NemoLib-Java-V2

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Description

The nemolib library includes tools specifically designed for executing the NemoProfile algorithm. Classes have also been designed with parallelization in mind.

Installation and Use in Linux

**Prerequisites

• A Linux operating environment.
• JDK version 8 or higher
• Maven version 3.0 or higher Use the mvn package command from the root directory to generate a jar file in the target subdirectory containing the nemolib library. Any classes which implement nemolib should use the statement import edu.uwb.nemolib;.

git clone https://github.com/Kimw6/NemoLib-Java-V2/

cd NemoLib-Java-V2/nemolib-master

mvn package

Installation and Use in Windows

• Prerequisites: Netbeans IDE and jdk 8.x version (jdk 9.x not work)

• Download and install Cygwin (follow the link to learn how to install gcc and g++) http://preshing.com/20141108/how-to-install-the-latest-gcc-on-windows/

• Systems->advanced->Environment Variables From the path variable, add C:\Cygwin64\bin (for 64 bit) or (3) C:\cygwin\bin (for 32 bit)

• NemoLib install From https://github.com/Kimw6/NemoLib-Java-V2/ Download NemoLib as zip file. Open the project in the NetBeans, build the library. With default setting, the library is, nemolib-master/target/ nemolib-0.1-SNAPSHOT.jar

Example Program (testing the library)

An example program can be found at https://github.com/Kimw6/NemoLib-Java-V2-Testing

The example java main file can be also found at /src/main/java/edu/uwb/nemolib_examples/network_motif_detector/

Documentation

JavaDocs are auto-generated when Maven creates the project.

Future Project Ideas

• Parallelize random graph analysis (embarassingly parallel).
• Complete parallelization using MPI.
• Implement SubgraphCollect by adding subgraph induction functionality.
• Implement the nauty algorithm in Java and include it as a dependency in nemolib.
• Research other graph/network parallelziation libraries and implement NemoProfile to compare.
• Write unit tests.