Gb User: Paul Fisher

108?size=160x160

Name: Paul Fisher

Joined: Thursday 26 July 2007 @ 16:46:52 (BST)

Last seen: Thursday 20 November 2008 @ 16:59:04 (GMT)

Email (public): fisherp [at] cs.manchester.ac.uk

Website: http://www.cs.man.ac.uk/~fisherp/

Location: Manchester, United Kingdom

37 Friends

2 Groups (admin)

10 Groups (member)

1 Blogs

2 Packs

4 Files

22 Workflows

1 Favourite

Paul Fisher has been credited 86 times

Paul Fisher has an average rating of:

4.2 / 5

(17 ratings in total)

for their items

I am a third year PhD student. Our research focuses on using QTL and microarray data, looking at the level of biological pathway, to identify novel links between Genotype and Phenotype.  


Other contact details:

Not specified

Interests:

Workflows
QTL analysis
Microarrays
Biological pathway analysis
In silico automation
Protein 3D structure prediction
Disease gene identification

Field/Industry: Bioinformatics

Occupation/Role(s): 3rd Year PhD Student

Organisation(s):

University of Manchester

 

Note: some items may not be visible to you, due to viewing permissions.


Contents (click to expand/contract)
Taverna 1

Original Uploader

Workflow Retrieve Protein Sequence (v1)

Created: 30/07/08 @ 16:36:56

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieve_protein_sequence_31678_1
Retrieves a protein sequence in Fasta format from Genbank

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

Viewed: 396 times | Downloaded: 229 times

Tags (5):
Show View Download Download (v1)

Taverna 1

Original Uploader

Workflow Pathway to Pubmed (v2)

Created: 09/03/08 @ 15:03:12 | Last updated: 08/07/08 @ 12:13:06

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Pathway_to_pubmed_25676_2
This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

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

Viewed: 769 times | Downloaded: 532 times

Tags (10):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Human Pathways from Diff Expressed Genes (v1)

Created: 08/02/08 @ 14:30:18 | Last updated: 08/02/08 @ 14:30:19

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Human_pathways_from_diff_expressed_genes_4391_1
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data

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

Viewed: 576 times | Downloaded: 6 times

Tags (17):
Show View

Taverna 1

Original Uploader

Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 14/05/08 @ 15:43:23

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

Microarray_cel_file_to_candidate_pathways_1844_2
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

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

Viewed: 792 times | Downloaded: 2 times

Tags (17):
Show View

Taverna 1

Original Uploader

Workflow Add Mesh String to Biological Process (v2)

Created: 03/10/07 @ 18:36:28

License: Creative Commons Attribution-NoDerivs 3.0 License

Add_mesh_string_to_biological_process_12549
No description

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

Viewed: 1810 times | Downloaded: 612 times

Tags (2):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Perfrom a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Last updated: 02/08/08 @ 14:35:11

License: Creative Commons Attribution-NoDerivs 3.0 License

Perfrom_a_text_based_search_through_pubmed_2447_3
This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Rating: 3.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 959 times | Downloaded: 30 times

Tags (7):
Show View

Taverna 1

Original Uploader

Workflow Parse UniProt text file (v2)

Created: 03/10/07 @ 18:36:08 | Last updated: 13/11/07 @ 16:08:44

License: Creative Commons Attribution-NoDerivs 3.0 License

Parse_uniprot_text_file_9226
This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers.

Rating: 3.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 609 times | Downloaded: 590 times

Tags (1):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Perform a search through NCBI eUtils eSearch (v2)

Created: 03/10/07 @ 18:36:07 | Last updated: 13/11/07 @ 16:11:50

License: Creative Commons Attribution-NoDerivs 3.0 License

Perform_a_search_through_ncbi_eutils_esearch_8923
This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term

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

Viewed: 837 times | Downloaded: 716 times

Tags (4):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow BLAST using DDBJ service (v2)

Created: 03/10/07 @ 18:36:06 | Last 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

Viewed: 973 times | Downloaded: 755 times

Tags (5):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Simpliy a BLAST text file (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 13/11/07 @ 16:28:08

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

Viewed: 929 times | Downloaded: 705 times

Tags (11):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:06 | Last 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

Viewed: 756 times | Downloaded: 729 times

Tags (6):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Last updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_from_diff_expressed_genes_22895_3
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

Viewed: 1153 times | Downloaded: 1072 times

Tags (19):
Show View Download Download (v3)

Taverna 1

Original Uploader

Workflow Remove null values (v2)

Created: 03/10/07 @ 18:36:05 | Last updated: 13/11/07 @ 16:20:42

License: Creative Commons Attribution-NoDerivs 3.0 License

Remove_null_values_27982
This workflow removes any null values from a list of strings

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

Viewed: 703 times | Downloaded: 613 times

Tags (4):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Remove duplicate strings (v2)

Created: 03/10/07 @ 18:36:03 | Last updated: 13/11/07 @ 16:25:42

License: Creative Commons Attribution-NoDerivs 3.0 License

Remove_duplicate_strings_10375
This workflow takes in two list of strings and then concatenates them together. Any duplicates that are present are then removed, and the resulting file is returned back to the user.

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 688 times | Downloaded: 603 times

Tags (5):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Back translate a protein sequence into a dna sequence (v2)

Created: 03/10/07 @ 18:36:03 | Last updated: 13/11/07 @ 16:17:30

License: Creative Commons Attribution-NoDerivs 3.0 License

Back_translate_a_protein_sequence_into_a_dna_sequence_19857
This workflow back translates a protein sequence into a DNA sequence.

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

Viewed: 465 times | Downloaded: 436 times

This Workflow has no tags!

 Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Mouse Pathways and Gene annotations for QTL Phenotype (v3)

Created: 03/10/07 @ 18:36:02 | Last updated: 20/02/08 @ 16:05:45

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_and_gene_annotations_for_qtl_phenotype_28303_3
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Rating: 4.5 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 1

Viewed: 1431 times | Downloaded: 1448 times

Tags (12):
Show View Download Download (v3)

Taverna 1

Original Uploader

Workflow Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype (v2)

Created: 03/10/07 @ 18:36:00 | Last updated: 20/02/08 @ 16:03:59

License: Creative Commons Attribution-NoDerivs 3.0 License

Pathways_and_gene_annotations_for_qtl_phenotype_25510
No description

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

Viewed: 609 times | Downloaded: 657 times

Tags (1):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Entrez Gene to KEGG Pathway (v2)

Created: 03/10/07 @ 18:36:00 | Last updated: 13/11/07 @ 16:16:10

License: Creative Commons Attribution 3.0 License

Entrez_gene_to_kegg_pathway_7493
This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.7 / 5 (3 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1587 times | Downloaded: 981 times

Tags (8):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow Transcribe a DNA sequence into an RNA sequence (v2)

Created: 03/10/07 @ 18:35:58 | Last updated: 13/11/07 @ 16:16:54

License: Creative Commons Attribution-NoDerivs 3.0 License

Transcribe_a_dna_sequence_into_an_rna_sequence_27205
This workflow transcribes a DNA sequence into an RNA sequence

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

Viewed: 627 times | Downloaded: 601 times

Tags (4):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow KEGG pathways common to both QTL and microarray based investigations (v2)

Created: 03/10/07 @ 18:35:58 | Last updated: 13/11/07 @ 16:22:14

License: Creative Commons Attribution-NoDerivs 3.0 License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations_27627
This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype

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

Viewed: 888 times | Downloaded: 731 times

Tags (11):
Show View Download Download (v2)

Taverna 1

Original Uploader

Workflow HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Last updated: 04/04/08 @ 12:14:21

License: Creative Commons Attribution-NoDerivs 3.0 License

Microarray_cel_file_to_candidate_pathways_17032_4
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Rating: 5.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1747 times | Downloaded: 1636 times

Tags (12):
Show View Download Download (v4)

New/Upload

Log in / Register

Username or Email:

Password:

Remember me:

OR

Use OpenID:


(eg: name.myopenid.com)

Need an account?
Click here to register

Forgot Password?

Popular Tags
25 tags
[All Tags]

Copyright (c) 2007 - 2008 The University of Manchester and University of Southampton

Front Page

Home

About Us

Mailing List

Contact Us

API

Publications

Taverna Workflow Workbench

Google Coop Search


Invite people to myExperiment

myGrid

BioCatalogue

JISC

Microsoft

Powered by:

Rails

Icons:
Silk icon set 1.3