CISBIO Software Resources

A wide range of bioinformatics software and databases is available from the . 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

  • BSS Software Resources

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 .

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

pySoloa 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.

ethoscopeThe 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.

rethomicsR package to study data from high-throughput animal behaviour monitoring