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🍃 SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.
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README.md

Build Status License: GPL v3 MMTF support DOI

SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.

Many aspects of the API are under development. API changes are frequent, never the less we try to keep them minimal.

Quick start

SiNGA is deployed to the Maven Central Repository. Simply add the desired modules to your pom.xml:

<dependencies>
    <dependency>
        <groupId>bio.singa</groupId>
        <artifactId>singa-[module]</artifactId>
        <version>0.5.0</version>
    </dependency>
    <!-- more dependencies -->
</dependencies>

Documentation

The full JavaDocs are available at singa-bio.github.io/singa-doc.

Requirements

Make sure you have the following tools and libraries installed:

  • Java 8 or later

For p-value calculation for Fit3D:

  • R installation 3.4.x or later
  • local package installation privileges or the sfsmisc package pre-installed

Contributors

Projects using SiNGA

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