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ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
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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 ).

Caveat

COBRAparser currently does not work with Java 9 due to an incompatibility in its dependency. Please use Java 8.

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.

Build

After cloning or updating this project run configureSQLiteDB to download and prepare the correct version of BiGG Models database from Dropbox.
Afterwards ModelPolisher can be built using Gradle, choosing one of four relevant tasks provided:

  • fatJar: (default, if running Gradle without a specified task): builds ModelPolisher with dependencies and SQLite version of BiGG packaged
  • lightJar: with dependencies, without SQLite DB
  • slimJar: without dependencies, but with SQLite DB included
  • bareJar: without dependencies and SQLite DB

To build the fatJar use

gradle fatJar

which builds the jar in ./target/

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.

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