singa-all

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

License	GNU GPL v3
GroupId	de.bioforscher.singa
ArtifactId	singa-all
Last Version	0.3.3
Release Date	May 2, 2018
Type	pom
Description	singa-all SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.
Project URL	https://github.com/cleberecht/singa
Source Code Management	https://github.com/cleberecht/singa

Download singa-all

Filename	Size
singa-all-0.3.3.pom	7 KB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/de.bioforscher.singa/singa-all/ -->
<dependency>
    <groupId>de.bioforscher.singa</groupId>
    <artifactId>singa-all</artifactId>
    <version>0.3.3</version>
    <type>pom</type>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/de.bioforscher.singa/singa-all/
implementation 'de.bioforscher.singa:singa-all:0.3.3'

Gradle Kotlin

// https://jarcasting.com/artifacts/de.bioforscher.singa/singa-all/
implementation ("de.bioforscher.singa:singa-all:0.3.3")

Apache Buildr

'de.bioforscher.singa:singa-all:pom:0.3.3'

Apache Ivy

<dependency org="de.bioforscher.singa" name="singa-all" rev="0.3.3">
  <artifact name="singa-all" type="pom" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='de.bioforscher.singa', module='singa-all', version='0.3.3')
)

Scala SBT

libraryDependencies += "de.bioforscher.singa" % "singa-all" % "0.3.3"

Leiningen

[de.bioforscher.singa/singa-all "0.3.3"]

Dependencies

compile (1)

Group / Artifact	Type	Version
org.slf4j : slf4j-api	jar	1.7.21

test (2)

Group / Artifact	Type	Version
junit : junit	jar	4.12
org.slf4j : slf4j-log4j12	jar	1.7.21

Project Modules

• ../singa-core
• ../singa-mathematics
• ../singa-features
• ../singa-chemistry
• ../singa-javafx
• ../singa-simulation
• ../singa-structure
• ../singa-sequence

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>0.7.0</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

• Christoph Leberecht | christoph.leberecht(at)hs-mittweida.de | https://github.com/cleberecht
• Florian Kaiser | contact(at)fkaiser.bio | https://github.com/fkaiserbio

Projects using SiNGA

• Fit3D - template-based detection of small structural motifs | https://github.com/fkaiserbio/fit3d
• MMM - template-free detection of substructure conservation | https://github.com/fkaiserbio/mmm
• PNAtor - generation of PNA aptamer structures | https://github.com/eisold/PNAtor

Versions

Version
0.3.3 May 2, 2018
0.3.2 Mar 15, 2018
0.3.1 Dec 21, 2017
0.2.3 Oct 25, 2017
0.2.2 Sep 12, 2017
0.2.1 Aug 2, 2017
0.2.0 Jul 18, 2017
0.1.3 Jun 30, 2017