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SBML
SBML (the Systems Biology Markup Language) is an XML-based format for communicating and storing representations of biological processes. Its aim is to be a lingua franca for representing models in biology. SBML is suitable for models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.
Here are 122 public repositories matching this topic...
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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Jun 25, 2021 - Python
memote – the genome-scale metabolic model test suite
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Jun 12, 2021 - HTML
paulstapor
commented
Jul 16, 2020
Currently, values for the llh, gradient, the computed trajectories of states and observables, or the sensitivities are checked in unit tests.
Unfortunately, some bugs, such as incorrect Jacobians or switched minus signs in the Newton solver, will not necessarily affect those quantities. However, they will substantially impact solver performance, by causing way too many steps to be taken. Hence, w
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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Jun 23, 2021 - JavaScript
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
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
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
Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
visualization
systems-biology
networkx
pysb
network-visualization
jupyter-widget
cytoscapejs
sbml
sbgn
tellurium
bionetgen
jupyterlab-extension
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Jun 25, 2021 - Jupyter Notebook
The official PySCeS project source code repository.
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Feb 25, 2021 - Python
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.
testing
simulation
systems-biology
test-automation
ode
stochastic
testing-tools
sbml
testing-framework
sbml-models
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Feb 24, 2021 - JavaScript
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
systems-biology
model-checking
knowledge-representation
sbml
bigg-models-knowledgebase
model-annotation
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Nov 18, 2020 - Java
3
JanHasenauer
commented
Mar 23, 2020
https://journals.plos.org/ploscompbiol/article?rev=1&id=10.1371/journal.pcbi.1006944
Complexity estimate: medium
The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
java
api
library
simulation
solver
linear-programming
simulations
ordinary-differential-equations
numerical-simulations
ode-solver
steady-state
sbml
flux-balance-analysis
time-series-analysis
constraint-based-modeling
fba
sbml-model
systems-biology-simulation
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May 2, 2021 - HTML
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
optimization
systems-biology
ode
high-performance-computing
parameter-estimation
hacktoberfest
dynamical-modeling
sbml
petab
amici
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Jun 24, 2021 - C++
Julia interface to the Systems Biology Markup Language (SBML) library
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Jun 27, 2021 - Julia
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
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Oct 13, 2020 - Java
AntonJuliusRabe
commented
Jun 22, 2018
methods handling menu bar actions are defined in MenuController and ready to be connected to basic methods like open, save and validate. Just for us to have something we can show It set handleOpen to call open from the imported controller package for now.
LibSBMLSim: A library for simulating SBML models
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Jun 21, 2021 - C
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.
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Jun 22, 2021 - C++
cy3sbml: SBML for Cytoscape 3
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Jun 4, 2021 - Java
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
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Dec 7, 2019 - Python
A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.
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May 17, 2018 - Java
Python package for building SBML models without needing to use libSBML.
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Jun 3, 2021 - Python
The environment variables in the
scripts/deploy_website.shscript assume a Travis environment and will need to be adjusted.