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Items tagged with "bioinformatics" (69)

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Network-member metabolomics

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

Data analysis and bioinformatics of metabolomic studies

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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.

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Network-member BioAssist_NL

Unique name: bioassist_nl Created: Wednesday 01 August 2007 @ 13:05:51 (BST)

Introduction ------------ BioAssist[1], organised by the Dutch 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]. [1]: http://www.nbic.nl/support/BioAssist [2]: http:/...

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Network-member SyMBA: Systems and Molecular Biology Data and Metadata Archive

Unique name: symba Created: Wednesday 12 September 2007 @ 11:30:41 (BST)

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...

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Network-member e-(bio)science tool group

Created: Tuesday 03 June 2008 @ 09:46:58 (BST)

Group for sharing bioinformatics tools that can enhance life science research.

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Blob A Taverna Users Guide

Created: 04/08/08 @ 17:40:21 | Updated: 04/08/08 @ 17:40:21

Credits: User Paul Fisher User Katy Wolstencroft User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

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File type: application/vnd.ms-powerpoint

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Workflows (63)

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Workflow EBI InterProScan (v2)

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

License: Creative Commons Attribution-NoDerivs 3.0 License

Ebi_interproscan_2846
EBI InterProScan. Stop fannying around with BLAST and use InterProScan instead.

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Genome annotation pipeline demonstrator workflow for Nucleic Acids Research (v2)

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

License: Creative Commons Attribution-NoDerivs 3.0 License

Genome_annotation_pipeline_demonstrator_workflow_for_nucleic_acids_research_26962
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

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Workflow BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:06 | Updated: 13/11/07 @ 16:14:48

License: Creative Commons Attribution-NoDerivs 3.0 License

Blastp_with_simplified_results_returned_28648
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.

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Simpliy a BLAST text file (v2)

Created: 03/10/07 @ 18:36:06 | Updated: 13/11/07 @ 16:28:07

License: Creative Commons Attribution-NoDerivs 3.0 License

Simpliy_a_blast_text_file_23463
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

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Workflow BLAST using DDBJ service (v2)

Created: 03/10/07 @ 18:36:06 | Updated: 13/11/07 @ 16:13:48

License: Creative Commons Attribution-NoDerivs 3.0 License

Blast_using_ddbj_service_29247
Perform a sequence similarity search using the BLAsT algorithm through the DDBJ web service

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:12 | Updated: 06/03/08 @ 17:01:32

License: Creative Commons Attribution-NoDerivs 3.0 License

Blastp_with_simplified_results_returned_14277
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

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Workflow EBI NCBI Blast (v2)

Created: 03/10/07 @ 18:36:22 | Updated: 03/10/07 @ 18:36:22

License: Creative Commons Attribution-NoDerivs 3.0 License

Ebi_ncbi_29268
EBI NCBI Blast

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Example of a conditional execution workflow (v2)

Created: 03/10/07 @ 18:36:30 | Updated: 27/01/08 @ 21:09:41

License: Creative Commons Attribution-NoDerivs 3.0 License

Example_of_a_conditional_execution_workflow_9051
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: 4 | Citations: 0

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Workflow Multiple Blastp (v2)

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

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 License

Multiple_blastp_7288_2
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: 0 | Citations: 0

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Workflow DataBiNS - Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs (v2)

Created: 04/12/07 @ 23:43:01 | Updated: 04/12/07 @ 23:45:25

Credits: User Fong Chun Chan

License: Creative Commons Attribution-Share Alike 3.0 License

Databins_with_kegg_pathways_20321_2
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Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BiomartAndEMBOSSAnalysis (v2)

Created: 05/03/08 @ 14:01:16 | Updated: 27/03/08 @ 12:14:09

License: Creative Commons Attribution 3.0 License

Biomartandembossanalysis_32163_2
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: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Fetch Dragon images from BioMoby (v2)

Created: 05/03/08 @ 14:09:35 | Updated: 25/03/08 @ 14:41:59

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Fetch_dragon_images_from_biomoby_1077_2
Fetch images and annotations of snapdragons

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Retrieve sequence in EMBL format (v2)

Created: 05/03/08 @ 14:11:18 | Updated: 31/03/08 @ 15:19:06

Credits: User Franck Tanoh User Tomoinn

License: Creative Commons Attribution 3.0 License

Retrieve_sequence_in_embl_format_22581_2
This workflow retrieves a sequence associated with its features in embl format given a sequence id.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Retrieve SNPs from regions around known genes (v1)

Created: 05/03/08 @ 14:12:32 | Updated: 29/07/08 @ 15:18:38

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Retrieve_snps_from_regions_around_known_genes_12046_1
Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Fetch PDB flatfile from RCSB server (v1)

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

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 License

Fetch_pdb_flatfile_from_rcsb_server_27474_1
Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow GBSeq test (v2)

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

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 License

Gbseq_test_23328_2
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

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Workflow EBI_InterProScan (v2)

Created: 31/05/08 @ 11:38:57 | Updated: 25/06/08 @ 06:30:59

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_interproscan_16782_2
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow EBI_InterProScan_with_prompts (v1)

Created: 31/05/08 @ 11:40:34 | Updated: 31/05/08 @ 11:40:34

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 License

Ebi_interproscan_with_prompts_27955_1
Run an InterProScan analysis using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). This workflow wraps the EBI_InterProScan workflow to provide a basic user interface which prompts for the required inputs: protien sequence and user e-mail. Other parameters are allowed to default.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow EBI_ClustalW2_phylogentic_tree (v1)

Created: 31/05/08 @ 13:07:34 | Updated: 31/05/08 @ 13:07:34

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_clustalw2_phylogentic_tree_28905_1
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: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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