Gb User: Paul Fisher

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Name: Paul Fisher

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

Last seen: Monday 29 June 2009 @ 17:18:48 (BST)

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

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

Location: Manchester, United Kingdom

40 Friends

6 Groups (admin)

11 Groups (member)

1 Blogs

3 Packs

22 Files

82 Workflows

2 Favourites

Paul Fisher has been credited 166 times

Paul Fisher has an average rating of:

4.2 / 5

(17 ratings in total)

for their items

I am a fourth year PhD student. My research focuses on using QTL and microarray data, looking at the level of biological pathway, to identify novel links between Genotype and Phenotype. I am conducting these correlations thorugh the use of web services and workflows.

These have been tested on African Trypanosomiasis in both Cattle and mice, Lung Cancer, infection of a mouse with Trichuris muris, and Colitis / Inflammatory bowel disease.


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): 4th Year PhD Student

Organisation(s):

University of Manchester

 

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Taverna 1

Original Uploader

Workflow NCBI Gi to Kegg Pathways (v1)

Created: 08/06/09 @ 18:39:38

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Ncbi_gi_to_kegg_pathways
This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

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

Viewed: 96 times | Downloaded: 49 times

Tags (6):
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Taverna 1

Original Uploader

Workflow inchi to Chebi (v1)

Created: 22/05/09 @ 16:07:51 | Last updated: 22/05/09 @ 16:07:52

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Inchi_to_chebi
This workflow converts an inchi string to a chebi id.

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

Viewed: 8 times | Downloaded: 1 time

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Taverna 1

Original Uploader

Workflow Pathways and Gene annotations for Arabidopsis affy data (v2)

Created: 05/03/09 @ 15:15:59 | Last updated: 06/03/09 @ 17:18:14

Credits: User Paul Fisher User Peter Li

Attributions: Workflow Mouse Pathways and Gene annotations for QTL Phenotype

License: Creative Commons Attribution-NoDerivs 3.0 License

Pathways_and_gene_annotations_for_arabidopsis_affy_data
This workflow searches for genes obtained from affymetrix probeset identifiers. 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 pathway database.

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

Viewed: 152 times | Downloaded: 1 time

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Taverna 1

Original Uploader

Workflow Get Kegg Gene information (v2)

Created: 05/01/09 @ 13:20:34 | Last updated: 26/01/09 @ 18:06:13

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Get_kegg_gene_information
This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

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

Viewed: 158 times | Downloaded: 58 times

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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: 271 times | Downloaded: 77 times

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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: 334 times | Downloaded: 91 times

Tags (10):
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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: 161 times | Downloaded: 4 times

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Taverna 1

Original Uploader

Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:54

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 ch...

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

Viewed: 155 times | Downloaded: 3 times

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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: 143 times | Downloaded: 29 times

Tags (2):
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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: 241 times | Downloaded: 4 times

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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: 50 times | Downloaded: 40 times

Tags (1):
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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: 149 times | Downloaded: 76 times

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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: 224 times | Downloaded: 90 times

Tags (5):
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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: 138 times | Downloaded: 80 times

Tags (11):
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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: 157 times | Downloaded: 53 times

Tags (6):
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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: 3 | Citations: 1

Viewed: 235 times | Downloaded: 69 times

Tags (18):
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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: 36 times | Downloaded: 31 times

Tags (4):
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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: 34 times | Downloaded: 24 times

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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: 21 times | Downloaded: 23 times

This Workflow has no tags!

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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: 345 times | Downloaded: 96 times

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

Viewed: 51 times | Downloaded: 24 times

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Taverna 1

Original Uploader

Workflow Entrez Gene to KEGG Pathway (v3)

Created: 03/10/07 @ 18:36:00 | Last updated: 27/02/09 @ 14:49:42

License: Creative Commons Attribution 3.0 License

Entrez_gene_to_kegg_pathway
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: 3 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 291 times | Downloaded: 157 times

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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: 27 times | Downloaded: 34 times

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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: 112 times | Downloaded: 64 times

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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: 1 | Citations: 0

Viewed: 415 times | Downloaded: 162 times

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