model creation and simulation package.
Galibrate
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8
Parameter estimation and model calibration using Genetic Algorithm optimization in Python.
Heta Compiler
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8
Software tool for the compilation of Heta-based QSP modeling platform
Pydyno
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8
Tool that uses tropical algebra concepts to 'decompose' species trajectories in the protein-protein interactions that drive changes of concentration in time
Sbml Org Website
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8
The source code and issue tracker for the SBML.org website.
Julia Theosysbio
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8
Pycotools
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7
A Python Toolbox for COPASI
Wc_lang
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7
Language for describing whole-cell models as reaction networks
Moccasin
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7
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
Advancesyntoolkit
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7
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
Intro_to_param_estim
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7
Parameter estimation of ODE models describing biological processes
Xitosbml
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7
XitoSBML - the spatial SBML plugin for ImageJ
Sbmlme
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7
Encoding ME models in SBML
River
⭐
7
R package for RIVER (RNA-Informed Variant Effect on Regulation)
1-100 of 131 search results
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