Software

CISBIO Software Resources

A wide range of bioinformatics software and databases is available from the Bioinformatics Data Science Group. CISBIO has developed various pieces of software to facilitate its research into systems biology and bioinformatics. Some of these items are listed below:

CISBIO Software Resources

Proteomics Tools

  • Phyre2 – Protein structure prediction server 
  • SuSPect – Prediction of variant phenotype   
  • PINALOG Alignment of interactomes
  • CombFunc Protein Function Prediction
  • 3DLigandSite an automated method for the prediction of ligand binding sites
  • 3D Garden Global and Restrained Docking Exploration Nexus

Microarray Data Analysis Tools

  • MMBGX - a tool to predict alternative splicing from Exon array data more accurately (publication)

Data Management Software

Commercial Imaging Software bought with CISBIC funding

Commercial Imaging Software bought with CISBIC funding (contact film-service@imperial.ac.uk)

Commercial Data Analysis Software supported by the Bioinformatics Data Science Group

Commercial Data Analysis Software supported by the Bioinformatics Data Science Group.

Genome Visualisation

Genome Visualisation (contact Derek Huntley)

Theoretical Systems Biology Tools

Phylogenetric software

treespace  (on CRAN): Statistical Exploration of Landscapes of Phylogenetic Trees. Tools for the exploration of distributions of phylogenetic trees.

TransPhylo (with Xavier Didelot, hosted on his github): Reconstruction of transmission trees using genomic data.

treetop (on github): Label and compare topologies of (for now binary) rooted trees.

phybreak (with Don Klinkenburg in Holland, and Xavier Didelot ): Analysis of Outbreaks with Sequence Data. Implementation the outbreak analysis method described by Klinkenberg et al (2016) 

 

Ethomics and sleep

pySolo: a multi-platform software for sleep/activity analysis in Drosophila. pySolo aims at improving sharing – and communication – among researchers in the field ofsleep in invertebrates. Works with TriKinetics software.

ethoscope: The ethoscope platform is a collection of interconnected tools allowing biologists to design experiments, acquire and analyse a large amount of behavioural data. Provides a hardware and software solution.

rethomics: R package to study data from high-throughput animal behaviour monitoring