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
- Microarray Data Analysis Tools
- Data Management Software
- Commercial Imaging Software bought with CISBIC funding
- Commercial Data Analysis Software supported by the Bioinformatics Data Science Group
- Genome Visualisation
- Theoretical Systems Biology Tools
- Phylogenetric software
- Ethomics and sleep
- MMBGX - a tool to predict alternative splicing from Exon array data more accurately (publication)
- BSS Software Resources
Commercial Imaging Software bought with CISBIC funding (contact film-service@imperial.ac.uk)
- SimplePCI / HCImage (Hamamatsu) for image acquisition and analysis
- Autoquant (Mediacybernetics) for deconvolution
- Definiens XD (Definiens) for advanced image analysis
Commercial Data Analysis Software supported by the .
Genome Visualisation (contact Derek Huntley)
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)
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