Software Projects

Post date: 6-feb-2012 20.52.23

M-Finder

  • GoD: a software tool for ranking genes with respect to diseases. https://sites.google.com/site/geneontologyprioritization/

  • GO-WAR: a software tool for extracting weighted association rules from Gene Ontology Database. https://sites.google.com/site/weightedrules/

  • HPO-Miner: a software tool for extracting weighted association rules from HPO Ontology.

  • M-FINDER is a framework for the analysis of functional association patterns on protein interaction networks. http://bionet.ecs.baylor.edu/mfinder

  • Align-MCL is a framework for local network alignment. https://sites.google.com/site/alignmcl/.

  • Align-Nemo: Is a local network Aligner. http://sourceforge.net/projects/alignnemo/.

  • IMPRECO IMproving PREdiction of PRotEin COmplexes), is a distributed architecture for the prediction of protein complexes https://sites.google.com/site/pietrohiramguzzi/Home/research/

  • myMCL is a web system for prediction of protein complexes based on a web application and the use of markov clustering

  • micro-CS Is a distributed system based on web services architecture for preprocessing and annotation of Affymetrix Microarray Data http://bioingegneria.unicz.it/m-cs.

  • micro-Analyzer Is the evolution of micro-CS for preprocessing and integrated analysis of genomic and expression microarray data http://sourceforge.net/projects/microanalyzer/ (26),

  • DMET-Analyzer Is a software tool for DMET Data Analysis https://sourceforge.net/projects/dmetanalyzer/files/.

  • DMET-MINER: is a software tool for extracting association rules from DMET data. https://sites.google.com/site/dmetminer/

  • coreSNP Is a multithread high performance system for genomic data analysis on cluster.

  • cloud4SNP is a cloud software for SNP data analysis based on DataMining Cloud Framework (35).

  • VeNet Is a software tool for biological network analysis based on vector space embedding.

  • CytoMCL http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=Cytomcl .

  • CytoSevishttps://sites.google.com/site/cytosevis/(61).

    • JProt Align is a cross platform Interface to the TM-Align Software. It provides: Alignment of Protein Structure Visualization of Superimposed structures.

    • Wiki Project Page Download

SNP-Analyzer

A software tool implementing a novel algorithm for extracting knowledge from SNP-DMET data.

https://sourceforge.net/projects/snpanalyzer

(SNP-DMET Data Analyzer), for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i) to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (dbSNP). It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way.

micro-CS

Micro cs is a Tool for Managing Affymetrix Binary Files through the TIGR TM4 Suite.

DNA microarrays are used to measure gene expression levels of genes. After microarray images are scanned and raw expression data are generated, the typical workflow of analysis is structured on six main phases: (i) summarization, (ii) quality control, (iii) normalization, (iv) filtering, (v) statistical analysis, and (vi) biological interpretation. Eg., summarization aims to recognize different genes in raw data, associating to different probes (regions of pixels in images) the unique gene that generated them. Nevertheless, many existing tools, such as the well known TMeV, part of TM4 Suite (www.tm4.org), currently are not able to automatically summarize recent arrays, such as the Affymetrix ones. micro-CS is a tool that automatizes the summarization, normalization and annotation of Affymetrix microarray data, extending the TMeV tool.

Now Micro-CS has been evolved into Micro Analyzer https://sourceforge.net/projects/microanalyzer/JProtAlign