Explore @sys-bio Open Source projects

UW Sauro Lab (@sys-bio)

sys-bio

Stars
248
Global Org. Rank 35,899 (Top 12 %)
Registered almost 11 years ago
Most used languages

Python
30.3 %

Jupyter Notebook
21.2 %

C++
15.2 %

Component Pascal 9.1 %

JavaScript
9.1 %

Pascal 6.1 %

C
6.1 %

CMake 3.0 %
Location 🇺🇸 United States
Country Total Rank 26,057
Country Ranking

Component Pascal 10

Pascal 190

CMake 538

Jupyter Notebook
6,420

C++
6,501

Python
7,182

C
8,743

tellurium

Python Environment for Modeling and Simulating Biological Systems

antimony

simplesbml

Python package for building SBML models without needing to use libSBML.

libOmexMeta

libOmexMeta is a library aimed at providing developer-level support for reading, writing, editing and managing semantic annotations for biosimulation models.

AMAS

AMAS (Automatic Model Annotation System): (currently) predicting annotations of species and reactions of models in SBML format.

Jupyter Notebook

SBbadger

teUtils

Tellurium Utilities

libroadrunner-deps

Dependencies for libroadrunner

sidewinder

A client side web application for building and simulating of biological reactions based on SBML.

libsbml-draw

Reads in an SBML file, and displays the network by generating a layout or using an existing layout. The SBML layout info can be saved to a new file.

IridiumSimulator

Interactive desktop simulator for systems biology

libSBMLVisual

libSBNW is a network viewer which supports autolayout of reaction networks and uses libSBML for reading/writing models.

ModelingTutorial

MPA 2023 Reproducibility + Tellurium Workshop

Jupyter Notebook

rrplugins

Plugins for Telluirum

reproducible-biomodel-case-study

Reproducible case studies from BioModels

Jupyter Notebook

temp-biomodels

Temporary place for coordination of updating existing Biomodels

Component Pascal

phrasedml

Git mirror of https://sourceforge.net/projects/phrasedml/

network-modeling-summer-school-2021

Jupyter Notebook

ReproduciblePaper

Component Pascal

libxml2

rr-libstruct

sedml2py

SedML to Python converter

SBviper

Unit tests for models in systems biology

Jupyter Notebook

SBstoat

Parameter optimization using Tellurium

Jupyter Notebook

SRES

Component Pascal

tellurium-notebooks

Notebook Examples for Tellurium

Jupyter Notebook

InteractiveModels

Models and simulator for Interactive modeling site: https://sites.google.com/view/interactive-modeling/home

BRSindy

Generalized Bayesian Reactive Sindy Algorithm

pySBML2Matlab

makesbml

Simple site to convert antimony to sbml

frequencyResponse

Computes frequency response for a SBML model

libantimonyjs

JavaScript version of the antimony library to support human-readable, human-writable modular model definition language.

vscode-antimony

Extensions for Antimony development in Visual Studio Code.