LibSBGN

Software support library for the Systems Biology Graphical Notation (SBGN).

Documentation about LibSBGN and the development process is available from the Wiki
https://github.com/sbgn/sbgn/wiki/LibSBGN
Documentation about SBGN is available from the SBGN homepage
http://sbgn.org

How to cite

Software support for SBGN maps: SBGN-ML and LibSBGN
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.
Bioinformatics, 28(15):2016-2021, 2012 PubMed

Using libsbgn

As of milestone 3, thanks to jitpack.io, it is easy to use libsbgn right away withL

gradle:

Step 1. Add the JitPack repository to your build file

Add it in your root build.gradle at the end of repositories:

allprojects {
    repositories {
        ...
        maven { url 'https://jitpack.io' }
    }
}

Step 2. Add the dependency

dependencies {
        implementation 'com.github.sbgn:libsbgn:Tag'
}

Maven

Step 1. Add the JitPack repository to your build file

<repositories>
    <repository>
        <id>jitpack.io</id>
        <url>https://jitpack.io</url>
    </repository>
</repositories>

Step 2. Add the dependency

<dependency>
    <groupId>com.github.sbgn</groupId>
    <artifactId>libsbgn</artifactId>
    <version>Tag</version>
</dependency> 

sbt

Add it in your build.sbt at the end of resolvers:

resolvers += "jitpack" at "https://jitpack.io"

Step 2. Add the dependency

libraryDependencies += "com.github.sbgn" % "libsbgn" % "Tag"

leiningen

Add it in your project.clj at the end of repositories:

:repositories [["jitpack" "https://jitpack.io"]]

Step 2. Add the dependency

:dependencies [[com.github.sbgn/libsbgn "Tag"]] 

Share this release:

Example code

If you would like to see how to use libsbgn, have a look at some of the examples:

• reading SBGN
• writing SBGN
• writing SBGN with annotation glyph
• reading SBGN render information
• writing SBGN render information

How to build

To build the java version of LibSBGN, you need to have installed:

• Git download
• Java JDK download
• Ant download

Building with Maven

First clone the repository via

git clone https://github.com/sbgn/libsbgn.git
cd libsbgn

then compile using mvn install.

Building with Ant

Add Git, Java JDK, and Ant to your path

First clone the repository via

git clone https://github.com/sbgn/libsbgn.git
cd libsbgn

Get the latest stable release otherwise you will work with the unstable development version

git fetch
git checkout milestone-2

Than build the library with ant from the source directory

ant -f ant-build-script.xml

This will result in the creation of /dist/org.sbgn.jar which you can include in your project.

To build the documentation in /docs/ use

ant -f ant-build-script.xml doc

To run the tests use

ant -f ant-build-script.xml test

Files

Here is an explanation of the directories in this project:

cpp_binding    - C++ version of LibSBGN  
example-files  - some example SBGN-ML files, larger and more complete than the test-cases  
licenses       - license information  
org.sbgn       - LibSBGN source code (Java version)  
resources      - general resources, including XML Schema (SBGN.xsd)  
specifications - Auto-generated documentation for the XML Schema  
test-files     - SBGN-ML test cases and reference images  
tools          - 
validation     - schematron validation rules, test-cases and resources  

Authors

Alice Villeger
Augustin Luna
Frank Bergmann
Martijn van Iersel
Sarah Boyd
Tobias Czauderna
Stuart Moodie
Matthias König

Contact

Contact our mailinglist:
sbgn-libsbgn@lists.sourceforge.net

Our official website:
https://github.com/sbgn/libsbgn