Dräger Lab

Dräger Lab's repositories

ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

Language:JavaMIT23 14 94

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.

Language:HTMLLGPL-3.022 8 54

KEGGtranslator

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.

Language:JavaLGPL-3.019 6 10

EscherConverter

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Language:JavaMIT15 7 35

pymCADRE

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

Language:Jupyter NotebookGPL-3.013 2 4

refinegems

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).

Language:Jupyter NotebookMIT11 1 94

SBTabEditor

Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.

Language:JavaMIT9 10 42

SBOannotator

SBOannotator: A Python tool for the automated assignment of Systems Biology Onotology terms

Language:PythonGPL-3.08 3 1

insilico

InSilico

Language:JavaMIT7 4 9

SBMLme

Encoding ME models in SBML

Language:JavaMIT7 60

TFpredict

Identification and structural characterization of transcription factors based on supervised machine learning

Language:JavaGPL-3.07 3 6

SPECIMEN

Automated pipeline for strain-specific metabolic modeling based on a high-quality template model.

Language:Jupyter NotebookGPL-3.05 3 19

MassChargeCuration

Python module to automatically curate the mass and charge assignments for metabolites in a metabolic model.

Language:Jupyter Notebook4 2 8

S_aureus_GEMs_Collection

In this resporitory, all modifications made within the publication "Curating and comparing 114 Strain-Specific Genome-Scale Models of Staphylococcus aureus" are documented.

Language:Jupyter Notebook4 3 2

SBMLsimulator

An efficient Java™ solver implementation for SBML

Language:JavaLGPL-3.04 4 2

SBMLsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

Language:HTMLGPL-3.04 6 12

ModelEditingTools

A collection of tools for working with models in SBML format

Language:JavaMIT3 20

SABINE

Prediction of the binding specificity of transcription factors using support vector regression

Language:JavaGPL-3.03 2 3

MPClient

Client library for the MPServer

Language:Python2 20

R-DRUGS

Rationalized Discovery of Robust antiviral targets Using Genome-scale model Systems

Language:Jupyter NotebookMIT2 30

VisSim

Easily usable JavaFx-based inSilico module for dynamic Systems Biology Markup Language (SBML) model simulation visualization. Provides an intuitive Graphical User Interface for dynamic processing based on SBSCL.

Language:JavaMIT2 30

C_striatum_GEMs

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

Language:HTMLMIT1 1 8

C_striatum_wetlab

This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

Language:Jupyter Notebook1 2 8

FERN

FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java.

Language:JavaLGPL-3.01 3 1

SBVC

Systems Biology Visualizer and Converter

Language:JavaLGPL-3.01 30

BOFdat

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

Language:Jupyter NotebookNOASSERTION000

MPServer

Server Implementation for the Model Polisher

Language:Clojure000

pymCADRE-1

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

Language:Jupyter NotebookGPL-3.0000

SBSCL-demo

A demo repository with example code for using the Systems Biology Simulation Core Library (SBSCL).

Language:JavaMIT02 1

Table2Model

A parser for systems biology models published in a table form that produces standardized files, such as SBML.

Language:JavaMIT020