Workflows

XPath Pubmed Ids (2)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: Paul Fisher

Attributions: XPath Pubmed Ids

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes found from a set of differentially expressed probestes, in Human, Homo sapiens. The workflow requires an input human affymetrix probeset identifiers. 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 pathway database.

Created: 2011-03-24 | Last updated: 2011-03-24

Credits: Paul Fisher

Extract unique proteins from blast results (4)

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The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.This workflow allows you to configure a BioMart query to fetch sequ...

Created: 2011-03-24 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Attributions: Parse unique proteins from Blast file

Drug Re-Purposing Workflow (6)

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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...

Created: 2011-03-25 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

ADR-S (2)

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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...

Created: 2011-03-28 | Last updated: 2011-08-09

Credits: Anna Bauer-Mehren

Threshold BLAST results (2)

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Thresholds tab-delimited BLAST results to a certain percent identity.

Created: 2011-03-28 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

NCBI Gi to Kegg Pathways (1)

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"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."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.

Created: 2011-03-28 | Last updated: 2011-03-28

Credits: Alibukhari

KEGG Pathways and Additional Information f... (2)

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Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

Created: 2011-03-29 | Last updated: 2011-03-30

Credits: Morgan Taschuk

Attributions: extract_uniprot_embl_gi.xml

gene subset extract (1)

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This workflow functions for matching a set of genes as a part of whole gene data set and aim to extract the subset as a separate list.

Created: 2011-03-29 | Last updated: 2011-03-29

Credits: Naser Paul Fisher

Print Analysis Information to HTML (2)

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Takes in a lot of parameters in order to construct an HTML header to display the information.

Created: 2011-03-29 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Compile Protein FASTA from Target to Drug ... (1)

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Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target.

Created: 2011-03-30 | Last updated: 2011-03-30

Credits: Morgan Taschuk Andrewsmeaton

Vaccine Targets Workflow (3)

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Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: T...

Created: 2011-03-30 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Diabetes_workflow (1)

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No description

Created: 2011-03-31 | Last updated: 2011-03-31

Credits: Munasultan Banu

Diabetes Gene and SNP identification (1)

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Created: 2011-03-31 | Last updated: 2011-03-31

IDDM Workflow (1)

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Created: 2011-03-31 | Last updated: 2011-03-31

Credits: Banu Munasultan

Vaccine drug targeting (1)

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Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Matthieu Alexncl Kristiangardner123 Paulshreeve Matt Collison

Diabetes patways and SNPs (1)

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Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Sudeep Sahadevan

Drug Repurposing Targets (1)

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No description

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Matthieu Alexncl Kristiangardner123 Paulshreeve Matt Collison

IDDM_Workflow (1)

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No description

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Munasultan

Print Protein Information to HTML (1)

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Takes in a lot of parameters in order to construct an HTML table to display the information.

Created: 2011-04-01

Credits: Morgan Taschuk

UniProt to Gene Ontology (1)

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Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from Gene Ontology and outputs it in text format.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Use UniProt to retrieve InterPro data (1)

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Used parsed Uniprot results (see workflowUsed parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from InterPro.

Created: 2011-04-01

Credits: Morgan Taschuk

Parsed UniProt to PubMed (1)

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Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Quality control processing of GEO datasets (2)

The workflow performs a quality control process on gene expression data sets stored in the Gene Expression Omnibus database. The QC process is performed using Bioconductor R packages. A variety of statistics are produced by the workflow including a diagnostic plot from snm normalisation and nucleotide composition bias.

Created: 2011-04-06 | Last updated: 2011-04-11

Credits: Peter Li Bhmecham

Blast Report from ID (1)

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This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced...

Created: 2011-04-07 | Last updated: 2011-04-07

Credits: Hectorj2f