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Showing 4527 results. Use the filters on the left and the search box below to refine the results.
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4059?size=60x60 Gb Aleksandra Pawlik
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Blob REST Service Tutorial

Created: 2013-09-05 12:12:56

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

REST Services Tutorial to be used for the workshop at Bonn University 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 55 times | Downloaded: 42 times

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Taverna 2
Uploader
3377?size=60x60 Gb Jon Giddy

Workflow Print R expression (3)

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This is a very small nested workflow to convert an R expression to the same textual representation that you see displayed when using the R command line.

Created: 2013-09-05 | Last updated: 2013-10-16

Credits: User Jon Giddy

Uploader
4059?size=60x60 Gb Aleksandra Pawlik
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Blob Shims and Beanshells - tutorial

Created: 2013-09-05 09:49:45

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Shims and Beanshell - introductory tutorial for the workshop at Bonn University 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 41 times | Downloaded: 36 times

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4059?size=60x60 Gb Aleksandra Pawlik
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Blob RShell tutorial

Created: 2013-09-05 09:46:43

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

RShell Tutorial by Peter Li - to be used for the workshop at Bonn University, 4-6 September 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 53 times | Downloaded: 48 times

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Taverna 2
Uploader
4059?size=60x60 Gb Aleksandra Pawlik

Workflow BioVeL workshop reduced full workflow (1)

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The workflow is a reduced version of the main workflow. It can be used to call web services to support biodiversity research. It fetches data from GBIF. The occurrences are then used to create a model using OpenModeller, test the model and to project the model. The projection of the model is currently a "native projection" i.e. it uses the same layers as those used to create the model. The services within the workflow will allow non-native projections

Created: 2013-09-04

Credits: User Katy Wolstencroft User Alan Williams

Attributions:

Taverna 2
Uploader
3377?size=60x60 Gb Jon Giddy

Workflow Convert Taverna list of RExpr to R list - v2 (2)

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This workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions. This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break. The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for...

Created: 2013-09-04 | Last updated: 2013-10-14

Credits: User Jon Giddy Network-member BioVeL

Taverna 2
Uploader
Avatar Raul Palma

Workflow Hello World (1)

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One of the simplest workflows possible, outputting the String Constant "Hello world!"One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2013-09-04

Credits: User Raul Palma

Creator
Avatar Raul Palma
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Pack myPack


Created: 2013-09-04 10:57:02 | Last updated: 2013-09-04 11:06:30

test pack

2 items in this pack

Comments: 0 | Viewed: 16 times | Downloaded: 7 times

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4059?size=60x60 Gb Aleksandra Pawlik
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Blob Introduction to Taverna -part2 - Bonn 2013

Created: 2013-09-03 22:28:51

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to Taverna workflows: myExperiment, nested workflows, Spreadsheet import, BioMart, exploring workflow engine. This is a tutorial for the workshop at Bonn University 4-6 September 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 66 times | Downloaded: 66 times

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Taverna 2
Uploader
4059?size=60x60 Gb Aleksandra Pawlik

Workflow Pathway to Pubmed (1)

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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.

Created: 2013-09-03

Credits: User Alan Williams User Paul Fisher

Attributions: Workflow Pathway to Pubmed

Taverna 2
Uploader
4059?size=60x60 Gb Aleksandra Pawlik

Workflow UnigeneID to KEGG Pathways (1)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2013-09-03

Credits: User Katy Wolstencroft User Alan Williams User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

Uploader
4059?size=60x60 Gb Aleksandra Pawlik
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Blob Introduction to Taverna - Bonn 2013

Created: 2013-09-03 20:22:55

Credits: User Katy Wolstencroft User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to building workflows with Taverna - tutorial for the workshop at Bonn University, 4-6 September 2013

File type: PowerPoint presentation

Comments: 0 | Viewed: 58 times | Downloaded: 60 times

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3185?size=60x60 Gb Alex Hardisty
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Blob Empty profile

Created: 2013-09-03 10:04:03 | Last updated: 2015-02-03 12:07:53

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

A basic empty profile that does not allow additional semantic annotation

File type: Taverna Component Profile

Comments: 0 | Viewed: 86 times | Downloaded: 40 times

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Uploader
Avatar Gb Robert Muetzelfeldt
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Blob Systo diagram widget

Created: 2013-09-02 23:05:28 | Last updated: 2013-09-18 20:27:41

Credits: User Robert Muetzelfeldt

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Test - Systo diagram widgetSee http://www.systo.org to find out more about Systo.

File type: JavaScript

Comments: 0 | Viewed: 16 times | Downloaded: 12 times

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Avatar Gb Robert Muetzelfeldt
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Blob Miniworld model as a Javascript object literal

Created: 2013-09-02 22:59:00 | Last updated: 2013-09-02 22:59:26

Credits: User Robert Muetzelfeldt

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Miniworld model

File type: JavaScript

Comments: 0 | Viewed: 21 times | Downloaded: 14 times

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Creator
4185?size=60x60 Nl Eleni
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Pack HD data interpretation


Created: 2013-09-02 13:18:22 | Last updated: 2015-04-03 21:14:41

This workflow pack, was created in order to further analyse and interpret the results from workflow pack 485 (HD chromatin analysis). The workflows in this pack are using the anni web services, implemented by the Biosemantics group. 

6 items in this pack

Comments: 0 | Viewed: 96 times | Downloaded: 21 times

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Taverna 2
Uploader
4185?size=60x60 Nl Eleni

Workflow Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2013-08-31

Credits: User Eleni Network-member BioSemantics

Uploader
4185?size=60x60 Nl Eleni
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Blob workflow sketch Hd chromatin analysis

Created: 2013-08-30 12:01:45 | Last updated: 2013-11-04 19:18:11

Credits: User Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Sketch that demonstrates how the workflows of our chromatin analysis in HD are connected with each other, plus a short explanation for each one. 

File type: PNG image

Comments: 0 | Viewed: 37 times | Downloaded: 25 times

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Uploader
4059?size=60x60 Gb Aleksandra Pawlik
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Blob Nested UnigeneID_to_KEGG in Import and Convert

Created: 2013-08-29 14:09:53

Credits: User Katy Wolstencroft User Alan Williams User Paul Fisher

Attributions: Workflow UnigeneID to KEGG Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an example of a nested workflow, created for the training purposes.

File type: Trident (Package)

Comments: 0 | Viewed: 37 times | Downloaded: 16 times

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Uploader
4059?size=60x60 Gb Aleksandra Pawlik
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Blob GalaxyGeneList - long : datafile for training

Created: 2013-08-29 10:25:07

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Chip-Seq gene list example used for training purposes. This is the original version of the file  (approx 400 entries). Warning! Running this file in some workflows may  take up to 30 minutes! If you want to use it for training, you may want to reconsider and use the shorter version of the file which is also uploaded.

File type: Excel workbook

Comments: 0 | Viewed: 33 times | Downloaded: 17 times

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Uploader
4059?size=60x60 Gb Aleksandra Pawlik
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Blob GalaxyGeneList - short : datafile for training

Created: 2013-08-29 10:20:47 | Last updated: 2013-08-29 10:22:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Chip-Seq gene list example used for training purposes. This is a shorter version of the file (20 entries) as running the original file (the longer one with approx 400 entries) takes up to 30 minutes.

File type: Excel workbook

Comments: 0 | Viewed: 53 times | Downloaded: 95 times

This File has no tags!

Creator
4185?size=60x60 Nl Eleni
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Pack HD chromatin analysis


Created: 2013-08-28 12:17:37 | Last updated: 2016-10-28 15:02:27

This pack is comprised by all workflows used for the integration and the analysis of Huntington's Disease (HD) gene expression data and epigenetic datasets in order to establish links between HD and epigenetic regulation in disease.  

6 items in this pack

Comments: 0 | Viewed: 93 times | Downloaded: 22 times

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Taverna 2
Uploader
Avatar De Sonja Holl

Workflow EBI NCBI BLAST filter e-value and length (1)

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The workflow queries the NCBI BLAST web service and extracts the e-values and length of the results. One of the sub-workflows filters the length first and afterwards the e-value and the other sub-workflow filters first the e-value and then the length. As the result may be different, this workflow was used for optimization purposes to find the sub-workflow performing best.

Created: 2013-08-23 | Last updated: 2014-02-06

Credits: User Sonja Holl

Attributions: Workflow EBI_NCBI_BLAST

Taverna 2
Uploader
1780?size=60x60 Gb Donal Fellows

Workflow SCAPE Assess Metrics (1)

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Assesses whether a set of metrics satisfy some provided Quality Level Definition (QLD). The QLD is given as a Schematron schema, and is evaluated by the Java tool library Jing. Jing (http://www.thaiopensource.com/relaxng/jing.html) is assumed to be installed in the current directory.

Created: 2013-08-22 | Last updated: 2013-08-22

Bioclipse Scripting Language
Uploader
4506?size=60x60 Nl Egon Willighagen

Workflow Find Labels in WikiPathways that are IUPAC... (1)

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This scripts parses a directory with WikiPathways GPML files. For each "label" it checks if the label contains an IUPAC name (using OPSIN), calculated the InChIKey (using JNI-InChI/CDK), and looks up a ChemSpider identifiers (using the ChemSpider web service).

Created: 2013-08-20

Credits: User Egon Willighagen

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