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Items tagged with "bioinformatics" (129)

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Groups (12)
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Network-member metabolomics


Created: Thursday 29 November 2007 @ 11:50:47 (GMT)

Data analysis and bioinformatics of metabolomic studies

2 shared items   |   0 announcements

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Network-member 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

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Network-member 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

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Network-member SyMBA: Systems and Molecular Biology Data ...

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

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Network-member 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

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Network-member 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

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Network-member 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

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Network-member 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

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Network-member Bioclipse

Unique name: bioclipse
Created: Monday 13 September 2010 @ 10:29:24 (GMT)

 Group around Bioclipse Scripting Language workflows.

2 shared items   |   0 announcements

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Network-member 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

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Network-member 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/    

22 shared items   |   1 announcements

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Latest announcement:: This is not the workshop group!

Network-member Bonn workshop 2012


Created: Wednesday 29 August 2012 @ 11:39:39 (GMT)

This group is a shared space for material related to the "in silico experimentation using e-labs" at Bonn University, 3-5 Spetember 2012

19 shared items   |   0 announcements

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Files (11)
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Blob LIFEsparks biotechnology network

Created: 19/10/08 @ 11:05:10 | Last updated: 19/10/08 @ 11:12:58

Credits: User 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

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Blob Popfly Blocks for Protein Characteristics and Predic...

Created: 27/11/08 @ 10:20:35 | Last updated: 01/12/08 @ 07:11:27

Credits: User 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: 52 times | Downloaded: 18 times

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Blob Popfly Blocks for Protein Characteristics and Predic...

Created: 27/11/08 @ 10:18:47 | Last updated: 01/12/08 @ 07:12:41

Credits: User 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: 22 times | Downloaded: 13 times

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Blob Popfly Blocks for Protein Characteristics and Predic...

Created: 27/11/08 @ 10:17:41 | Last updated: 01/12/08 @ 07:13:40

Credits: User 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: 26 times | Downloaded: 13 times

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Blob Popfly Blocks for Protein Characteristics Mashup 1

Created: 27/11/08 @ 10:11:14 | Last updated: 01/12/08 @ 07:14:32

Credits: User 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: 25 times | Downloaded: 11 times

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Blob Popfly Blocks for Protein Prediction Mashup 1

Created: 27/11/08 @ 10:13:29 | Last updated: 01/12/08 @ 07:15:28

Credits: User 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

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Blob Popfly Blocks for Protein Prediction Mashup 2

Created: 27/11/08 @ 10:15:10 | Last updated: 01/12/08 @ 07:16:18

Credits: User 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: 22 times | Downloaded: 13 times

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Blob Protein Analysis Popfly Blocks

Created: 27/11/08 @ 10:03:04 | Last updated: 01/12/08 @ 07:17:33

Credits: User 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: 32 times | Downloaded: 14 times

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Blob The general plan and guidelines for BioAssist from O...

Created: 26/10/09 @ 10:15:03

Credits: User 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

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Blob ProStack Screencast: Segmentation of Images of Gene ...

Created: 20/05/10 @ 19:48:40

Credits: User 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: 16 times | Downloaded: 7 times

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Workflows (101)
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Workflow EBI InterProScan (2)

Created: 03/10/07 @ 18:35:46

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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: 523 times | Downloaded: 154 times

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Workflow Genome annotation pipeline demonstrator wo... (2)

Created: 03/10/07 @ 18:35:47

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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: 592 times | Downloaded: 178 times

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Workflow BLASTP with simplified results returned (2)

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

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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: 344 times | Downloaded: 115 times

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Workflow Simplify a BLAST text file (2)

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

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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: 392 times | Downloaded: 151 times

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Workflow BLAST using DDBJ service (2)

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

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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: 640 times | Downloaded: 234 times

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Workflow BLASTP with simplified results returned (2)

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

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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: 240 times | Downloaded: 64 times

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Workflow Example of a conditional execution workflow (2)

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

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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: 128 times | Downloaded: 58 times

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Workflow Multiple Blastp (2)

Created: 20/11/07 @ 16:58:38 | Last updated: 10/01/08 @ 12:09:38

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 517 times | Downloaded: 165 times

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Workflow BiomartAndEMBOSSAnalysis (4)

Created: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 3.0 Unported License

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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: 1256 times | Downloaded: 421 times

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Workflow Fetch Dragon images from BioMoby (3)

Created: 05/03/08 @ 14:09:35 | Last updated: 14/07/10 @ 16:46:37

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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Fetch images and annotations of snapdragons

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 326 times | Downloaded: 112 times

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Workflow Retrieve sequence in EMBL format (3)

Created: 17/06/09 @ 16:51:32

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

License: Creative Commons Attribution 3.0 Unported License

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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: 330 times | Downloaded: 108 times

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Workflow Fetch PDB flatfile from RCSB server (1)

Created: 05/03/08 @ 14:13:24 | Last updated: 31/03/08 @ 16:01:41

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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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: 307 times | Downloaded: 121 times

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Workflow GBSeq test (2)

Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

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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: 249 times | Downloaded: 93 times

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Workflow EBI_InterProScan (3)

Created: 26/10/08 @ 20:33:34 | Last updated: 01/04/11 @ 08:52:28

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 1444 times | Downloaded: 401 times

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Workflow EBI_InterProScan_with_prompts (1)

Created: 31/05/08 @ 11:40:34 | Last updated: 01/04/11 @ 08:57:45

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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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: 88 times | Downloaded: 51 times

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Workflow EBI_ClustalW2_phylogentic_tree (2)

Created: 07/04/09 @ 20:09:32

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 311 times | Downloaded: 115 times

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Original Uploader

Workflow EBI_ClustalW_alignment_tree (2)

Created: 31/05/08 @ 13:53:04 | Last updated: 03/12/10 @ 13:34:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree

License: Creative Commons Attribution 3.0 Unported License

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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: 194 times | Downloaded: 89 times

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Workflow EBI_blastpgp_PSI-BLAST (1)

Created: 31/05/08 @ 14:39:22

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 133 times | Downloaded: 65 times

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Workflow EBI_dbfetch_fetchBatch (1)

Created: 31/05/08 @ 20:59:46

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 111 times | Downloaded: 73 times

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Workflow Protein_search_fetch_align_tree (2)

Created: 07/04/09 @ 20:13:19

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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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: 463 times | Downloaded: 154 times

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Workflow EBI_Phobius (2)

Created: 01/06/08 @ 11:08:45 | Last updated: 02/06/08 @ 21:39:06

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 118 times | Downloaded: 66 times

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Original Uploader

Workflow EBI_InterProScan_tmhmm_signalp (4)

Created: 26/10/08 @ 20:50:10 | Last updated: 01/04/11 @ 08:56:37

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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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: 219 times | Downloaded: 89 times

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Original Uploader

Workflow Protein_alignment_transmembrane (1)

Created: 01/06/08 @ 12:20:29

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 Unported License

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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: 208 times | Downloaded: 59 times

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Original Uploader

Workflow Sequence_or_ID (1)

Created: 01/06/08 @ 14:15:12

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 161 times | Downloaded: 69 times

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Workflow tmap_single_sequence (2)

Created: 01/06/08 @ 14:27:12 | Last updated: 02/06/08 @ 21:38:13

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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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: 147 times | Downloaded: 45 times

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Original Uploader

Workflow Protein_transmembrane_prediction (2)

Created: 26/10/08 @ 21:16:10 | Last updated: 01/04/11 @ 08:57:10

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan_tmhmm_signalp Workflow EBI_Phobius Workflow tmap_single_sequence

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_ClustalW2 (2)

Created: 07/04/09 @ 20:06:03 | Last updated: 06/12/10 @ 11:00:19

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_Kalign (1)

Created: 02/06/08 @ 21:28:56 | Last updated: 06/12/10 @ 11:39:52

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_WU-BLAST (1)

Created: 30/05/08 @ 22:47:18 | Last updated: 06/12/10 @ 10:51:04

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.  

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Workflow EBI WU-BLAST with program and database sel... (3)

Created: 04/07/09 @ 11:39:54 | Last updated: 06/12/10 @ 10:56:44

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_FASTA (1)

Created: 30/05/08 @ 23:50:46 | Last updated: 06/12/10 @ 10:52:25

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.  

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Workflow EBI FASTA with prompts (3)

Created: 30/05/08 @ 23:53:16 | Last updated: 06/12/10 @ 10:53:23

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_NCBI_BLAST (1)

Created: 31/05/08 @ 08:38:46 | Last updated: 06/12/10 @ 10:54:16

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_NCBI_BLAST_with_prompts (1)

Created: 31/05/08 @ 08:40:29 | Last updated: 06/12/10 @ 10:55:09

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_MPsrch (1)

Created: 02/06/08 @ 21:49:11 | Last updated: 06/12/10 @ 10:38:42

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.  

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Workflow EBI_MAFFT (1)

Created: 03/06/08 @ 05:55:43 | Last updated: 06/12/10 @ 11:38:58

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow EBI_ScanPS (1)

Created: 03/06/08 @ 05:57:09 | Last updated: 06/12/10 @ 10:37:50

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.  

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Workflow EBI_MUSCLE (1)

Created: 03/06/08 @ 06:16:22 | Last updated: 06/12/10 @ 11:04:03

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.  

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Workflow EBI_TCoffee (1)

Created: 03/06/08 @ 06:31:37 | Last updated: 06/12/10 @ 11:02:53

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.  

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Workflow getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

Created: 05/06/08 @ 16:00:38 | Last updated: 16/06/08 @ 11:40:46

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow EBI_MaxSprout (2)

Created: 05/06/08 @ 21:44:00 | Last updated: 06/06/08 @ 05:58:16

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow Structure_or_ID (1)

Created: 06/06/08 @ 05:57:31

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow Nucleotide_ORF_translation (1)

Created: 06/06/08 @ 20:13:04

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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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).

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Workflow Fasta_string_to_fasta_list (1)

Created: 06/06/08 @ 21:41:28

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Split a string containing a set of sequences in fasta format into a list for fasta formated sequences.

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Workflow Nucleotide_InterProScan (4)

Created: 26/10/08 @ 21:10:09 | Last updated: 01/04/11 @ 08:54:21

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow EBI_Blast2InterPro (2)

Created: 26/10/08 @ 20:45:45 | Last updated: 22/08/12 @ 11:22:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST Workflow EBI_dbfetch_fetchBatch Workflow Fasta_string_to_fasta_list Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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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...

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Workflow NCBI_QBLAST (2)

Created: 07/06/08 @ 15:05:00 | Last updated: 07/06/08 @ 17:11:36

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow Sequence_or_ID_or_GI (1)

Created: 07/06/08 @ 16:58:14

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow EBI_DaliLite (1)

Created: 07/06/08 @ 17:16:37

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

Created: 08/06/08 @ 13:53:39 | Last updated: 08/06/08 @ 14:10:02

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

License: Creative Commons Attribution 3.0 Unported License

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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

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Workflow EBI_PICR_Sequence_to_ID (1)

Created: 08/06/08 @ 14:03:07

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow EBI_dbfetch_UniParc (1)

Created: 08/06/08 @ 14:05:40

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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).

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Workflow EBI_Fetch_InterPro_Matches_UniParc (1)

Created: 08/06/08 @ 14:08:47

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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).

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Workflow EBI_CENSOR (2)

Created: 17/06/08 @ 20:42:46 | Last updated: 25/06/08 @ 06:16:03

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow tRNAscan (1)

Created: 28/06/08 @ 09:57:33

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID_or_GI

License: Creative Commons Attribution 3.0 Unported License

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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).

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Workflow EBI_OLS_TermInfo (1)

Created: 09/07/08 @ 05:36:40

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow EBI_IntAct (1)

Created: 09/07/08 @ 06:01:17

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Find protein binary interactions using the EBI's IntAct service. See http://www.ebi.ac.uk/intact/ for further details.

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Workflow Retrieve Protein Sequence (1)

Created: 30/07/08 @ 16:36:55 | Last updated: 03/12/09 @ 16:54:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

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Workflow mustang provides structural alignment of t... (3)

Created: 20/08/08 @ 14:41:21 | Last updated: 25/08/08 @ 15:40:45

Credits: User Steffen Möller

Attributions: Workflow Fetch PDB flatfile from RCSB server

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow Retrieve Single Molecule from ZINC - struc... (1)

Created: 24/08/08 @ 22:52:25 | Last updated: 25/08/08 @ 21:57:16

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow dbfetch tutorial (1)

Created: 22/09/08 @ 01:05:36

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow runFunCUT (1)

Created: 03/10/08 @ 10:54:45 | Last updated: 03/10/08 @ 11:49:17

Credits: User José Manuel Rodríguez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow Download Entries from PubChem (1)

Created: 30/03/09 @ 09:20:42 | Last updated: 30/03/09 @ 09:34:37

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow Retrieve Pathways and Compound information... (1)

Created: 30/03/09 @ 09:22:36 | Last updated: 30/03/09 @ 09:39:23

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow Search InChI in NCBI eSearch (pccompound) (1)

Created: 30/03/09 @ 09:26:25 | Last updated: 30/03/09 @ 09:47:00

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow MassBank to KEGG (1)

Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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)

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Workflow Nucleotide InterProScan for the BioExtract... (3)

Created: 16/04/09 @ 15:26:57 | Last updated: 01/07/09 @ 08:32:34

Credits: User Carol Lushbough User Hamish McWilliam

Attributions: Workflow Nucleotide_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow EBI_dbfetch_fetchData (1)

Created: 28/08/09 @ 11:45:50 | Last updated: 28/08/09 @ 11:49:08

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Sample workflow illustrating the use of the EBI's WSDbfetch service in Triana.

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Workflow EBI_dbfetch_fetchBatch (1)

Created: 28/08/09 @ 11:55:10

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Sample workflow illustrating the use of EBI's WSDbfetch service with Triana.

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Workflow Fetch Dragon images from BioMoby (1)

Created: 14/07/10 @ 16:20:46 | Last updated: 14/07/10 @ 16:20:48

Credits: User EdwardKawas User Tomoinn

Attributions: Workflow Fetch Dragon images from BioMoby

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Fetch images and annotations of snapdragons

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Workflow retrieve protein sequence and do a BLAST a... (1)

Created: 21/07/10 @ 13:10:40 | Last updated: 21/07/10 @ 13:10:41

Credits: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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  

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Workflow retrieve protein sequence and do a high sp... (1)

Created: 21/07/10 @ 13:16:00 | Last updated: 21/07/10 @ 13:23:12

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow retrieve protein sequence and do a BLAST w... (1)

Created: 21/07/10 @ 13:24:56 | Last updated: 01/09/10 @ 17:37:48

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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    

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Workflow retrieve nucleotide sequence and do a BLAS... (1)

Created: 21/07/10 @ 13:56:08 | Last updated: 21/07/10 @ 13:58:41

Credits: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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    

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Workflow retrieve nucleotide sequence and do a high... (4)

Created: 21/07/10 @ 14:08:32 | Last updated: 07/09/10 @ 10:04:55

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow retrieve nucleotide sequence and do a BLAS... (1)

Created: 21/07/10 @ 14:21:50 | Last updated: 21/07/10 @ 14:21:52

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow retrieve nucleotide sequence and do a VecS... (1)

Created: 21/07/10 @ 14:36:36 | Last updated: 01/09/10 @ 17:35:20

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow retrieve protein sequence and do a high sp... (1)

Created: 01/09/10 @ 17:16:24 | Last updated: 01/09/10 @ 17:18:45

Credits: User Lebreton

Attributions: Workflow 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

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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

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Workflow retrieve protein sequence and do a BLAST f... (1)

Created: 01/09/10 @ 17:22:14 | Last updated: 01/09/10 @ 17:22:37

Credits: User Lebreton

Attributions: Workflow retrieve protein sequence and do a BLAST and extract position from DDBJ Web services

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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  

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Workflow retrieve nucleotide sequence and do a high... (1)

Created: 01/09/10 @ 17:26:07 | Last updated: 01/09/10 @ 17:26:39

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow retrieve nucleotide sequence and do a BLAS... (1)

Created: 01/09/10 @ 17:31:29 | Last updated: 01/09/10 @ 17:33:51

Credits: User Lebreton

Attributions: Workflow retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 

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Workflow NCBI BLAST (SOAP) (1)

Created: 29/11/10 @ 20:46:58 | Last updated: 29/11/10 @ 20:47:00

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow NCBI BLAST (SOAP) (1)

Created: 29/11/10 @ 20:03:13 | Last updated: 29/11/10 @ 20:03:14

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow InterProScan (SOAP) (1)

Created: 03/12/10 @ 07:41:47 | Last updated: 03/12/10 @ 07:41:48

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow InterProScan (SOAP) (1)

Created: 03/12/10 @ 08:20:21 | Last updated: 03/12/10 @ 08:20:24

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow InterProScan (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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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.

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Workflow EMBL-EBI ClustalW2 (SOAP) (1)

Created: 06/12/10 @ 13:16:52

Attributions: Workflow EBI_ClustalW2

License: Creative Commons Attribution 3.0 Unported License

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Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

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Workflow [untitled] (1)

Created: 26/04/11 @ 14:50:37 | Last updated: 26/04/11 @ 15:04:28

Credits: User Dennis Leenheer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow Generate Atom Signatures of molecules give... (1)

Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow Scoring small molecules for metabolite lik... (2)

Created: 13/05/11 @ 17:22:28 | Last updated: 18/03/12 @ 16:41:39

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 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...

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Workflow Plotting distribution of natural product l... (1)

Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 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...

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Workflow Get names of proteins similar to RNA bindi... (1)

Created: 18/05/11 @ 15:24:56 | Last updated: 18/05/11 @ 15:39:02

Credits: User hindlem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow Download Structures from PubChem given che... (1)

Created: 24/05/11 @ 13:13:52 | Last updated: 24/05/11 @ 14:19:24

Credits: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.  

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Avatar Baj

Workflow NGS sample workflow with data (1)

Created: 24/06/11 @ 11:42:57 | Last updated: 24/06/11 @ 12:17:00

Credits: User Baj

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 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.    

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Workflow ADR-S (2)

Created: 28/03/11 @ 11:34:18 | Last updated: 09/08/11 @ 22:38:12

Credits: User Anna Bauer-Mehren

License: GNU General Public License (GPL) 2.0

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  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...

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Workflow BATWING (1)

Created: 25/08/11 @ 19:39:58 | Last updated: 25/08/11 @ 19:57:37

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow Extract Gene Sequence with Kepler (1)

Created: 05/10/11 @ 05:04:40 | Last updated: 05/10/11 @ 05:04:42

Credits: User Wdsnellg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow Match gene lists based on information in l... (7)

Created: 17/04/12 @ 08:55:46 | Last updated: 25/04/12 @ 07:54:26

Credits: User Marco Roos User Reinout van Schouwen User Eleni User Kristina Hettne Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Explain concept scores

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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[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...

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Workflow DatabaseID_to_ConceptID (4)

Created: 25/06/12 @ 20:48:28 | Last updated: 14/09/12 @ 10:03:01

Credits: User Marco Roos User Martijn Schuemie User Reinout van Schouwen Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Resources: Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ... Comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Workflow NCBI Protein Clustal Omega Alignment (1)

Created: 31/08/12 @ 19:18:55

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

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Packs (5)

Pack FunCUT package


Created: 03/10/08 @ 16:47:15 | Last updated: 03/10/08 @ 16:48:55

Input example and FunCUT workflow

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Pack 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...

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Pack 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...

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Pack 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...

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Pack 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...

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