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psmbionet

Parallel SMBioNet (PSMBioNet)

1.    Introduction

2.    Multicore version for Windows

3.    Multicore version for Linux

4.    Cluster based version for Linux

5.    Credits

6.    Acknowledgements

7.    Contact

 

1     Introduction

Parallel SMBioNet (PSMBioNet) is a parallel implementation for parameter estimation of Biological Regulatory Networks (BRNs). It uses the existing implementation of SMBioNet (Selection of models for Biological Networks).  For parallelization, PSMBioNet uses java based library MPJExpress.
PSMBioNet is available for Windows and Linux for multicore and Cluster based Platforms. The multicore version can used computational capabilities of modern desktop and laptop processors to reduce processing time required for parameter estimation of large biological networks. The cluster based version can be installed on specialized Cluster computers or Supercomputers.

2    Multicore version for Windows

Pre-requisites

PSMBioNet has been tested with Microsoft Windows 7
Download and Install Java Runtime Environment (JRE)
Download and Install MPJ Express 0.44. For detailed instructions to install MPJ Express, please read User Guide for Windows.

Download

How to Run

Create input file containing genes, proteins and their interactions. Download SMBioNet user guide to create an input file
Execute the following command to launch PSMBioNet
mpjrun.bat -np 2 PSMBIONET input_file
This command will launch PSMBioNet with 2 threads to process the input_file. The logical parameter space is explored exhaustively by multiple threads and finally, the results are stored in input_file.out.
 

3    PSMBioNet – Multicore version for Linux

Pre-requisites

Make sure Java is installed and available in the path
Download and Install MPJ Express 0.44. For detailed instructions to install MPJ Express, please read User Guide for Linux

Download

How to Run

Create input file containing genes, proteins and their interactions. Download SMBioNet user guide to create an input file.
Execute the following command to launch PSMBioNet
mpjrun.sh -np 2 PSMBIONET input_file
 

4    PSMBioNet – Cluster based version for Linux

 

5     Credits

PSMBioNet has been developed by Tariq Saeed under the supervision of Dr. Jamil Ahmad

6    Acknowledgements

We acknowledge the support from Dr. Adrien Richard for providing source codes of SMBioNet.

7     Contact

For any question, comment or suggestion, please write to: tariq [at] rcms.nust.edu.pk and dr.ahmad.jamil [at] gmail.com