ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
doc/img
gradle/wrapper
lib
licenses
resources
scripts
src
test/edu/ucsd/sbrg/bigg
.gitignore
.travis.yml
BuildSBMLFix.xml
LICENSE
Notes for contributors.md
README.md
THIRD-PARTY.txt
assembly.xml
build.gradle
gradlew
gradlew.bat
pom.xml

README.md

ModelPolisher

Annotating Systems Biology Models

Authors: Andreas Dräger, Thomas J. Zajac, Matthias König

Build Status Stable version DOI License (MIT)

ModelPolisher accesses the BiGG Models knowledgebase to annotate and autocomplete SBML models. Thereby, the program mainly relies on BiGG identifiers for model components. Moreover, it fixes some apparent errors in the models.

ModelPolisher is primarily a command-line based tool. You can run it locally using your installation of BiGG Models database (see https://github.com/SBRG/bigg_models). A list of all available command-line options is printed when starting ModelPolisher with the option -?, i.e., by typing java -jar ModelPolisher-VERSION.jar -?, where "VERSION" needs to be replaced with the current release version of the program. If you run into trouble with larger files, especially java.lang.OutOfMemoryError: GC overhead limit exceeded, please use the JVM Xmx flag (e.g., java -Xmx4G -jar ModelPolisher-VERSION.jar ).

How to cite ModelPolisher?

The online version of ModelPolisher is described in this article: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149263

The article "BiGG Models: A platform for integrating, standardizing and sharing genome-scale models" describes BiGG Models knowledge-base including ModelPolisher.

Usage

After cloning or updating this project, make sure to delete bigg.zip and bigg.sqlite within the folder resources. Afterwards run configureSQLiteDB to download and prepare the correct version of BiGG Models database from Dropbox.

Licenses

ModelPolisher is distributed under the MIT License (see LICENSE). An Overview of all dependencies is provided in THIRD-PARTY.txt, their respective licenses can be found in the licenses folder.