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In-silico Fragmentation of Naringenin (v2)

Created: 05/02/10 @ 14:03:44 | Last updated: 08/02/10 @ 12:19:24

Credits: http://sneumann.pip.verisignlabs.com/

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Original Uploader

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In-silico Fragmentation of Naringenin (v2)

Created: 05/02/10 @ 14:03:44 | Last updated: 08/02/10 @ 12:19:24

Credits: http://sneumann.pip.verisignlabs.com/

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Viewed: 12 times | Downloaded: 6 times

Original Uploader

Marco Roos

BioAID_DiseaseDiscovery (v3)

Created: 12/11/07 @ 22:39:04 | Last updated: 15/12/08 @ 20:47:51

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

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M.B.Mon...

Workflow for Protein Sequence Analysis (v1)

Created: 09/01/08 @ 12:03:04 | Last updated: 09/01/08 @ 12:31:29

Credits: M.B.Monteiro

Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

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

Viewed: 689 times | Downloaded: 229 times

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Paul Fisher

HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Last updated: 26/11/09 @ 17:34:25

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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 returned 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: 558 times | Downloaded: 203 times

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Paul Fisher

Pathways and Gene annotations for QTL region (v5)

Created: 03/10/07 @ 18:36:02 | Last updated: 20/11/09 @ 10:33:28

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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: 5 | Reviews: 0 | Comments: 2 | Citations: 1

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Paul Fisher

KEGG Pathway to Pubmed (v2)

Created: 09/03/08 @ 15:03:12 | Last updated: 03/12/09 @ 16:52:10

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.   Example input for this workflow is as follows (new line separated): path:mmu04530    Tight junction - Mus musculus (mouse) path:mmu04540    Gap junction - Mus musculus (mouse) path:mmu04730    Long-term depre...

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Andrea Wiggins

Success-Abandonment-Classification (v3)

Created: 06/02/08 @ 14:35:42 | Last updated: 02/07/08 @ 17:15:25

Credits: Andrea Wiggins James Howison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves data from FLOSSmole and from the Notre Dame SourceForge repository to compute project statistics based on releases, downloads and project lifespan. Project statistics are then used to classify projects according to the criteria set up in English & Schweik, but comparison criteria are parameterized so that a different set of criterion thresholds can be used to evaluate the project characteristics.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 624 times | Downloaded: 5883 times

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Alan Williams

Example of a conditional execution workflow (v1)

Created: 05/03/08 @ 13:55:46 | Last updated: 25/03/08 @ 14:46:19

Credits: Tomoinn

License: Creative Commons Attribution 3.0 Unported License

If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak.

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

Viewed: 763 times | Downloaded: 235 times

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Paul Fisher

Entrez Gene to KEGG Pathway (v4)

Created: 03/10/07 @ 18:36:00 | Last updated: 04/12/09 @ 16:04:39

Credits: Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

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: 4 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 443 times | Downloaded: 219 times

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Alan Williams

BiomartAndEMBOSSAnalysis (v4)

Created: 05/03/08 @ 14:01:18 | Last updated: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 3.0 Unported License

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: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 530 times | Downloaded: 198 times

Original Uploader

Mark Borkum

QR code (matrix code) generator (v4)

Created: 07/10/07 @ 17:17:04 | Last updated: 16/07/08 @ 01:46:14

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The latest (and greatest) version of the QR code generator workflow. This workflow uses the QR code service provided by the ChemTools project.

Rating: 1.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 219 times | Downloaded: 165 times

Original Uploader

Paul Fisher

Get Kegg Gene information (v2)

Created: 05/01/09 @ 13:20:34 | Last updated: 14/12/09 @ 12:05:23

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

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

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Original Uploader

Marco Roos

BioAID_DiseaseDiscovery (v3)

Created: 12/11/07 @ 22:39:04 | Last updated: 15/12/08 @ 20:47:51

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 1921 times | Downloaded: 242 times

Original Uploader

Paul Fisher

Perform a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Last updated: 03/12/09 @ 16:39:20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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. Example input for this workflow is given as: 9215629

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

Viewed: 358 times | Downloaded: 6 times

Original Uploader

Franck Tanoh

Retrieve_abstract_from_Medline (v1)

Created: 17/09/08 @ 15:22:56 | Last updated: 17/09/08 @ 15:24:22

Credits: Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow retrieves Medline Abstracts given PMIDs (PubMed id) You can use: 9879 as input example to test this workflow

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

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Original Uploader

Hamish McWilliam

EBI_Whatizit (v1)

Created: 09/07/08 @ 05:14:28 | Last updated: 09/07/08 @ 05:14:29

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf). Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.

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

Viewed: 110 times | Downloaded: 42 times