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Items tagged with "bioinformatics" (126)

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Workflows (99)

Taverna 1 Original Uploader Duncan Hull	EBI InterProScan (v2) Created: 03/10/07 @ 18:35:46 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License EBI InterProScan. Stop fannying around with BLAST and use InterProScan instead. Rating: 4.0 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 499 times \| Downloaded: 143 times Tags (4): bioinformatics \| sanger sequencing \| satellite \| scaffold	View Download (v2)
Taverna 1 Original Uploader Duncan Hull	Genome annotation pipeline demonstrator workflow for Nucleic Acids Research (v2) Created: 03/10/07 @ 18:35:47 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Part of a workflow by Hannah Tipney, adapted by Duncan Hull using GenScan, RepeatMasker and BLAST. http://dx.doi.org/10.1093/nar/gkl320 Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 549 times \| Downloaded: 162 times Tags (5): bioinformatics \| segregation \| sequence \| sequence assembly \| sequence tagged site	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLASTP with simplified results returned (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:28:50 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV... Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 323 times \| Downloaded: 106 times Tags (6): bioinformatics \| BLAST \| ddbj \| sequence \| similarity \| simplifier	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Simplify a BLAST text file (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 28/07/09 @ 13:01:45 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc. Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 357 times \| Downloaded: 140 times Tags (11): bioinformatics \| BLAST \| gene identifier \| gi \| matrix \| sequence \| similarity \| simple \| simplifier \| substitution \| summary	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLAST using DDBJ service (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:31:20 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP... Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 579 times \| Downloaded: 213 times Tags (5): bioinformatics \| BLAST \| ddbj \| sequence \| similarity	View Download (v2)
Taverna 1 Original Uploader Franck Tanoh	BLASTP with simplified results returned (v2) Created: 03/10/07 @ 18:36:12 \| Last updated: 06/03/08 @ 17:01:32 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow Performs a blastp search on protein sequence, extracts sequence id within the blast report and retrives the corresponding seuqences. Rating: 4.0 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 192 times \| Downloaded: 58 times Tags (3): bioinformatics \| BLAST \| sequence	View Download (v2)
Taverna 1 Original Uploader Hong Chang Bum	EBI NCBI Blast (v2) Created: 03/10/07 @ 18:36:22 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License EBI NCBI Blast Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 3 \| Citations: 0 Viewed: 252 times \| Downloaded: 92 times Tags (3): bioinformatics \| scaffold \| SEG	View Download (v2)
Taverna 1 Original Uploader Franck Tanoh	Example of a conditional execution workflow (v2) Created: 03/10/07 @ 18:36:30 \| Last updated: 27/01/08 @ 21:09:41 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License If the input is true the workflow returns the temperature in Celsius, if false the temperature in Fahrenheit is returned. Rating: 3.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 111 times \| Downloaded: 57 times Tags (2): bioinformatics \| design pattern	View Download (v2)
Taverna 1 Original Uploader Kieren Lythgow	Multiple Blastp (v2) Created: 20/11/07 @ 16:58:38 \| Last updated: 10/01/08 @ 12:09:38 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a workflow to automate multiple BLASTp jobs on a large list of protein sequences in FASTA format. Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 482 times \| Downloaded: 157 times Tags (4): bioinformatics \| BLAST \| protein \| sequence	View Download (v2)
Taverna 1 Original Uploader Fong Chun Chan	DataBiNS - Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs (v2) Created: 04/12/07 @ 23:43:01 \| Last updated: 04/12/07 @ 23:45:25 Credits: Fong Chun Chan License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 435 times \| Downloaded: 128 times Tags (12): bioinformatics \| biomoby \| entrez \| hapmap \| kegg \| Kegg Pathways \| ls-snp \| OMIM \| pdb \| pubmed \| snps \| swiss prot	View Download (v2)
Taverna 1 Original Uploader Alan Williams	BiomartAndEMBOSSAnalysis (v4) Created: 15/09/09 @ 15:11:11 License: Creative Commons Attribution 3.0 Unported License Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1157 times \| Downloaded: 391 times Tags (6): bioinformatics \| biomart \| emboss \| example \| mygrid \| taverna	View Download (v4)
Taverna 1 Original Uploader Alan Williams	Fetch Dragon images from BioMoby (v3) Created: 05/03/08 @ 14:09:35 \| Last updated: 14/07/10 @ 16:46:37 Credits: Tomoinn License: Creative Commons Attribution 3.0 Unported License Fetch images and annotations of snapdragons Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 305 times \| Downloaded: 108 times Tags (8): annotation \| bioinformatics \| biomoby \| example \| image \| mygrid \| snapdragon \| taverna	View Download (v3)
Taverna 1 Original Uploader Alan Williams	Retrieve sequence in EMBL format (v3) Created: 17/06/09 @ 16:51:32 Credits: Franck Tanoh Tomoinn Stuart Owen License: Creative Commons Attribution 3.0 Unported License This workflow retrieves a sequence associated with its features in embl format Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 307 times \| Downloaded: 100 times Tags (8): bioinformatics \| example \| mygrid \| rendering \| retrieval \| sequence \| soaplab \| taverna	View Download (v3)
Taverna 1 Original Uploader Alan Williams	Fetch PDB flatfile from RCSB server (v1) Created: 05/03/08 @ 14:13:24 \| Last updated: 31/03/08 @ 16:01:41 Credits: Tomoinn License: Creative Commons Attribution 3.0 Unported License Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein. Rating: 3.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 288 times \| Downloaded: 109 times Tags (8): bioinformatics \| example \| mygrid \| pdb \| protein \| protein structure \| rcsb \| taverna	View Download (v1)
Taverna 1 Original Uploader Alan Williams	GBSeq test (v2) Created: 05/03/08 @ 14:15:35 \| Last updated: 31/03/08 @ 15:55:09 Credits: Franck Tanoh License: Creative Commons Attribution 3.0 Unported License This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 241 times \| Downloaded: 90 times Tags (9): bioinformatics \| example \| mygrid \| ncbi \| nucleotide \| protein \| retrieval \| shim \| taverna	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_InterProScan (v3) Created: 26/10/08 @ 20:33:34 \| Last updated: 01/04/11 @ 08:52:28 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform an InterProScan ... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 1237 times \| Downloaded: 374 times Tags (10): bioinformatics \| ebi \| gff \| go terms \| interpro \| interproscan \| protein annotation \| protein domain \| protein family \| protein motif	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_InterProScan_with_prompts (v1) Created: 31/05/08 @ 11:40:34 \| Last updated: 01/04/11 @ 08:57:45 Credits: Hamish McWilliam Attributions: EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run an InterProScan anal... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 50 times Tags (7): bioinformatics \| ebi \| go terms \| interpro \| interproscan \| protein annotation \| user_interaction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW2_phylogentic_tree (v2) Created: 07/04/09 @ 20:09:32 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 1 \| Comments: 1 \| Citations: 0 Viewed: 280 times \| Downloaded: 102 times Tags (7): bioinformatics \| clustal \| clustalw \| ebi \| neighbor-joining \| phylogenetic tree \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW_alignment_tree (v2) Created: 31/05/08 @ 13:53:04 \| Last updated: 03/12/10 @ 13:34:43 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree License: Creative Commons Attribution 3.0 Unported License Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 176 times \| Downloaded: 83 times Tags (10): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| sequence alignment \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_blastpgp_PSI-BLAST (v1) Created: 31/05/08 @ 14:39:22 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 123 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastpgp \| ebi \| ncbi blast \| PSI-BLAST \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_dbfetch_fetchBatch (v1) Created: 31/05/08 @ 20:59:46 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License From a list of sequence entry identifiers and a database name, fetch the sequences in fasta format using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 103 times \| Downloaded: 70 times Tags (3): bioinformatics \| dbfetch \| ebi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Protein_search_fetch_align_tree (v2) Created: 07/04/09 @ 20:13:19 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 419 times \| Downloaded: 140 times Tags (15): alignment \| bioinformatics \| BLAST \| clustal \| clustalw \| dbfetch \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| protein \| sequence alignment \| sequence similarity search \| tree \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Phobius (v2) Created: 01/06/08 @ 11:08:45 \| Last updated: 02/06/08 @ 21:39:06 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 113 times \| Downloaded: 62 times Tags (8): bioinformatics \| ebi \| gff \| phobius \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_InterProScan_tmhmm_signalp (v4) Created: 26/10/08 @ 20:50:10 \| Last updated: 01/04/11 @ 08:56:37 Credits: Hamish McWilliam Attributions: EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Use the TMHMM and Signal... Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 203 times \| Downloaded: 83 times Tags (8): bioinformatics \| ebi \| gff \| interproscan \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v4)
Taverna 1 Original Uploader Hamish McWilliam	Protein_alignment_transmembrane (v1) Created: 01/06/08 @ 12:20:29 Credits: Hamish McWilliam Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch License: Creative Commons Attribution 3.0 Unported License Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 190 times \| Downloaded: 57 times Tags (16): alignment \| bioinformatics \| clustal \| clustalw \| dbfetch \| ebi \| emboss \| emboss tmap \| FASTA \| multiple sequence alignment \| protein \| protein annotation \| sequence alignment \| sequence similarity search \| transmembrane \| transmembrane prediction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Sequence_or_ID (v1) Created: 01/06/08 @ 14:15:12 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format. If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 144 times \| Downloaded: 60 times Tags (6): bioinformatics \| dbfetch \| ebi \| emboss \| emboss seqret \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	tmap_single_sequence (v2) Created: 01/06/08 @ 14:27:12 \| Last updated: 02/06/08 @ 21:38:13 Credits: Hamish McWilliam Attributions: Sequence_or_ID License: Creative Commons Attribution 3.0 Unported License Simple workflow using tmap to find transmembrane regions, using a single sequence as input. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 116 times \| Downloaded: 44 times Tags (9): bioinformatics \| ebi \| emboss \| emboss tmap \| gff \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Protein_transmembrane_prediction (v2) Created: 26/10/08 @ 21:16:10 \| Last updated: 01/04/11 @ 08:57:10 Credits: Hamish McWilliam Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Transmembrane and signal... Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 3 \| Citations: 0 Viewed: 320 times \| Downloaded: 91 times Tags (11): bioinformatics \| ebi \| emboss \| emboss tmap \| gff \| interproscan \| phobius \| protein \| protein annotation \| transmembrane \| transmembrane prediction	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW2 (v2) Created: 07/04/09 @ 20:06:03 \| Last updated: 06/12/10 @ 11:00:19 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 servi... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 506 times \| Downloaded: 240 times Tags (7): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| sequence alignment	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Kalign (v1) Created: 02/06/08 @ 21:28:56 \| Last updated: 06/12/10 @ 11:39:52 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 73 times \| Downloaded: 45 times Tags (6): alignment \| bioinformatics \| ebi \| kalign \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_WU-BLAST (v1) Created: 30/05/08 @ 22:47:18 \| Last updated: 06/12/10 @ 10:51:04 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params. Note: the WSWUBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement WU-BLAST services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 208 times \| Downloaded: 78 times Tags (5): bioinformatics \| BLAST \| ebi \| sequence similarity search \| wu-blast	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI WU-BLAST with program and database selection prompts. (v3) Created: 04/07/09 @ 11:39:54 \| Last updated: 06/12/10 @ 10:56:44 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). This workflow wraps the EBI_WU-BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. The values presented in the selection menus for the program and database are obtained from the service, using the provided me... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 169 times \| Downloaded: 82 times Tags (6): bioinformatics \| BLAST \| ebi \| sequence similarity search \| user_interaction \| wu-blast	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_FASTA (v1) Created: 30/05/08 @ 23:50:46 \| Last updated: 06/12/10 @ 10:52:25 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement FASTA services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 85 times \| Downloaded: 49 times Tags (6): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI FASTA with prompts (v3) Created: 30/05/08 @ 23:53:16 \| Last updated: 06/12/10 @ 10:53:23 Credits: Hamish McWilliam Attributions: EBI_FASTA License: Creative Commons Attribution 3.0 Unported License Run a FASTA analysis using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). This workflow wraps the EBI_FASTA workflow to provide a basic user interface which prompts for the required inputs: sequence, database, FASTA program and user e-mail. Other parameters (e.g. matrix, gap penalties, etc.) are allowed to default. Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new developme... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 44 times Tags (7): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch \| user_interaction	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST (v1) Created: 31/05/08 @ 08:38:46 \| Last updated: 06/12/10 @ 10:54:16 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement NCBI BLA... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 312 times \| Downloaded: 154 times Tags (6): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST_with_prompts (v1) Created: 31/05/08 @ 08:40:29 \| Last updated: 06/12/10 @ 10:55:09 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution 3.0 Unported License Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 73 times Tags (7): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search \| user_interaction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MPsrch (v1) Created: 02/06/08 @ 21:49:11 \| Last updated: 06/12/10 @ 10:38:42 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch). Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 43 times Tags (7): bioinformatics \| ebi \| mpsrch \| protein \| protein annotation \| sequence similarity search \| smith-waterman	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MAFFT (v1) Created: 03/06/08 @ 05:55:43 \| Last updated: 06/12/10 @ 11:38:58 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MAFFT services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 94 times \| Downloaded: 55 times Tags (6): alignment \| bioinformatics \| ebi \| mafft \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ScanPS (v1) Created: 03/06/08 @ 05:57:09 \| Last updated: 06/12/10 @ 10:37:50 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool. Note: the WSScanPS service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 58 times \| Downloaded: 38 times Tags (6): bioinformatics \| ebi \| protein \| scanps \| sequence similarity search \| smith-waterman	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MUSCLE (v1) Created: 03/06/08 @ 06:16:22 \| Last updated: 06/12/10 @ 11:04:03 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used. Note: the WSMuscle service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MUSCLE services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 57 times Tags (6): alignment \| bioinformatics \| ebi \| multiple sequence alignment \| muscle \| sequence alignment	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_TCoffee (v1) Created: 03/06/08 @ 06:31:37 \| Last updated: 06/12/10 @ 11:02:53 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used. Note: the WSTCoffee service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement T-COFFEE services (REST or SOAP) should be used instead. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 127 times \| Downloaded: 61 times Tags (6): alignment \| bioinformatics \| ebi \| multiple sequence alignment \| sequence alignment \| t-coffee	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage (v2) Created: 05/06/08 @ 16:00:38 \| Last updated: 16/06/08 @ 11:40:46 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License uses InChI's retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 128 times \| Downloaded: 62 times Tags (8): accurate mass \| bioinformatics \| chemspider \| compound info + image \| mass spectrometry \| massbank \| metabolomics \| systems biology	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MaxSprout (v2) Created: 05/06/08 @ 21:44:00 \| Last updated: 06/06/08 @ 05:58:16 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License Generation of protein backbone and side chain co-ordinates from a C(alpha) trace using the MaxSprout tool. The EBI's WSMaxsprout service (see http://www.ebi.ac.uk/Tools/webservices/services/maxsprout) is used to access the tool. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 40 times Tags (6): backbone \| bioinformatics \| ebi \| pdb \| protein \| structure	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Structure_or_ID (v1) Created: 06/06/08 @ 05:57:31 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 379 times \| Downloaded: 37 times Tags (8): bioinformatics \| dbfetch \| ebi \| pdb \| protein \| protein structure \| structure \| structure retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Nucleotide_ORF_translation (v1) Created: 06/06/08 @ 20:13:04 Credits: Hamish McWilliam Attributions: Sequence_or_ID License: Creative Commons Attribution 3.0 Unported License From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 183 times \| Downloaded: 96 times Tags (8): bioinformatics \| ebi \| emboss \| emboss getorf \| nucleotide sequence \| nucleotide translation \| open reading frame \| ORF	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Fasta_string_to_fasta_list (v1) Created: 06/06/08 @ 21:41:28 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Split a string containing a set of sequences in fasta format into a list for fasta formated sequences. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 91 times \| Downloaded: 43 times Tags (2): bioinformatics \| fasta format	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Nucleotide_InterProScan (v4) Created: 26/10/08 @ 21:10:09 \| Last updated: 01/04/11 @ 08:54:21 Credits: Hamish McWilliam Attributions: EBI_InterProScan EBI_NCBI_BLAST Nucleotide_ORF_translation Fasta_string_to_fasta_list Sequence_or_ID License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run InterProScan using a... Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 358 times \| Downloaded: 119 times Tags (11): bioinformatics \| BLAST \| ebi \| interpro \| interproscan \| ncbi blast \| nucleotide sequence \| nucleotide translation \| open reading frame \| protein \| protein annotation	View Download (v4)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Blast2InterPro (v2) Created: 26/10/08 @ 20:45:45 \| Last updated: 01/04/11 @ 08:55:49 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST EBI_dbfetch_fetchBatch Fasta_string_to_fasta_list EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform a BLAST search a... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 245 times \| Downloaded: 94 times Tags (11): bioinformatics \| BLAST \| dbfetch \| ebi \| go terms \| interpro \| interproscan \| protein \| protein annotation \| sequence similarity search \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	NCBI_QBLAST (v2) Created: 07/06/08 @ 15:05:00 \| Last updated: 07/06/08 @ 17:11:36 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Perform an NCBI BLAST sequence similarity search using NCBI's QBLAST service (see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 136 times \| Downloaded: 70 times Tags (5): bioinformatics \| BLAST \| ncbi \| ncbi blast \| sequence similarity search	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Sequence_or_ID_or_GI (v1) Created: 07/06/08 @ 16:58:14 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License Get a sequence in fasta format given one of: An NCBI GI number (e.g. 75251068). An entry identifier in database:identifier format (e.g. uniprot:Q96247). 3. A sequence entry in a format supported by EMBOSS seqret. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 118 times \| Downloaded: 60 times Tags (9): bioinformatics \| dbfetch \| ebi \| efetch \| fasta format \| gi \| ncbi \| sequence identifier \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_DaliLite (v1) Created: 07/06/08 @ 17:16:37 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Pairwise structure comparison using the DaliLite tool. The EBI's WSDaliLite web service (see http://www.ebi.ac.uk/Tools/webservices/services/dalilite) is used to access the tool. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 49 times Tags (7): bioinformatics \| ebi \| pairwise structure comparison \| pdb \| protein \| protein structure \| structure	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_PICR_Sequence_to_UniParc_and_InterPro (v2) Created: 08/06/08 @ 13:53:39 \| Last updated: 08/06/08 @ 14:10:02 Credits: Hamish McWilliam Attributions: EBI_dbfetch_UniParc EBI_Fetch_InterPro_Matches_UniParc EBI_PICR_Sequence_to_ID License: Creative Commons Attribution 3.0 Unported License Given a protein sequence get some information about it: Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this s... Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 158 times \| Downloaded: 57 times Tags (13): bioinformatics \| dbfetch \| ebi \| fasta format \| gi \| interpro \| picr \| protein \| sequence identifier \| sequence retrieval \| uniparc \| uniprot archive \| upi	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_PICR_Sequence_to_ID (v1) Created: 08/06/08 @ 14:03:07 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Map a protein sequence to the known identifiers of identical sequences. Uses the EBI's PICR web service (see http://www.ebi.ac.uk/Tools/picr/) to perform the mapping. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 72 times \| Downloaded: 39 times Tags (9): bioinformatics \| ebi \| gi \| picr \| protein \| sequence identifier \| uniparc \| uniprot archive \| upi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_dbfetch_UniParc (v1) Created: 08/06/08 @ 14:05:40 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License From a list of UniParc entry identifers get the complete entries using the EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 53 times \| Downloaded: 33 times Tags (9): bioinformatics \| dbfetch \| ebi \| protein \| sequence identifier \| sequence retrieval \| uniparc \| uniprot archive \| upi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Fetch_InterPro_Matches_UniParc (v1) Created: 08/06/08 @ 14:08:47 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License For a UniParc (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) identifier/accession fetch the assocated InterPro Matches from SRS@EBI (see http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+IPRMC_UNIPARC). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 65 times \| Downloaded: 34 times Tags (9): bioinformatics \| ebi \| interpro \| protein \| protein annotation \| srs \| uniparc \| uniprot archive \| upi	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_CENSOR (v2) Created: 17/06/08 @ 20:42:46 \| Last updated: 25/06/08 @ 06:16:03 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool. Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 152 times \| Downloaded: 50 times Tags (6): bioinformatics \| censor \| ebi \| nucleotide sequence \| protein \| repeat masking	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	tRNAscan (v1) Created: 28/06/08 @ 09:57:33 Credits: Hamish McWilliam Attributions: Sequence_or_ID_or_GI License: Creative Commons Attribution 3.0 Unported License Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE). This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 152 times \| Downloaded: 56 times Tags (6): bioinformatics \| nucleotide sequence \| nucleotide sequence annotation \| tRNA \| trnascan \| trnascan-se	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_OLS_TermInfo (v1) Created: 09/07/08 @ 05:36:40 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Get details of an ontology term given its identifer. This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 43 times Tags (9): bioinformatics \| ebi \| gene ontology \| GO \| go terms \| ols \| ontologies \| ontology \| ontology lookup service	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_IntAct (v1) Created: 09/07/08 @ 06:01:17 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Find protein binary interactions using the EBI's IntAct service. See http://www.ebi.ac.uk/intact/ for further details. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 117 times \| Downloaded: 57 times Tags (7): binary \| bioinformatics \| ebi \| intact \| protein \| protein annotation \| protein interaction	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Retrieve Protein Sequence (v1) Created: 30/07/08 @ 16:36:55 \| Last updated: 03/12/09 @ 16:54:02 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 384 times \| Downloaded: 128 times Tags (5): bioinformatics \| neuroscience \| newcastle \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Steffen Möller	mustang provides structural alignment of two proteins (v3) Created: 20/08/08 @ 14:41:21 \| Last updated: 25/08/08 @ 15:40:45 Credits: Steffen Möller Attributions: Fetch PDB flatfile from RCSB server License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 149 times \| Downloaded: 62 times Tags (5): alignment \| bioinformatics \| grid \| pdb \| protein structure	View Download (v3)
Taverna 1 Original Uploader Steffen Möller	Retrieve Single Molecule from ZINC - structure and figure (v1) Created: 24/08/08 @ 22:52:25 \| Last updated: 25/08/08 @ 21:57:16 Credits: Steffen Möller License: Creative Commons Attribution-Share Alike 3.0 Unported License The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds. With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data inst... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 125 times \| Downloaded: 60 times Tags (4): bioinformatics \| docking \| ligand \| structure	View Download (v1)
Taverna 1 Original Uploader Steffen Möller	dbfetch tutorial (v1) Created: 22/09/08 @ 01:05:36 Credits: Steffen Möller License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is alw... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 98 times \| Downloaded: 41 times Tags (3): bioinformatics \| sequence retrieval \| structure retrieval	View Download (v1)
Taverna 1 Original Uploader José Manuel Rodríguez	runFunCUT (v1) Created: 03/10/08 @ 10:54:45 \| Last updated: 03/10/08 @ 11:49:17 Credits: José Manuel Rodríguez License: Creative Commons Attribution-Share Alike 3.0 Unported License MOBY Web Services (synchronous and asynchronous) that describe the FunCUT method. Is recommended use asynchronous MOBY services because the method needs huge range of time. FunCUT Method Short Description: Annotates homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups) FunCUT (Abascal and Valencia, 2003. PROTEINS: Structure, Function, and Genetics 53:683– 692 (2003)) is application based on the study... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 111 times \| Downloaded: 0 times Tags (4): bioinformatics \| inb \| protein annotation \| protein family	View
Taverna 1 Original Uploader Michael Gerlich	Download Entries from PubChem (v1) Created: 30/03/09 @ 09:20:42 \| Last updated: 30/03/09 @ 09:34:37 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results. Adding support for downloading this XML file and writing it to filesystem is planned. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 74 times \| Downloaded: 52 times Tags (4): bioinformatics \| compound info + image \| pubchem \| pug	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	Retrieve Pathways and Compound information from KEGG (v1) Created: 30/03/09 @ 09:22:36 \| Last updated: 30/03/09 @ 09:39:23 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 39 times Tags (3): bget \| bioinformatics \| pathway	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	Search InChI in NCBI eSearch (pccompound) (v1) Created: 30/03/09 @ 09:26:25 \| Last updated: 30/03/09 @ 09:47:00 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 93 times \| Downloaded: 47 times Tags (12): bioinformatics \| compound \| compound info + image \| database \| image \| inchi \| information \| ncbi \| pccompound \| pubchem \| search \| xml	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	MassBank to KEGG (v1) Created: 30/03/09 @ 09:30:32 \| Last updated: 30/03/09 @ 09:49:13 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 198 times \| Downloaded: 0 times Tags (21): bget \| bioinformatics \| chemspider \| compound \| compound info + image \| database \| eutils \| image \| inchi \| information \| mass spectrometry \| massbank \| metabolomics \| ncbi \| pathway \| pccompound \| pubchem \| pug \| search \| summary \| xml	View
BioExtract Server Original Uploader Carol Lushbough	Nucleotide InterProScan for the BioExtract Server (v3) Created: 16/04/09 @ 15:26:57 \| Last updated: 01/07/09 @ 08:32:34 Credits: Carol Lushbough Hamish McWilliam Attributions: Nucleotide_InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 149 times \| Downloaded: 89 times Tags (5): bioinformatics \| BLAST \| blastp \| ebi \| interproscan	View Download (v3)
Triana Original Uploader Hamish McWilliam	EBI_dbfetch_fetchData (v1) Created: 28/08/09 @ 11:45:50 \| Last updated: 28/08/09 @ 11:49:08 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Sample workflow illustrating the use of the EBI's WSDbfetch service in Triana. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 54 times \| Downloaded: 29 times Tags (4): bioinformatics \| dbfetch \| ebi \| sequence retrieval	View Download (v1)
Triana Original Uploader Hamish McWilliam	EBI_dbfetch_fetchBatch (v1) Created: 28/08/09 @ 11:55:10 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Sample workflow illustrating the use of EBI's WSDbfetch service with Triana. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 59 times \| Downloaded: 18 times Tags (5): bioinformatics \| dbfetch \| ebi \| example \| structure retrieval	View Download (v1)
Taverna 1 Original Uploader EdwardK...	Fetch Dragon images from BioMoby (v1) Created: 14/07/10 @ 16:20:46 \| Last updated: 14/07/10 @ 16:20:48 Credits: EdwardKawas Tomoinn Attributions: Fetch Dragon images from BioMoby License: Creative Commons Attribution-Share Alike 3.0 Unported License Fetch images and annotations of snapdragons Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 11 times Tags (8): annotation \| bioinformatics \| biomoby \| example \| image \| mygrid \| snapdragon \| taverna 1	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:10:40 \| Last updated: 21/07/10 @ 13:10:41 Credits: Lebreton Attributions: BLAST using DDBJ service License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 10 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| services \| xml	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:16:00 \| Last updated: 21/07/10 @ 13:23:12 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 13 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST with options from DDBJ Web services (v1) Created: 21/07/10 @ 13:24:56 \| Last updated: 01/09/10 @ 17:37:48 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html exxample accession : Q9NRA8 database : UNIPROT program : blastp param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 11 times Tags (5): bioinformatics \| BLAST \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:56:08 \| Last updated: 21/07/10 @ 13:58:41 Credits: Lebreton Attributions: BLAST using DDBJ service License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 9 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services (v4) Created: 21/07/10 @ 14:08:32 \| Last updated: 07/09/10 @ 10:04:55 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 28 times \| Downloaded: 16 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v4)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services (v1) Created: 21/07/10 @ 14:21:50 \| Last updated: 21/07/10 @ 14:21:52 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 10 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a VecScreen from DDBJ Web services (v1) Created: 21/07/10 @ 14:36:36 \| Last updated: 01/09/10 @ 17:35:20 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a VecScreen from DDBJ Web services : A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 11 times Tags (4): bioinformatics \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a high speed BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:16:24 \| Last updated: 01/09/10 @ 17:18:45 Credits: Lebreton Attributions: retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 13 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:22:14 \| Last updated: 01/09/10 @ 17:22:37 Credits: Lebreton Attributions: retrieve protein sequence and do a BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 11 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:26:07 \| Last updated: 01/09/10 @ 17:26:39 Credits: Lebreton License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 6 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve nucleotide sequence and do a BLAST from DDBJ Web services (v1) Created: 01/09/10 @ 17:31:29 \| Last updated: 01/09/10 @ 17:33:51 Credits: Lebreton Attributions: retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve nucleotide sequence and do a BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 8 times Tags (5): bioinformatics \| BLAST \| nucleotide \| sequence \| services	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:46:58 \| Last updated: 29/11/10 @ 20:47:00 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 16 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 2 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:03:13 \| Last updated: 29/11/10 @ 20:03:14 Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 44 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 2 Original Uploader Hamish McWilliam	InterProScan (SOAP) (v1) Created: 03/12/10 @ 07:41:47 \| Last updated: 03/12/10 @ 07:41:48 Attributions: EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 17 times Tags (11): bioinformatics \| ebi \| interpro \| interproscan \| protein \| protein annotation \| protein domain \| protein family \| protein motif \| transmembrane \| transmembrane prediction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	InterProScan (SOAP) (v1) Created: 03/12/10 @ 08:20:21 \| Last updated: 03/12/10 @ 08:20:24 Credits: Hamish McWilliam Attributions: EBI_InterProScan InterProScan (SOAP) License: Creative Commons Attribution 3.0 Unported License Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 23 times \| Downloaded: 11 times Tags (11): bioinformatics \| ebi \| interpro \| interproscan \| protein \| protein annotation \| protein domain \| protein family \| protein motif \| transmembrane \| transmembrane prediction	View Download (v1)
Taverna 2 Original Uploader Hamish McWilliam	EMBL-EBI ClustalW2 (SOAP) (v1) Created: 06/12/10 @ 13:16:52 Attributions: EBI_ClustalW2 License: Creative Commons Attribution 3.0 Unported License Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 19 times Tags (7): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Dennis Leenheer	[untitled] (v1) Created: 26/04/11 @ 14:50:37 \| Last updated: 26/04/11 @ 15:04:28 Credits: Dennis Leenheer License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 9 times Tags (16): bioinformatics \| biosemantics \| datamining \| global test \| GO \| kegg \| literature weighted global test \| mapping \| normalization \| rma \| sommation \| taverna \| taverna 2 \| textmining \| weighted global test \| workflow	View Download (v1)
Taverna 2 Original Uploader Kalai	Generate Atom Signatures of molecules given SDF as input (v1) Created: 13/05/11 @ 17:14:06 \| Last updated: 13/05/11 @ 19:47:24 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 46 times \| Downloaded: 19 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| synthetic \| taverna 2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Scoring small molecules for metabolite likeness/ Natural product likeness (v2) Created: 13/05/11 @ 17:22:28 \| Last updated: 18/03/12 @ 16:41:39 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1 Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 66 times \| Downloaded: 16 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| structure \| synthetic \| workflow \| workflows	View Download (v2)
Taverna 2 Original Uploader Kalai	Plotting distribution of natural product likeness scores (v1) Created: 13/05/11 @ 17:34:58 \| Last updated: 13/05/11 @ 17:35:08 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License Prerequisite: CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file. - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1 Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 13 times Tags (24): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader hindlem	Get names of proteins similar to RNA binding proteins (Simple example SADI workflow) (v1) Created: 18/05/11 @ 15:24:56 \| Last updated: 18/05/11 @ 15:39:02 Credits: hindlem License: Creative Commons Attribution-Share Alike 3.0 Unported License A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 11 times Tags (5): bioinformatics \| BLAST \| GO \| sadi \| uniprot	View Download (v1)
Taverna 2 Original Uploader Kalai	Download Structures from PubChem given chemical names (v1) Created: 24/05/11 @ 13:13:52 \| Last updated: 24/05/11 @ 14:19:24 Credits: Kalai Michael Gerlich Attributions: Download Entries from PubChem License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned. The pubchem compound_ID is then used to download structures from PubChem. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 19 times Tags (26): bioinformatics \| cheminformatics \| compound \| data \| download file \| esearch \| eutils \| file \| list \| ncbi \| open science \| open source \| pccompound \| split \| string \| structure \| structure retrieval \| synthetic \| taverna 2 \| taverna2 \| url2list \| workflow \| workflows \| wsdl \| xml \| xpath	View Download (v1)
KNIME Original Uploader Baj	NGS sample workflow with data (v1) Created: 24/06/11 @ 11:42:57 \| Last updated: 24/06/11 @ 12:17:00 Credits: Baj License: Creative Commons Attribution-Share Alike 3.0 Unported License Sample workflow for NGS data analysis This worklfow relies on community contributions that can be installed through the following update site: http://tech.knime.org/update/community-contributions/nightly specifically the KNIME NGS tools and the KNIME R Scripting extensions. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 136 times \| Downloaded: 36 times Tags (4): bioinformatics \| data \| sample \| workflow	View Download (v1)
Taverna 2 Original Uploader Anna Bauer-Mehren	ADR-S (v2) Created: 28/03/11 @ 11:34:18 \| Last updated: 09/08/11 @ 22:38:12 Credits: Anna Bauer-Mehren License: GNU General Public License (GPL) 2.0 The ADR-S pathway seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are pr... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 16 times Tags (5): adr \| adverse drug reaction \| bioinformatics \| drug safety \| signal	View Download (v2)
LONI Pipeline Original Uploader Pipeline	BATWING (v1) Created: 25/08/11 @ 19:39:58 \| Last updated: 25/08/11 @ 19:57:37 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License Batwing reads in multi-locus haplotype data, and model and prior distri- bution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also generates approximate posterior samples of the entire genealogical tree underly- ing the sample, including the tree hei... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 3 times Tags (7): batwing \| bioinformatics \| brain \| brain imaging \| genomics \| loni \| pipeline	View Download (v1)
Kepler Original Uploader Wdsnellg	Extract Gene Sequence with Kepler (v1) Created: 05/10/11 @ 05:04:40 \| Last updated: 05/10/11 @ 05:04:42 Credits: Wdsnellg License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a workflow which allows one to extract gene sequence information using the accession number as the input. Multiple outputs include a file output of sequence header information, as well as one output window of base pair count, ratios and gene sequence. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 13 times Tags (3): bioinformatics \| gene \| ist600	View Download (v1)
Taverna 2 Original Uploader Marco Roos	Match gene lists based on information in literature (v7) Created: 17/04/12 @ 08:55:46 \| Last updated: 25/04/12 @ 07:54:26 Credits: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics Attributions: ExplainScores demo License: Creative Commons Attribution-Share Alike 3.0 Unported License [THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic... Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 6 times Tags (11): association \| bioinformatics \| biology \| concept \| concept mining \| concept web \| literature \| protein \| proteins \| semantic \| uniprot	View Download (v7)

Packs (5)

Creator: José Manuel Rodríguez	FunCUT package Created: 03/10/08 @ 16:47:15 \| Last updated: 03/10/08 @ 16:48:55 Input example and FunCUT workflow 1 item in this pack Comments: 0 \| Viewed: 145 times \| Downloaded: 0 times Tags: bioinformatics \| protein annotation \| protein family	View
Creator: Paul Fisher	Open Data: Bilateral Perisylvian Polymicrogyria Created: 16/11/10 @ 16:20:43 \| Last updated: 23/09/11 @ 10:55:08 This pack contains freely accessible data for scientific researchers to try and identify key genes linked to Bilateral Perisylvian Polymicrogyria. For those who want more information about this condition before they download the data, please see this link, which describes the condition and traits: http://omim.org/entry/300388?search=bilateral%20perisylvian%20polymicrogyria The results conatined within this pack are the output from running a scientific workflow that identifies candidate genes... 7 items in this pack Comments: 0 \| Viewed: 124 times \| Downloaded: 21 times Tags: bilateral perisylvian polymicrogyria \| bioinformatics \| chromosome \| cosine vector space \| data-driven \| epilepsy \| genotype \| homo sapiens \| human \| Kegg Pathways \| phenotype \| text mining; term extraction; entity recognition \| trait	View Download
Creator: Kalai	Natural product likeness filter Created: 13/05/11 @ 19:35:39 \| Last updated: 29/08/11 @ 14:25:47 Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work... 3 items in this pack Comments: 0 \| Viewed: 34 times \| Downloaded: 18 times Tags: bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna 2 \| taverna2 \| workflow \| workflows	View Download
Creator: Wdsnellg	Extract Gene Sequence Information with Kepler Created: 05/10/11 @ 04:58:33 \| Last updated: 05/10/11 @ 06:11:56 This workflow and pack were designed for a class project. The Kepler based workflow allows one to extract specific information from a gene sequence by using the accession ID as input. By using two web services created for the DNA Data Bank of Japan (DDBJ, http://www.xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en), one can extract the sequence header information as an output file, as well as retrieve the sequence, base pair count, and base pair ratios in... 5 items in this pack Comments: 0 \| Viewed: 2 times \| Downloaded: 1 time Tags: bioinformatics \| gene \| ist600	View Download
Creator: Marco Roos	wf4ever Deliverable 6.3 Pack Created: 02/12/11 @ 09:31:26 \| Last updated: 02/12/11 @ 10:21:03 This pack contains (references to) the workflows for GWAS analysis by workflows that perform pathway and GO analysis and biosemantics data interpretation (a special form of text mining). This pack aggregates the deliverable materials for month 8 for Work Package 6. The workflows have not been published in the scientific domain yet, so its content cannot yet be made public. They are available upon request, in particular for reviewers. Please contact Kristina Hettne or Marco Roos (see credit... 6 items in this pack Comments: 0 \| Viewed: 6 times \| Downloaded: 0 times Tags: bioinformatics \| biosemantics \| ensembl \| gene \| genes \| GO \| gwas \| interpretation \| pathway \| pathways \| wf4ever	View

Groups (11)

Administrator: Mariebrown	metabolomics Created: Thursday 29 November 2007 @ 11:50:47 (GMT) Data analysis and bioinformatics of metabolomic studies 2 shared items \| 0 announcements Members (21): Mar... Tsamv Pra... Rak... Saa... Mic... Peter Leopold Andy Tseng Aniraj Suza Adam Jay... Ruchi Michael Gerlich Duncan Hull Paul Dobson htt... Tabma Mkb... mro... Egon Willighagen Peter Li Tags: bioinformatics \| Kegg Pathways \| phenotype	View
Administrator: Fong Chun Chan	Biomoby Unique name: biomoby Created: Tuesday 04 December 2007 @ 09:48:10 (GMT) This is a group for those involved in the Biomoby world. Whether you are a developer or simple a user of it, you can join this group to keep up to date on the latest Biomoby news. 0 shared items \| 0 announcements Members (12): Fong Chun Chan Mdm... Dun... Hch... Saa... Barend Aniraj Carol Lushbough Suza Adam Heiko Schoof Michael Gerlich Ktolle Tags: bioinformatics \| biomoby	View
Administrator: Marco Roos	BioAssist_NL Unique name: bioassist_nl Created: Wednesday 01 August 2007 @ 13:05:51 (GMT) NBIC's BioAssist program BioAssist[1], organised by the Netherlands BioInformatics Centre (NBIC[2]), is a program for support and dissemination of bioinformatics tools and expertise in the Netherlands. It advocates the use of e-science standards such as web services and workflow. It is associated with the projects VL-e[3] and BioRange[4]. Links: http://www.nbic.nl/support/BioAssist... 4 shared items \| 0 announcements Members (19): Marco Roos Ishtiaq AHMAD Rob Hooft Jbot Barbera van Schaik Mic... Wim spee Barend Alexg Angela Luijf Markf Tabma Péter Horvatovich Pieter Neerincx Morris Swertz Maurice Bouwhuis Harm Nijveen Antoine van Kampen M. Scott Marshall Tags: bioinformatics \| NBIC \| support	View
Administrator: Allyson Lister	SyMBA: Systems and Molecular Biology Data and Metadata Archive Unique name: symba Created: Wednesday 12 September 2007 @ 11:30:41 (GMT) SyMBA was originally developed to be a high-throughput data archive for the data created at CISBAN at Newcastle University, but is now a project applicable for many in the biology & bioinformatics community. New developers are always welcome. SyMBA is a data and metadata archive that is based on the Functional Genomics Object Model(FuGE) and which archives, stores, and retrieves raw high-t... 0 shared items \| 0 announcements Members (9): Allyson Lister Elh... Abh... Aida Aniraj Suza Adam Dswan Neil Wipat Frank Gibson Tags: bioinformatics \| data integration \| database \| fuge \| open-source \| software \| sourceforge \| systems biology	View
Administrator: Marco Roos	e-(bio)science tool group Created: Tuesday 03 June 2008 @ 09:46:58 (GMT) Group for sharing bioinformatics tools that can enhance life science research. 3 shared items \| 0 announcements Members (4): Marco Roos M. Scott Marshall Katy Wolstencroft Morris Swertz Tags: bioinformatics \| e-science \| support	View
Administrator: Marco Roos	CWA users Unique name: CWA_Users Created: Tuesday 01 September 2009 @ 16:35:48 (GMT) Group for (potential) users of the Concept Web. See below for information on CWA taken from the Concept Web Alliance Blog. Also see other CWA groups here on myExperiment. Please request to join this group if you are (i) a scientist working in application fields such as life science, (ii) interested in computer support for sharing knowledge between (computational) experiments and between scie... 1 shared item \| 0 announcements Members (8): Marco Roos Ara... Mat... Christine Chichester Franck Tanoh Katy Wolstencroft Bla... Peter 't Hoen Tags: bioinformatics \| semantic_web \| utility	View
Administrator: Rob Hooft	NBIC Central Engineering Team Unique name: c Created: Friday 11 September 2009 @ 08:21:17 (GMT) The software production factory for NBIC, making tools developed in academic environments available to a larger audience 1 shared item \| 0 announcements Members (4): Rob Hooft Hailiang (Leon) Mei Bharat Singh Dmitry Katsubo Tags: bioinformatics \| NBIC \| programming	View
Administrator: Andrew David King	Baywatch Solutions Unique name: teambncl Created: Wednesday 10 March 2010 @ 18:39:50 (GMT) MyExperiment Group for the Team Baywatch (Solutions). Newcastle University, 2010 MSc Bioinformatics e-Science Group B. 2010 Prize Winners!!! 10 shared items \| 1 announcements Members (6): Andrew David King Aks... Haakon berven Fergus Monica Bhaskar Peter Hebden Tags: bioinformatics \| csc8308 \| e-science \| msc \| newcastle	View
Administrator: Egon Willighagen	Bioclipse Unique name: bioclipse Created: Monday 13 September 2010 @ 10:29:24 (GMT) Group around Bioclipse Scripting Language workflows. 2 shared items \| 0 announcements Members (6): Egon Willighagen Christoph Steinbeck Abh... De maas htt... jonalv Tags: bioclipse \| bioinformatics \| cheminformatics \| chemistry	View
Administrator: Katy Wolstencroft	Bonn eScience Workshop Created: Wednesday 16 March 2011 @ 10:43:40 (GMT) This group contains workflows and other resources for the Bonn e-Science workshop. Use this space for sharing with other members of the group. Finished workflow 'solutions' will also be posted here as the course progresses 32 shared items \| 0 announcements Members (14): Katy Wolstencroft Jane Mabey Gilsenan Mun... Banu Sonja Holl Bot... Sudeep Sahadevan Naser Harsha gurulingappa Dong Kathrin Klee Fabian Hoffmann Heiko Schoof Paul Fisher Tags: bioinformatics \| e-science \| functional genomics \| tutorial	View
Administrator: Alan Williams	BioVeL Unique name: biovel Created: Saturday 06 August 2011 @ 15:38:58 (GMT) Group for sharing workflows relating to BioVeL - Biodiversity Virtual e-Laboratory - FP7-283359 BioVeL For more information visit http://www.biovel.eu/ 18 shared items \| 1 announcements Members (40): Alan Williams Abraham Nieva Vassilis Protonotarios Oskar Kindvall Khalid Bamdad Dashtban Daniel Bolgheroni Kar... regiov Miki Kertész Yde... Norman Morrison Vhe... Dora Krasser Che... Sar... Xlrfrb Pasquale Notarangelo Ferenc HORVATH Ger... Maria Paula Balcazar-Vargas Antonio Fernandez Jon Giddy Pai... Vic... Robert Kulawik Zoltan BARCZA Katy Wolstencroft Hans Carole Goble Saa... Bio... Gue... Renzo Alex Hardisty Giacinto Donvito Robert Haines Ian Dunlop Shoaib Sufi David Withers Tags: biodiversity \| bioinformatics \| biovel Latest announcement:: This is not the workshop group!	View

Files (11)

Uploader: Paul Fisher	A Taverna Users Guide Created: 04/08/08 @ 17:40:21 Credits: Paul Fisher Katy Wolstencroft Franck Tanoh License: Creative Commons Attribution-Share Alike 3.0 Unported License No description File type: PowerPoint presentation Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 89 times \| Downloaded: 109 times Tags: bioinformatics \| microarray \| mining \| neuroscience \| newcastle \| sleeping sickness \| summary \| web services	View Download
Uploader: Suza Adam	LIFEsparks biotechnology network Created: 19/10/08 @ 11:05:10 \| Last updated: 19/10/08 @ 11:12:58 Credits: Suza Adam License: Creative Commons Attribution-Share Alike 3.0 Unported License The LIFEsparks biopartnering social forum aims to boost the commercial success of Southern African initiatives and start-up companies focused the life sciences sector (biotechnology and medical devices), vis-a-vis allowing participants to share ideas, knowledge and to present their business and or investment opportunities to potential partners and funders. File type: JPEG image Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 60 times \| Downloaded: 28 times Tags: africa \| agricultural biotechnology \| animal biotechnology \| biofuels \| bioinformatics \| biopartnering \| biotech funding \| biotech investment \| biotech startup \| biotechnology \| bloemfontein \| cape town \| cell therapy \| clinical trails \| clinical trials \| diagnostics \| drug development \| durban \| environmental biotechnology \| escience \| food technology \| forest biotechnology \| green plastics \| industrial sustainability \| johannesburg \| life sciences \| medical devices \| microarray \| nanobiotechnology \| personalised medicine \| pharmacology \| phytopharma \| pretoria \| professional network \| projects \| r&d \| rapiddiscovery.biz \| rapidremedial.biz \| research \| social media \| sosial network \| south africa \| suza adam \| therapeutics \| vaccines \| venture capital	View Download
Uploader: Felicity	Popfly Blocks for Protein Characteristics and Prediction Mashup 3 Created: 27/11/08 @ 10:20:35 \| Last updated: 01/12/08 @ 07:11:27 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License Popfly blocks for Protein Characteristics and Prediction Mashup 3. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Characteristics%20and%20Prediction%203 File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 49 times \| Downloaded: 17 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Felicity	Popfly Blocks for Protein Characteristics and Prediction Mashup 2 Created: 27/11/08 @ 10:18:47 \| Last updated: 01/12/08 @ 07:12:41 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License Popfly blocks for Protein Characteristics and Prediction Mashup 2. The mashup can be viewed at: http://www.popfly.com/users/fsn/Protein%20Characteristics%20and%20Prediction%202 File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 19 times \| Downloaded: 12 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Felicity	Popfly Blocks for Protein Characteristics and Prediction Mashup 1 Created: 27/11/08 @ 10:17:41 \| Last updated: 01/12/08 @ 07:13:40 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License Popfly blocks for Protein Characteristics and Prediction Mashup 1. The mashup can be viewed at: http://www.popfly.com/users/fsn/Protein%20Characteristics%20and%20Prediction%201 File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 21 times \| Downloaded: 12 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Felicity	Popfly Blocks for Protein Characteristics Mashup 1 Created: 27/11/08 @ 10:11:14 \| Last updated: 01/12/08 @ 07:14:32 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License Popfly blocks for Protein Characteristics Mashup 1. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Characteristics%20Mashup%201 File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 22 times \| Downloaded: 10 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Felicity	Popfly Blocks for Protein Prediction Mashup 1 Created: 27/11/08 @ 10:13:29 \| Last updated: 01/12/08 @ 07:15:28 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License Popfly blocks for Protein Prediction Mashup 1. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Prediction%20Mashup%201 File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 21 times \| Downloaded: 18 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Felicity	Popfly Blocks for Protein Prediction Mashup 2 Created: 27/11/08 @ 10:15:10 \| Last updated: 01/12/08 @ 07:16:18 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License Popfly blocks for Protein Prediction Mashup 2. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Prediction%20Mashup%201 File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 19 times \| Downloaded: 12 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Felicity	Protein Analysis Popfly Blocks Created: 27/11/08 @ 10:03:04 \| Last updated: 01/12/08 @ 07:17:33 Credits: Felicity License: Creative Commons Attribution-Share Alike 3.0 Unported License A zip file containing Popfly blocks for protein analysis. It also includes a file explaining the function of each block as well as a list of mashups in which these blocks have been used. File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 28 times \| Downloaded: 13 times Tags: bioinformatics \| mashups \| protein	View Download
Uploader: Barend	The general plan and guidelines for BioAssist from October 2009-? Created: 26/10/09 @ 10:15:03 Credits: Barend License: Creative Commons Attribution-Share Alike 3.0 Unported License This document has been accepted at the NBIC management team meeting of 22 October 2009, and will serve as ageneral guideline to run the BioAssist program of NBIC. It might be a good idea to read the short document before you contact BioAssist for support in the scope of your 'code' or 'content' interests. Barend Mons File type: application/x-download Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 18 times \| Downloaded: 15 times Tags: bioinformatics \| management \| NBIC \| software engineering \| support	View Download
Uploader: Konstantin Kozlov	ProStack Screencast: Segmentation of Images of Gene Expression Patterns Created: 20/05/10 @ 19:48:40 Credits: Konstantin Kozlov License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License ProStack (Processing of Stacks) is a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. This video demonstrates the workflow for extraction of quantitative information on gene expression from confocal images. ProStack home page: urchin.spbcas.ru/downloads/ProStack/ProStack.htm Download:sourceforge.net/projects/prostack/ File type: AVI video Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 7 times \| Downloaded: 6 times Tags: bioinformatics \| gene expression \| image processing \| prostack \| segmentation \| workflow	View Download