https://github.com/sbgn/libsbgn
Libraries for the Systems Biology Graphical Notation (SBGN); Java and C++
https://github.com/sbgn/libsbgn
ant java maven sbgn
Last synced: 6 months ago
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Libraries for the Systems Biology Graphical Notation (SBGN); Java and C++
- Host: GitHub
- URL: https://github.com/sbgn/libsbgn
- Owner: sbgn
- License: other
- Created: 2016-06-10T01:54:26.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2024-10-08T13:51:18.000Z (over 1 year ago)
- Last Synced: 2025-08-04T02:04:24.433Z (11 months ago)
- Topics: ant, java, maven, sbgn
- Language: HTML
- Homepage:
- Size: 36.8 MB
- Stars: 16
- Watchers: 12
- Forks: 8
- Open Issues: 20
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.txt
- License: LICENSE.txt
Awesome Lists containing this project
README
# LibSBGN
[](https://jitpack.io/#sbgn/libsbgn)
[](https://github.com/sbgn/libsbgn/actions/workflows/jdk8-maven.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk11-maven.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk16-maven.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk17-maven.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk21-maven.yml)
[](https://github.com/sbgn/libsbgn/actions/workflows/jdk8-ant.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk11-ant.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk16-ant.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk17-ant.yml) [](https://github.com/sbgn/libsbgn/actions/workflows/jdk21-ant.yml)
Software support library for the [Systems Biology Graphical Notation (SBGN)](http://www.sbgn.org).
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](https://www.ncbi.nlm.nih.gov/pubmed/22581176)
## Using libsbgn
As of milestone 3, thanks to [jitpack.io](https://jitpack.io/#sbgn/libsbgn), 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
jitpack.io
https://jitpack.io
Step 2. Add the dependency
com.github.sbgn
libsbgn
Tag
### 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](org.sbgn/examples/org/sbgn/ReadExample.java)
* [writing SBGN](org.sbgn/examples/org/sbgn/WriteExample.java)
* [writing SBGN with annotation glyph](org.sbgn/examples/org/sbgn/WriteExampleAnnotation.java)
* [reading SBGN render information](org.sbgn/examples/org/sbgn/ReadExampleWithRender.java)
* [writing SBGN render information](org.sbgn/examples/org/sbgn/WriteRenderExtensionExample.java)
## How to build
To build the java version of LibSBGN, you need to have installed:
* Git [download](https://git-scm.com/downloads)
* Java JDK [download](http://www.oracle.com/technetwork/java/javase/downloads/index-jsp-138363.html)
* Ant [download](https://ant.apache.org/bindownload.cgi)
### 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