#
systems-biology
Here are 346 public repositories matching this topic...
Curated (meta)list of resources for Biology.
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Jun 1, 2021
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software
biology
dsl
systems-biology
ode
reaction-network
differential-equations
sde
chemical-reactions
gillespie-algorithm
systems-biology-simulation
rate-laws
scientific-machine-learning
sciml
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Jul 22, 2021 - Julia
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.
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Jul 23, 2021 - Python
LogIN-
commented
Apr 29, 2020
It would help to have download option to get a list of used packages:
For example:
Download list of ML Packages used in Model Training, with all corresponding citations in CSV Format.
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
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Jun 1, 2021 - HTML
bioinformatics
systems-biology
networks
domain-specific-language
biological-expression-language
pybel
networks-biology
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Jul 7, 2021 - Python
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
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Jul 22, 2021 - R
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
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Jul 22, 2021 - Component Pascal
A Python framework for structural systems biology
structural-biology
protein-structure
systems-biology
cobrapy
constraint-based-modeling
structural-systems-biology
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Dec 7, 2020 - Python
An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
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May 5, 2021 - C++
FFroehlich
commented
Apr 13, 2021
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
systems-biology
metabolic-models
metabolic-reconstruction
constraint-based-modeling
metabolic-engineering
gap-filling
human-metabolism
genome-scale-models
sysbio
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Jul 15, 2021 - MATLAB
The consensus GEM for Saccharomyces cerevisiae
python
biology
matlab
systems-biology
consensus
reconstruction
hacktoberfest
yeast
metabolic-models
genome-scale-models
saccharomyces-cerevisiae
yeast-gem
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Jul 2, 2021 - MATLAB
a modeling environment tailored to parameter estimation in dynamical systems
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Jul 20, 2021 - MATLAB
A web application to visualize and edit pathway models
visualization
editor
bioinformatics
biology
layout
systems-biology
pathways
network-visualization
pathway-analysis
newt
web-based-visualization
sbml
sbgn
sif
pathway-models
celldesigner
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Jul 22, 2021 - JavaScript
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
bioinformatics
systems-biology
tcga
cancer-genomics
pathways
network-visualization
pathway-analysis
cancer-pathways
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Jul 11, 2021 - TypeScript
For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
science
data
synthetic-biology
opendata
systems-biology
semantic-web
isa
publication
fair
datamanagement
biohackcovid20
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Jul 23, 2021 - Ruby
An interactive web portal for exploring immuno-oncology data
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Feb 26, 2021 - R
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
systems-biology
modelling
parameter-estimation
hacktoberfest
data-format
sbml
sbml-model
combine-archive
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May 14, 2021
Python package to study microbial communities using metabolic modeling.
python
flux
community
modeling
systems-biology
biochemistry
microbiome
cobra
microbiota
cobrapy
metabolic-models
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Jul 7, 2021 - Python
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.
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Jun 25, 2021 - Java
A web based visualization tool for process description maps in SBGN
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Jul 16, 2021 - JavaScript
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
python
systems-biology
computational-biology
gene-expression
metabolism
cobra
cobrapy
metabolic-models
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Jan 11, 2019 - Python
StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
python
bioinformatics
systems-biology
console-application
stochastic-simulation-algorithm
kinetic-modeling
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Jul 12, 2021 - Python
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
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Mar 29, 2020 - AMPL
Toolbox for including enzyme constraints on a genome-scale model.
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Jul 2, 2021 - MATLAB
PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
optimization
matlab
systems-biology
parameter-estimation
uncertainty-quantification
profile-likelihood
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Mar 2, 2020 - MATLAB
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
systems-biology
moments
chemical-reaction-networks
stochastic-processes
gene-network
gillespie-algorithm
moment-equations
moment-closure
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Jul 22, 2021 - Julia
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