help-wanted
An issue that should be easy to implement for anyone in the community.
good first issue
This should be a good issue to start contributing to COBRApy.
#
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 128 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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Updated
May 21, 2022 - Python
memote – the genome-scale metabolic model test suite
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Updated
Feb 10, 2022 - HTML
Open
Lint petab models
FFroehlich
commented
Mar 1, 2022
CLI already lints, but programmatic interface doesn't lint by default. Model linting should definitely be performed when import fails to avoid having to reimplement validation checks in amici and provide helpful error messages.
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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Updated
Sep 9, 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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Updated
May 24, 2022
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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Updated
May 16, 2022 - Java
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
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Updated
Oct 31, 2021 - 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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Updated
May 10, 2022 - Jupyter Notebook
The official PySCeS project source code repository.
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Updated
May 29, 2022 - Python
Julia interface to the Systems Biology Markup Language (SBML) library
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May 28, 2022 - Julia
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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Updated
May 26, 2022 - 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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Updated
May 18, 2022 - Java
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
simulation
biology
modeling
biological-simulations
standards
vega
reproducibility
biosimulation
sbml
sed-ml
biochemical-networks
biosimulations
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Updated
May 30, 2022 - TypeScript
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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Updated
Jan 5, 2022 - HTML
2
JanHasenauer
commented
Mar 19, 2020
https://jvi.asm.org/content/84/13/6687.long
SBML: https://www.ebi.ac.uk/biomodels/BIOMD0000000546
Estimate of complexity: low
sthiele
opened
Jan 29, 2021
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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Updated
May 30, 2022 - C++
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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Updated
Feb 8, 2022 - Java
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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Updated
Apr 19, 2022 - C++
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
systems-biology
ode
differential-equations
chemical-reaction-networks
sbml
gillespie-algorithm
quantitative-systems-pharmacology
sciml
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Updated
May 30, 2022 - Julia
cy3sbml: SBML for Cytoscape 3
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Updated
Feb 1, 2022 - Java
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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Updated
Aug 10, 2021 - Java
Registry of containerized biosimulation tools that support a standard command-line interface
docker
simulation
systems-biology
computational-biology
reuse
reproducibility
combine
sbml
mathematical-model
sbo
sed-ml
omex
kinetic-model
kisao
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Updated
May 15, 2022 - Python
LibSBMLSim: A library for simulating SBML models
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Updated
Sep 14, 2021 - C
Problem description
When going through an I/O cycle with a model that has subsystems stored as groups, the members of each group in the sbml file get scrambled on each cycle, as those members are stored in
set()structures, which are unordered. This significantly hinders cobrapy to be used for updating a model that has groups and is stored in a Github repository, as hundreds of lines in