Topic: systems-biology Goto Github
Some thing interesting about systems-biology
Some thing interesting about systems-biology
systems-biology,Code repository for the book "Python for the Life Sciences" by Lancaster & Webster
Organization: amberbiology
Home Page: http://pythonforthelifesciences.com/
systems-biology,Fast stochastic simulator for chemical reaction networks
User: armavica
Home Page: https://armavica.github.io/rebop/
systems-biology,Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
User: augustinas1
Home Page: https://augustinas1.github.io/MomentClosure.jl/dev/
systems-biology,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
Organization: benchmarking-initiative
systems-biology,Multi-dimensional, trans-omics metabolic maps.
Organization: biosustain
Home Page: https://biosustain.github.io/shu
systems-biology,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!
Organization: cnapy-org
Home Page: https://cnapy-org.github.io/CNApy-guide/
systems-biology,COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Organization: copasi
Home Page: https://copasi.org
systems-biology,An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app
Organization: cri-iatlas
Home Page: https://www.cri-iatlas.org
systems-biology,📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
User: cthoyt
Home Page: https://github.com/cthoyt/doctoral-thesis/raw/master/main.pdf
systems-biology,Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
User: darrenjw
Home Page: https://darrenjw.github.io/work/smfsb/3e/
systems-biology,a modeling environment tailored to parameter estimation in dynamical systems
Organization: data2dynamics
Home Page: https://github.com/Data2Dynamics/d2d
systems-biology,A Python package for drug discovery by analyzing causal paths on multiscale networks
Organization: drug2ways
Home Page: https://drug2ways.readthedocs.io/en/latest/
systems-biology,An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
Organization: ecell
Home Page: https://ecell4.e-cell.org/
systems-biology,General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
User: florianhartig
Home Page: https://cran.r-project.org/web/packages/BayesianTools/index.html
systems-biology,:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
systems-biology,PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
Organization: genular
Home Page: https://atomic-lab.org
systems-biology,A python library for metabolic networks sampling and analysis
Organization: geomscale
systems-biology,PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
Organization: icb-dcm
Home Page: https://doi.org/10.1093/bioinformatics/btx676
systems-biology,python Parameter EStimation TOolbox
Organization: icb-dcm
Home Page: https://pypesto.readthedocs.io
systems-biology,A web application to visualize and edit pathway models
Organization: ivis-at-bilkent
Home Page: http://newteditor.org
systems-biology,PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Organization: ivis-at-bilkent
Home Page: https://www.pathwaymapper.org/
systems-biology,A web based visualization tool for process description maps in SBGN
Organization: ivis-at-bilkent
Home Page: http://www.cs.bilkent.edu.tr/~ivis/SBGNViz_sample_app/
systems-biology,Picotti lab data analysis package.
User: jpquast
Home Page: https://jpquast.github.io/protti/
systems-biology,StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Organization: klamt-lab
systems-biology,Julia interface to the Systems Biology Markup Language (SBML) library
Organization: lcsb-biocore
Home Page: https://lcsb-biocore.github.io/SBML.jl/stable
systems-biology,Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
Organization: lolab-msm
systems-biology,Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Organization: maayanlab
Home Page: http://biojupies.cloud
systems-biology,Python package to study microbial communities using metabolic modeling.
Organization: micom-dev
Home Page: https://micom-dev.github.io/micom
systems-biology,Workshop in omics integration and systems biology
Organization: nbisweden
Home Page: https://uppsala.instructure.com/courses/52162
systems-biology,COBRApy is a package for constraint-based modeling of metabolic networks.
Organization: opencobra
Home Page: http://opencobra.github.io/cobrapy/
systems-biology,PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Organization: petab-dev
Home Page: https://petab.readthedocs.io
systems-biology,🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
Organization: pybel
Home Page: http://pybel.readthedocs.io
systems-biology,Python framework for Systems Biology modeling
Organization: pysb
systems-biology,Curated (meta)list of resources for Biology.
User: raivivek
systems-biology,MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Organization: saeyslab
systems-biology,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.
Organization: sbmlteam
Home Page: https://sbml.org/software/jsbml/
systems-biology,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.
Organization: sbmlteam
Home Page: https://sbml.org/software/libsbml
systems-biology,A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Organization: sbrg
systems-biology,A Python framework for structural systems biology
Organization: sbrg
Home Page: http://ssbio.readthedocs.io/en/latest/
systems-biology,Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Organization: sciml
Home Page: https://docs.sciml.ai/Catalyst/stable/
systems-biology,CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
Organization: sciml
Home Page: https://docs.sciml.ai/CellMLToolkit/stable/
systems-biology,SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Organization: sciml
Home Page: https://docs.sciml.ai/SBMLToolkit/stable/
systems-biology,For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
Organization: seek4science
Home Page: http://www.seek4science.org
systems-biology,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.
Organization: sorgerlab
Home Page: http://indra.bio
systems-biology,A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions
User: stasaki
Home Page: https://stasaki.github.io/DEcode/
systems-biology,Toolbox for including enzyme constraints on a genome-scale model.
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/GECKO/
systems-biology,HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
Organization: sysbiochalmers
systems-biology,The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/RAVEN/
systems-biology,The consensus GEM for Saccharomyces cerevisiae
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/yeast-GEM/
systems-biology,StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
Organization: systemsbioinformatics
Home Page: http://stochpy.sourceforge.net/
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