Getting Started With Cyverse UK apps

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:
Search for CyVerse UK apps

Earlham Institute Apps

All EI apps are available within the DE, and run on CyVerse UK hardware.


gwasserbanner2
polymarker kallistobanner (copy)
mikado_banner2

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 *
Sequence Alignment
APPLES A set of tools to analyse promoter sequences on a genome-wide scale DE
Footprint Identification
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
Differencial Expression
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
Network Inference
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BHC A clustering algorithm for expression data originally made available in R, allows for the analysis of both time course or multiple static datasets DE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