Open Source Unix Shell Bio-Informatics Software

cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

To get access to the code, please check it out with svn as described in the code section.

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. This approach increases the confidence in PTES supporting reads. Reads emanating from template-switching events are often characterised by large indels when aligned to the transcriptome. PTESFinder uses additional filters to exclude reads with ambiguous alignments around PTES exon-exon junctions, further increasing confidence in these supporting reads. PTESFinder identifies more PTES structures than other published methods whilst maintaining high specificity.

PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.

TreeBASE is a database and web front end that stores phylogenetic trees and the data matrices used to generate them. The current iteration comprises a complete rewrite of the schema and web layer, and will include a web services layer.

A general purpose distributed hash table adapted for sequence analysis. This program searches for all maximal, exact unique n-mers from a given set of genomes. Originally, this program's primary use was to design resequencing microarrays.

The WISDOM project is a Grid based production environment used to deploy bio-informatics large scale applications.

This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function.

Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk