msneddon / nfsim
A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
☆17Updated 9 months ago
Alternatives and similar repositories for nfsim:
Users that are interested in nfsim are comparing it to the libraries listed below
- Rule-based modeling framework☆61Updated 5 months ago
- Dynamic Flux Balance analysis in Python☆11Updated 9 years ago
- A general-purpose, stochastic, biochemical reaction simulator for large reaction networks☆14Updated 9 months ago
- Encoding Dynamic Flux Balance Analysis in SBML☆11Updated 4 years ago
- An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuris…☆24Updated last year
- Symbolic Kinetic Models with Python☆31Updated last week
- ☆22Updated 2 years ago
- Gillespie Stochastic Simulation Algorithm☆14Updated 11 years ago
- An extension to the MDAnalysis library providing support for dealing with structural ensembles. There is currently support for calculatin…☆14Updated 6 years ago
- libRoadRunner: A high-performance SBML simulator☆45Updated last week
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆27Updated last year
- A primer on statistical mechanics for biochemists☆46Updated 2 years ago
- CHAP is a tool for the functional annotation of ion channel structures:☆21Updated last year
- The Integrative Modeling Platform☆76Updated this week
- MCell Monte Carlo Simulator of Cellular Microphysiology☆35Updated 2 weeks ago
- Release of the whole cell E. coli model.☆64Updated 3 months ago
- StochKit is an extensible tool for stochastic simulation tool with stochastic and multiscale algorithms.☆16Updated 4 years ago
- Software tool for metabolic modelling in Systems Biology☆10Updated 4 years ago
- Code used in the manuscript for De Novo Design of Bioactive Protein Switches☆16Updated 5 years ago
- Printing text using protein structures☆13Updated 3 years ago
- localCIDER - sequence analysis tool for disordered protein sequences☆23Updated last year
- Introduction to Biophysics, requires one semester of calculus-based Physics.☆26Updated last year
- Benchmarking common tasks on proteins in various languages and packages☆41Updated 4 years ago
- Container-based installation of pymol, with interaction through the browser via Jupyter notebook☆19Updated 5 years ago
- Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module☆22Updated 3 years ago
- Open Source Protein REdesign for You v3☆50Updated 3 months ago
- Learning Kinetic Models from Time Series Proteomics and Metabolomics Data☆28Updated 2 years ago
- LASSI - Lattice Simulation Engine For Stickers And Spacer Interactions☆16Updated 2 months ago
- A modular compiler for biological chemical reaction networks☆43Updated 2 weeks ago
- To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.☆23Updated last week