All content

Arabidopsis thaliana QTL Analysis (1)

• Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. 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 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: 2009-07-08 | Last updated: 2009-12-14

Credits: Paul Fisher

Retrieve sequence in EMBL format (1)

• Download

This workflow retrieves a sequence associated with its features in embl format

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Retrieve sequence in EMBL format

Demonstration of configurable iteration (1)

• Download

This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes Tomoinn

Attributions: Demonstration of configurable iteration

Execute GWorkflowDL workflow using Taverna... (1)

• Download

This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench. This workflow contains all the input parameters as string constants, so it can be started right away without user inputs.

Created: 2009-06-30

Credits: Andreas Hoheisel

Attributions: Execute GWorkflowDL workflow using Taverna 2

Execute GWorkflowDL workflow using Taverna 2 (1)

• Download

This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench.

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Andreas Hoheisel

Query dbsnp, transform to HTML (1)

• Download

Created: 2009-05-21 | Last updated: 2009-05-21

Credits: PL

View Download

Towards Genotype-Phenotype Correlations

Created: 2009-04-08 13:14:54 | Last updated: 2009-08-11 14:50:01

20 items in this pack

Comments: 0 | Viewed: 314 times | Downloaded: 82 times

LINTUL crop model (1)

• Download

Created: 2009-04-01

Credits: Robert Muetzelfeldt

Search InChI in NCBI eSearch (pccompound) (1)

• Download

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.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Download Entries from PubChem (1)

• Download

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.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Demo of ChemSpider InChi to SMILES webserv... (1)

• Download

Created: 2009-03-28 | Last updated: 2009-03-28

Credits: David De Roure

fetch_fasta (1)

• Download

This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: Jumblejumble

Biomart Protein Sequence Retrieval (1)

• Download

This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

Created: 2009-03-09

Credits: Kieren Lythgow

Sesame triplestore loader from a dereferen... (2)

• Download

Load triples obtained from an URL in N3 or XML format and load them into your local Sesame Triplestore locally installed and available at http://localhost/sesame. The http://localhost/sesame/servlets/uploadURL service of Sesame is used in HTTP POST mode.

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Workflow Pattern - Blocking Discriminator ... (1)

• Download

This workflow is a GWorkflowDL representation of a blocking discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored and the AND transition is blocked. The pattern is resets if both, A and B have been invoked. Then the next token on "begin" can be processed. Please note that the transitions "C", "ignore", and "release" have different priorities (represented by p0, p1, an...

Created: 2009-01-20

Credits: Andreas Hoheisel

Wash and filter molecules (1)

• Download

The Wash and Filter workflow performs some processing on incoming structures to filter out those wildcards or unspecified atom types, standardise stereo and charges, and various other adjustments. This is an advance on the filter used in the paper... Drug Discovery Today Volume 14, Issues 1-2, January 2009, Pages 31-40 ‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries  

Created: 2009-01-20

Credits: Paul Dobson

Author's collaborators according to pubmed (1)

• Download

SELECT distinct ?s2 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "author" .   ?s2 ?p2 ?s1 .   FILTER( regex(?s1, "pubmed") ) } followed by SELECT ?creator, count() FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 .   ?s1 ?p2 ?o2 .   FILTER( regex(?o2, "author"))   ?s1 ?creator . } ORDER BY DESC(count())

Created: 2009-01-20 | Last updated: 2009-01-20

Credits: Francois Belleau

Text search within sparql point (1)

• Download

This workflow make possible full text search within different sparql point made available by the Bio2RDF project.

Created: 2009-01-19

Credits: Francois Belleau

Workflow Pattern - Synchronization (AND-Join) (2)

• Download

This workflow is a GWorkflowDL representation of a synchronization (AND Join) that waits until A and B finish their execution. This workflow is equivalent to the following pseudo code: threadA = new Thread( end_A = A() ); threadB = new Thread( end_B = B() ); threadA.join(); threadB.join();

Created: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Structured Partial Join (1)

• Download

This workflow is a GWorkflowDL representation of a structured partial join (N-out-of-M join) that invokes D after N=2 invocations of A or B or C (M=3). All next (M-N) invocations of A or B or C are ignored. This is only one out of various possibilities to model this workflow pattern.

Created: 2009-01-06

Credits: Andreas Hoheisel

View

AIDA demo pack

Created: 2008-12-14 21:35:43 | Last updated: 2009-05-01 17:35:26

5 items in this pack

Comments: 0 | Viewed: 192 times | Downloaded: 0 times

View Download

Package: mapping oligonucleotides to an assembly

Created: 2008-12-11 12:02:47 | Last updated: 2009-01-22 09:06:26

5 items in this pack

Comments: 0 | Viewed: 253 times | Downloaded: 89 times

Affimetrix microarray: part two (perm) (1)

• Download

We use a permutation test to infer the significance of the differently expressed genes found by the ANOVA analysis. Permutation tests are computationally intensive, needing at least 1000 permutations per gene to obtain acceptable results. For large experiments, the in-built feature of running R/MAANOVA in a single cluster may not be enough. We are using WS- VLAM workflow management system [2] to create a Grid-enabled R/MAANOVA workflow (Grid-MAANOVA) that will simultaneously run in multiple c...

Created: 2008-12-05

Credits: Zhiming Zhao

Basic eSearch/eFetch cycle (1)

• Download

This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI. It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences. I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am ...

Created: 2008-12-04 | Last updated: 2008-12-04

Credits: Giovanni Dall'Olio

AUGUSTUS Workflow for predicting genes in ... (1)

• Download

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Currently, it has been trained to predict genes in human, Drosophila melagonaster, Arabidopsis thaliana, Brugia malayi, Aedes aegypti, Coprinus cinereus, Tribolium castaneum, Schistosoma mansoni, Tetrahymena thermophila, Galdieria sulphuraria and Zea mays. In addition the species parameters of the following species are a courtesy of Jason Stajich: Caenorhabditis elegans, Saccharomyces cerevisiae, Ustilago ma...

Created: 2008-11-25 | Last updated: 2008-12-05

Credits: MediGRID