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Odkrywanie reguł asocjacyjnych za pomocą... (1)

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Proces pokazuje wykorzystanie algorytmu FP-Growth do odkrywania reguÅ‚ asocjacyjnych. Należy zwrócić uwagÄ™ na to, że implementacja algorytmu FP-Growth akceptuje jedynie atrybuty binominalne, zatem zachodzi konieczność zamiany wszystkich atrybutów numerycznych i nominalnych na binominalne.

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

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

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Drug Target FASTA

Created: 2011-03-30 10:51:26 | Last updated: 2011-04-01 13:10:05

Credits: Morgan Taschuk Andrewsmeaton

Attributions: Compile Protein FASTA from Target to Drug file

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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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

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Taverna XPath practical slides .

Created: 2011-03-30 09:17:52 | Last updated: 2011-03-30 09:17:55

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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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

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

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

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

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

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Taverna Iteration training slides

Created: 2011-03-28 11:44:06 | Last updated: 2011-03-28 11:44:08

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 72 times | Downloaded: 52 times

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

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Bonn Taverna Training agenda March/April 2011

Created: 2011-03-28 11:31:38 | Last updated: 2011-03-28 11:31:39

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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Taverna Introduction

Created: 2011-03-28 11:29:08 | Last updated: 2011-03-28 11:29:10

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 76 times | Downloaded: 80 times

Gene function prediction in Macaca Fasciculus (1)

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This workflow searches for ORF regions in a specific gene (TOM1L1 in Macaca fasciculus testis) to predict candidate protein coding regions. Results from blastp are used to find which frames are closest to existing proteins in other species. rpsblast is used to predict the domains and the protein families that these sequences may belong to. This is used to predict the function of the protein.

Created: 2011-03-27 | Last updated: 2011-03-27

Credits: Kalpana

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

Comments: 0 | Viewed: 50 times | Downloaded: 30 times

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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

Comments: 0 | Viewed: 40 times | Downloaded: 33 times

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