sys-bio Goto Github PK

amas

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

antimony

antimonyeditor

Antimony Web Editor: A Web Editor for the Antimony Modeling Language

archive_roadrunner

This archives all the orphan branches on roadrunner

artificial_random_signaling_network

biomodelscache

A biomodels cache for faster lookup.

biomodelsstore

biopredynbench

Benchmark problems in dynamical modeling (Villaverde et a. 2015)

brsindy

Generalized Bayesian Reactive Sindy Algorithm

bzip2

CMake support for bzip2

cesium

check-subproject

A unit testing framework for C

codeforpublishedpapers

Contains folder that include code published with papers

complexsystems

Analysis of dynamical characteristics of reaction networks.

crbm-reproducibility-report

Python script to generate a CRBM report from a LaTeX template using Jinja2

demo

The official demo for libsbmljs

deps-for-travis

Debian builds for Travis

developing-a-workflow-for-creating-omex-files

egfr

egfr_reference_models

evolution

Tool used to create oscillatory networks. Generates reaction network models in Antimony, which can be easily converted to SBML (SBML.org) for further analysis. This is the main repository for Evolution, superseding the original one at https://github.com/ltatka/evolution.

evosimannealing

frequency_response_paper

Paper on frequency response

frequencyresponse

Computes frequency response for a SBML model

grn_generate_run

Analyzing and recreating DREAM 7: Network Topology and Parameter Inference Challenge

iconv

interactivemodels

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

iridiumsimulator

Interactive desktop simulator for systems biology

libantimonyjs

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

libomexmeta

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