TSMiner

What is it?

TSMiner is a software program to construct time-specific regulatory networks from time-series expression profiles using two groups of genes:
(1) genes encoding transcription factors (TFs) that are activated or repressed at a specific time;
(2) genes involved in biological pathways showing significant mutual interactions with these TFs.
TSMiner provides a network map with extensive interactive visualization operations to help users explore the time-specific regulatory networks.The core algorithms and interfaces of TSMiner were written in java language.

The release version

TSMiner version v1.0.0 (11/28/2018)

The first release version of TSMiner.

Software requirements

• Java 1.5 or later must be installed. Download link
• 1024 MB Java heap memory minimum.
• Operating systems: Platform independent

Running

• Once Java is installed, to start TSMiner in Microsoft Windows double click on TSMiner.jar.
• Otherwise start TSMiner from a command line while in the drem directory, enter the command: java -mx1024M -jar TSMiner.jar
• The data input and parameter settings are described in TSMiner manual.pdf.
• Download link:

Files

• Source code and Javadoc api for the source code are included in the 'sourcecode' directory.
• License files are included in 'license' directory.
• Gene ontology files and KEGG/Reactome pathway files are included in the 'Gene annotation file' directory.
• Example TF-gene interaction data are included in 'TF-gene file' directory.
• Example time-series expression data sets are included in 'Time-series data' directory.
• Example saved models are included in 'Saved model' directory.

Example

To run a case analysis of mouse liver regeneration (LR) with default settings.

• If in Microsoft Windows double click on the file 'Case_analysis_of_mouseLR.cmd' and press the 'Run' button in the main interface.
• Otherwise from a command line while in the TSMiner directory type the command: java -mx1024M -jar TSMiner.jar -d Case_analysis_of_mouseLR.txt, then press the 'Run' button.

The default parameters are shown in Defaults_for_case_analysis.txt.

Contact

For any questions please contact Dr. Mingfei Han (Email: free1234hm@163.com).

License

• This software product is developed by the National Center for Protein Sciences (Beijing)-Bioinformatics group. The TSMiner software makes use of several existing tools:
• the Dynamic Regulatory Events Miner (DREM) (Mol Syst Biol. 2007;3:74. Epub 2007 Jan 16.) which is distributed GPL v3.0 license
• the Piccolo toolkit (www.cs.umd.edu/hcil/piccolo) which is distributed under a BSD license
• the Batik software (http://xmlgraphics.apache.org/batik/) which is distributed under an Apache license
• Please review and agree to the DREM, Piccolo, and Batik licenses before using the TSMiner software. The detailed licenses are described in the license folder.