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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

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

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

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Example XML

Created: 2011-03-23 17:25:09 | Last updated: 2011-03-23 17:25:11

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

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Schema for flat file cross-referencing

Created: 2011-03-23 17:00:58 | Last updated: 2011-03-23 17:01:01

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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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

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XML Result from Pubmed Search

Created: 2011-03-23 11:49:33 | Last updated: 2011-03-23 11:49:36

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

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XPath Pubmed Ids (1)

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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

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

Credits: Paul Fisher

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Simulation results

Created: 2011-03-23 09:52:21 | Last updated: 2011-03-23 09:52:24

Credits: John Brookes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

Comments: 1 | Viewed: 43 times | Downloaded: 19 times

Wybór atrybutów na podsatwie algorytmu z... (1)

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Workflow pokazuje użycie algorytmu zachÅ‚annego do wyboru cech. Algorytm może wykonywać zarówno wyboru progresywnego (forward selection) jak i selekcji wstecznej (backward selection). Do oceny jakoÅ›ci rozwiÄ…zania algorytm wykorzystuje klasyfikator k-najbliższych sÄ…siadów i 10-krotnÄ… walidacjÄ™ krzyżowÄ….

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

Wybór atrybutów na podstawie algorytmu g... (1)

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Workflow przedstawia wykorzystanie algorytmu genetycznego do znalezienia optymalnego zbioru atrybutów. Wybór atrybutów odbywa siÄ™ na podstawie sprawdzenia jakoÅ›ci klasyfikacji. Wykorzystanym klasyfikatorem jest algorytm k-najbliższych sÄ…siadów, zbiór danych jest dzielony na zbiór uczÄ…cy i zbiór testujÄ…cy w proporcji 70%-30%. WyjÅ›ciowy algorytm genetyczny wykorzystuje populacje o rozmiarze 10, ograniczajÄ…c liczbÄ™ pokoleÅ„ do 30.

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

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Bilateral Perisylvian Polymicrogyria - Single Nucleo...

Created: 2011-03-17 11:21:06 | Last updated: 2011-03-17 11:21:12

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Pathways and Gene annotations forQTL region (2)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. 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 pathway ...

Created: 2011-03-17 | Last updated: 2011-08-30

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

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Bilateral Perisylvian Polymicrogyria

Created: 2011-03-17 10:56:15 | Last updated: 2011-03-17 11:16:53

Credits: Paul Fisher

Attributions: Pathway and Gene to Pubmed Pathways and Gene annotations forQTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

Comments: 0 | Viewed: 86 times | Downloaded: 43 times

InterproScan without Looping (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. This workflow will not work properly until we add looping.

Created: 2011-03-16 | Last updated: 2012-08-29

Credits: Katy Wolstencroft

Collaborative filtering recommender (1)

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This process executes a collaborative filtering recommender based on user to item score matrix. This recommender predicts one user’s score on some of his non scored items based on similarity with other users. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations and %{number_of_neighbors} defines the number of the most similar users taken into a...

Created: 2011-03-15 | Last updated: 2012-03-06

Content based recommender (1)

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This process is a special case of the item to item similarity matrix based recommender where the item to item similarity is calculated as cosine similarity over TF-IDF word vectors obtained from the textual analysis over all the available textual data. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations. The process internally uses an example set of...

Created: 2011-03-15 | Last updated: 2011-03-15

Item to item similarity matrix -based reco... (1)

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This process executes the recommendation based on item to item similarity matrix. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations. The process internally uses an item to item similarity matrix written in pairwise form (id1, id2, similarity). The process essentially filters out appearances of the required ID in both of the columns of the pairwis...

Created: 2011-03-15 | Last updated: 2011-03-15

Random recommender (1)

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This process does a random item recommendation; for a given item ID, from the example set of items, it randomly recommends a desired number of items. The purpose of this workflow is to produce a random recommendation baseline for comparison with different recommendation solutions, on different retrieval measures. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of ...

Created: 2011-03-15 | Last updated: 2011-03-15

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Output from workflow 1943 on 2011-03-13 in CSV format

Created: 2011-03-13 11:31:21

Credits: David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

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