CyVerse UK aims to provide scientific HPC services in an easy to use manner for all scientists. It is an extension of the US CyVerse project. For more details see the ‘About’ page. As we are currently in our development phase, most of the CyVerse UK apps are available within the Discovery Environment, but not all may actually run on CyVerse UK hardware. You shouldn’t need to worry about this, but it’s helpful to know that we will be making the two systems work more closely together in the future. Below you can find links to all apps described here in their respective environments.
You can also search for applications within the CyVerse Discovery Environment by using the “uk cyverse” keyword in the application search box:
Earlham Institute Apps
All EI apps are available within the DE, and run on CyVerse UK hardware.
Apps & the Testing Discovery Environment at Warwick
A full list of applications developed by the Warwick team is given in the table:
|Application Information||Description||Run on CyVerse *|
|APPLES||A set of tools to analyse promoter sequences on a genome-wide scale||DE|
|Wellington Bootstrap||An algorithm for the identification of regions occupied by proteins in DNase-seq data, performing a differential analysis between two samples||DE|
|Wellington Footprint||An algorithm for the identification of regions occupied by proteins in DNase-seq data||DE|
|GP2S||A differential expression algorithm for time series data with a two condition (eg. control/treated) experimental design||DE|
|Gradient Tool||An algorithm for the identification of the time of change from single condition time course expression data||DE|
|CSI||A network inference algorithm capable of inferring causal regulatory network models from time course expression data||DE|
|hCSI||An expansion of CSI network inference to handle multiple time course datasets||DE|
|oCSI||An expansion of CSI network inference to handle data from multiple organisms||DE|
|Clustering / Biclustering|
|BHC||A clustering algorithm for expression data originally made available in R, allows for the analysis of both time course or multiple static datasets||DE|
|TCAP||A clustering algorithm for time course expression data, identifies complex regulatory groups thanks to a rich information measure||DE|
|Wigwams||An algorithm for the extraction of gene groups co-regulated across subsets of multiple time course datasets||DE|
|Transcription Factor Motif Enrichment|
|HMT||A transcription factor binding site overrepresentation analysis algorithm for known motifs||DE|
|MEME-LaB||A transcription factor binding site overrepresentation analysis algorithm with novel motif discovery||DE|
* – A CyVerse account is required. Register here if necessary.
These applications are also accessible through the Warwick testing Discovery Environment. Please note this is not the same as the CyVerse DE, and is only for testing applications.
CIPRES Phylogeny Apps
CIPRES apps are supported by CyVerse UK to benefit UK users. Please see here for in depth documentation: CIPRES Phylogenetic Collection (BEAST2, MrBayes, RAxML). Please note that we are in the process of getting these apps published, so some are not currently available.
|Application Information||Description||Run on CyVerse UK *|
|MrBayes||Bayesian analysis of molecular sequences using MCMC||DE|
|BEAST||Bayesian analysis of molecular sequences using MCMC||Not available yet|
|BEAST2||Bayesian analysis of molecular sequences using MCMC||DE|
|RAxML||Bayesian analysis of molecular sequences using MCMC||DE|