Taverna Workbench allows users to construct complex analysis workflows from components located on both remote and local machines, run these workflows on their own data and visualize the results. To support this core functionality it also allows various operations on the components themselves such as discovery and description and the selection of personalized libraries of components previously discovered to be useful to a particular application.

IWWE&M is the Interactive Web Workflow Enactor & Manager, which is currently able to manage and enact (aka run, execute or launch) standard Taverna 1 workflows.

IWWE&M has been developed in a modular bottom-up way, so upper-layers should only depend on information from lower ones. This would enable, for instance, to add new workflow and enaction paradigms, or create alternate graphical interfaces.

Workflow download Input example download Outputs hmms Services runHMMBuild: Constructs a Hidden Markov Model from a multiple sequence alignment. getEnsemblIDsFromUniprot: Returns Ensembl cross references from an uniprot entry. getHomologiesFromEnsembl: Retrieves homologies from ENSEMBL. getSequencesFromENSEMBLHomology: Retrieves all sequence of an ENSEMBL homology. runClustalwFast: ClustalW multiple sequence alignments (fast method). Description This workflow creates HMM profiles from a group of ortologous sequences. Retrieve the ENSEMBL ids for the input sequence id. Search ENSEMBL homologs. Search ENSEMBL homologs. Multiple align the previous sequences. Build the HMM profile from the previous alingment. Approximate time 20 minutes aprox. Program This workflow works in Taverna 2.2.

Workflow download Input example download Outputs geneWise report (GFF format) Services loadPersistentFile: Loads a persistent object and returns its reference fromFastaToCommentedNASequence: Converts a sequence in Fasta format into a CommentedNASequence object. runNCBIFormatdb: Formats a database into NCBI BLAST format. runNCBIBlastp: Compares a protein sequence against a protein database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). parseBlastIDs: Parsers the identifiers of Blast report hits. getAminoAcidSequence: Retrieves an aminoacid sequence from an aminoacid database fromGenericSequenceCollectionToFasta: Converts a GenericSequence object into a multifasta object. runNCBIBlastAgainstDBFromFASTA: Compares a protein or dna sequence against a protein or dna database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST). runBlast2gene: Analysis of genomic regions containing completely or partially duplicated genes: it processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment from a BLAST report. overlappingFromBL2G: Filters Blast2gene report runGenewise: Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors Description This workflow helps to gene detection from genomic DNA sequence based on sequence comparison. Creation of a family of homologous proteins to the query protein by using BlastP. Converting the genomic area we are interested in into a compatible Blast database. Looking for related protein sequences into the target genomic area. Screaning them using Blast2gene to define candidate genomic regions. Filtering the results using GeneWise. Approximate time 24 hours aprox. Program This workflow runs web services located in MareNostrum and Altix machines. They can be called through: MobyLite API