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Items tagged with "workflow" (77)

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Network-member AP Biology

Unique name: apbiology
Created: Tuesday 30 October 2012 @ 18:36:04 (GMT)

 This group is for the students of the Quality Schools International Advanced Placement Biology course. Students are expected to critique and evalutate exisiting workflows and upload their own for discussion.

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Files (5)
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Blob Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

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Blob ProStack Screencast: Segmentation of Images of Gene ...

Created: 20/05/10 @ 19:48:40

Credits: User Konstantin Kozlov

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

ProStack (Processing of Stacks) is a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. This video demonstrates the workflow for extraction of quantitative information on gene expression from confocal images. ProStack home page: urchin.spbcas.ru/downloads/ProStack/ProStack.htm Download:sourceforge.net/projects/prostack/

File type: AVI video

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Blob Interaction with OMERO server from ProStack - screen...

Created: 03/08/10 @ 07:25:46 | Last updated: 03/08/10 @ 07:25:49

Credits: User Konstantin Kozlov

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The modules of ProStack image processing platform are described that allow to: browse OMERO datasets, fetch an image for processing in ProStack, insert a resulting image into the dataset.

File type: video/mp4

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Blob Workflow compact

Created: 06/10/11 @ 03:27:24 | Last updated: 06/10/11 @ 03:27:29

Credits: User Chrisser

License: Creative Commons Attribution 3.0 Unported License

This screenshot shows the "Elevation plot..." workflow with the nested workflows compact. img, #cubbies-overlay{ -moz-transition-property: margin, box-shadow, z-index; -moz-transition-duration: 0.1s; -webkit-transition-property: margin, box-shadow, z-index; -webkit-transition-duration: 0.1s; } .cubbies-selected{ z-index: 9999; box-shadow: 3px 3px 8px -1px blue !important; cursor: pointer !important; margin: -3px 3px 3px -3px; } .cubbies-selected:active{ box-shadow: 2px 2px 5px -1...

File type: JPEG image

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Blob "Elevation plot..." workflow, expanded view

Created: 06/10/11 @ 03:29:43 | Last updated: 06/10/11 @ 03:29:52

Credits: User Chrisser

License: Creative Commons Attribution 3.0 Unported License

this screenshot shows the entire workflow, with nested workflows expanded img, #cubbies-overlay{ -moz-transition-property: margin, box-shadow, z-index; -moz-transition-duration: 0.1s; -webkit-transition-property: margin, box-shadow, z-index; -webkit-transition-duration: 0.1s; } .cubbies-selected{ z-index: 9999; box-shadow: 3px 3px 8px -1px blue !important; cursor: pointer !important; margin: -3px 3px 3px -3px; } .cubbies-selected:active{ box-shadow: 2px 2px 5px -1px darkblue !important; ma...

File type: JPEG image

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Workflows (69)
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Workflow 1 (2)

Created: 06/11/07 @ 16:59:05 | Last updated: 20/11/07 @ 16:18:31

Credits: User Antoon Goderis User Carole Goble User A. Random Scientist Network-member try it out

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.

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

Viewed: 195 times | Downloaded: 98 times

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Workflow Taverna rendering of the PAN-STARRS workfl... (1)

Created: 30/04/09 @ 16:32:17

Credits: User Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Example inputs: CSVRootPath = /Users/paolo/Documents/myGRID/OPM/PC3/SampleData/J062941 JobID:J062941  

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Workflow Test SoapLab Service Availability (1)

Created: 29/05/09 @ 10:13:45 | Last updated: 29/05/09 @ 10:14:47

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow tests for all Taverna workflows stored at myExperiment wether theS oapLab services used still exists. For each SOAP/WSDL service it checks wether the SoapLab service can still be accessed. The output is among others a report of accessible SoapLab services inaccessible SoapLab services

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

Viewed: 48 times | Downloaded: 33 times

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Workflow Test SOAP/WSDL Service Availability (1)

Created: 29/05/09 @ 10:15:41

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow tests for all Taverna workflows stored at myExperiment wether the SOAP/WSDL services used still exists. For each SOAP/WSDL service it checks wether the WSDL file is still accessible and whether the operation is still exists. The output is among others a report of accessible services and operation, operations which WSDL file is not accessible, operations which WSDL file still exists, but the operation is not defined anymore. The last set needs to be checked by hand, because...

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

Viewed: 116 times | Downloaded: 50 times

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Workflow G-language Genome Analysis Environment - B... (2)

Created: 05/04/10 @ 06:15:53

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Given a numerical vector (array), this workflow calculates the maximum value (max) and its index (maxdex), minumum value (min) and its index (mindex), mean, sum, median, and standard deviation. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

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Workflow G-language Genome Analysis Environment - G... (2)

Created: 05/04/10 @ 06:20:58

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates and graphs the GC skew of a given genome sequence. Use this as a template for using more than 100 analysis programs implemented in G-language Genome Analysis Environment, which can be used in a similar manner. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 53 times | Downloaded: 23 times

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Workflow G-language Genome Analysis Environment - G... (2)

Created: 05/04/10 @ 06:24:02

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates and graphs the GC skew (by default, for keto bases, with window size of 1000) of a given genome sequence identifier. Here the genome sequence in Fasta format is downloaded through the Togo Web Service with RefSeq identifier. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 56 times | Downloaded: 37 times

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Workflow G-language Genome Analysis Environment - B... (2)

Created: 05/04/10 @ 06:13:16 | Last updated: 05/04/10 @ 06:13:17

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow shows simple sequence manipulation functions of G-language GAE, such as random shuffling, obtaining a reverse complement, and translation of nucleotide sequences, and showing basic composition statistics for nucleotide and amino acid sequences. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 29 times | Downloaded: 22 times

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Workflow G-language Genome Analysis Environment - G... (2)

Created: 05/04/10 @ 06:22:28

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates and graphs the GC skew of a given genome sequence (for the entire genome, for only the coding sequences, for only the intergenic regions, and for only the third codon positions), as well as the GC content with sliding windows. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 68 times | Downloaded: 27 times

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Workflow G-language Genome Analysis Environment - G... (3)

Created: 05/04/10 @ 06:17:25 | Last updated: 09/01/11 @ 06:08:19

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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This workflow calculates and graphs the AT skew of a given genome sequence, using options of gcskew program. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

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Workflow G-language Genome Analysis Environment - S... (2)

Created: 05/04/10 @ 06:26:41

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates the Student's T-test and Pearson/Spearman correlations. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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

Viewed: 53 times | Downloaded: 25 times

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Workflow G-language Genome Analysis Environment - R... (2)

Created: 30/03/10 @ 10:58:18 | Last updated: 30/03/10 @ 11:19:03

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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This workflow displays a documentation of G-language GAE programs. If you input the "keywords", this workflow searches for the keyword through the documentations. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

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Viewed: 54 times | Downloaded: 24 times

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Workflow Biomart and EMBOSS analysis (1)

Created: 03/07/09 @ 14:18:28 | Last updated: 03/07/09 @ 14:19:32

Credits: User Stian Soiland-Reyes

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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Workflow DataBiNS with Kegg ID (3)

Created: 09/07/09 @ 21:39:54 | Last updated: 22/11/10 @ 23:16:42

Credits: User Mark Wilkinson User Fong Chun Chan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

Rating: 5.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow DNA sequence analysis pilot (1)

Created: 10/07/09 @ 14:31:27 | Last updated: 30/11/09 @ 09:37:38

Credits: User Angela Luijf User Glatard

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

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  http://amc-app1.amc.sara.nl/twiki/bin/view/         Workflow-based  DNA sequence analysis on the Dutch Life Science Grid, presented as Application Showcase at the NBIC Conference 2009, Lunteren, The Netherlands, 17 & 18 March 2009. http://www.biomedgrid.it/programme may 15th 2009. Hands on workflow: grid-enabled medical imaging  (Johan Montagnat – Tristan Glatard)  

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Workflow Ex (1)

Created: 16/11/09 @ 12:37:25

Credits: User Mventosa

Attributions: Workflow EBI_InterProScan for Taverna 2

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Ex of exercise

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Workflow DNA sequence analysis pilot (Blat) (2)

Created: 20/11/09 @ 11:12:43 | Last updated: 30/11/09 @ 09:35:38

Credits: User Angela Luijf User Barbera van Schaik User Glatard

Attributions: Workflow DNA sequence analysis pilot

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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http://amc-app1.amc.sara.nl/twiki/bin/view/  Workflow-based  DNA sequence analysis on the Dutch Life Science Grid. This workflow is  based on http://www.myexperiment.org/workflows/840 , the last component (Blast analysis) is replaced by Blat analysis    

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Workflow G-language Genome Analysis Environment - B... (2)

Created: 05/04/10 @ 06:08:25 | Last updated: 05/04/10 @ 06:08:26

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta...

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

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Workflow Get KEGG gene descriptions and pathways (1)

Created: 30/04/10 @ 16:09:29 | Last updated: 30/04/10 @ 16:12:02

Credits: User Nadia Cerezo User Paul Fisher

Attributions: Workflow Get Kegg Gene information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identif...

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Workflow Phylogenetic Study Using the Bio Extract S... (2)

Created: 17/06/10 @ 16:34:50 | Last updated: 19/07/10 @ 20:00:00

Credits: User Kendra Giesey Network-member BioExtract Server for Genomics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced the...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1

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Workflow Protein Mutation Analysis Using the BioExt... (1)

Created: 22/07/10 @ 20:20:07 | Last updated: 22/07/10 @ 20:29:56

Credits: User Kendra Giesey User Yosr Bouhlal Network-member BioExtract Server for Genomics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow, created using the BioExtract Server, contains a protein query (using the NCBI Protein Database), Blastp, ClustalW, Transeq, Garnier, PepWindowWall, PepInfo, and Octanol. For this workflow, a mutated protein sequence needs to be selected. Once the corresponding non-mutated sequence has been queried, the Blastp tool can be used to find sequences similar to the one queried, and the ClustalW tool can be used to analyze whether the mutation is conserved within species.  The Tra...

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Workflow For loop sample for Trident v1.2 (1)

Created: 19/08/10 @ 18:29:19 | Last updated: 24/08/10 @ 17:27:34

Credits: Network-member Trident

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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  Please refere following link for more information http://tridentworkflow.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=138916

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Workflow Replicator Activity sample for Trident v1.2 (1)

Created: 03/09/10 @ 09:00:59 | Last updated: 03/09/10 @ 09:04:01

Credits: Network-member Trident

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The objective of this workflow is to explain the working of the Replicator activity in the Trident application. For detailed description of the worklfow please refer the following document. Sample Description

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Workflow IfEls Activity sample for Trident v1.2 (v1) (1)

Created: 03/09/10 @ 10:53:39 | Last updated: 03/09/10 @ 10:53:43

Credits: Network-member Trident

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The objective of this workflow is to explain the working of the If Else activity in the Trident application.  For more information on how to use the if else sample. Please refere the following document. IfElse-Sample Details

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Workflow Sample for explaining the feature: - Type ... (1)

Created: 03/09/10 @ 11:05:13 | Last updated: 03/09/10 @ 11:05:16

Credits: Network-member Trident

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The objective of this workflow is to explain the working of the Type Initializer in the Trident application.   For detailed information on type initializer and how it can be used please refer the following document:- http://tridentworkflow.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=138922  

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Viewed: 27 times | Downloaded: 9 times

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Workflow Phylogenetic analysis workflow (1)

Created: 12/03/11 @ 07:10:59 | Last updated: 12/03/11 @ 07:12:22

Credits: User Yosr Bouhlal

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow provides a simple phylogenetic analysis starting from a protein query using "MrBayes" program and according to the maximum likelihood model

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Workflow [untitled] (1)

Created: 26/04/11 @ 14:50:37 | Last updated: 26/04/11 @ 15:04:28

Credits: User Dennis Leenheer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

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Workflow Generate Atom Signatures of molecules give... (1)

Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

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Workflow Scoring small molecules for metabolite lik... (2)

Created: 13/05/11 @ 17:22:28 | Last updated: 18/03/12 @ 16:41:39

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

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Workflow Plotting distribution of natural product l... (1)

Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

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Workflow Download Structures from PubChem given che... (1)

Created: 24/05/11 @ 13:13:52 | Last updated: 24/05/11 @ 14:19:24

Credits: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

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Avatar Baj

Workflow Bash example from the NGS community contri... (1)

Created: 07/06/11 @ 15:44:41

Credits: User Baj

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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  BASH Simple workflow that executes "ls" on the command line in the directory "/".

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Avatar Baj

Workflow NGS sample workflow with data (1)

Created: 24/06/11 @ 11:42:57 | Last updated: 24/06/11 @ 12:17:00

Credits: User Baj

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Sample workflow for NGS data analysis This worklfow relies on community contributions that can be installed through the following update site: http://tech.knime.org/update/community-contributions/nightly specifically the  KNIME NGS tools and the KNIME R Scripting extensions.    

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Workflow tblastx non-redundant alignment (1)

Created: 30/06/11 @ 15:26:13 | Last updated: 04/07/11 @ 16:51:41

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species.   For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1.   Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2.   The output from ...

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Workflow Rave Usability Lab Workflow (1)

Created: 16/08/11 @ 16:40:01 | Last updated: 10/11/11 @ 16:08:49

Credits: User Liz Masterman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Workflow created when writing UX requirements for mobile interface to myExperiment and renamed for use in the usability lab.

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Workflow Image metadata extraction (1)

Created: 31/08/11 @ 12:02:29 | Last updated: 31/08/11 @ 12:02:31

Credits: User Harvey

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow invokes the gdalinfo service and will list various information about a GDAL supported raster dataset of the image ( GeoTIFF, PNG, JPEG and GIF.).

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Workflow TIFF to PNG (1)

Created: 31/08/11 @ 12:04:44 | Last updated: 31/08/11 @ 12:04:47

Credits: User Harvey

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow can convert Image format from TIFF to PNG. This workflow is one of the example for GENESI-DEC ontology.

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Viewed: 50 times | Downloaded: 13 times

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Workflow Convert GML to SVG (1)

Created: 31/08/11 @ 12:06:27 | Last updated: 31/08/11 @ 12:06:31

Credits: User Harvey

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow can convert the GML (Geography Markup Language) file to SVG image.

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Viewed: 42 times | Downloaded: 22 times

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Workflow The NOTCH2 workflow (1)

Created: 06/09/11 @ 09:24:22 | Last updated: 06/09/11 @ 09:26:48

Credits: User Pierre Lindenbaum

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

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Workflow World Population Density - IST 600 (1)

Created: 21/09/11 @ 05:51:09 | Last updated: 21/09/11 @ 05:51:06

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population. Based on "Population Histogram in R" by Alan R Williams

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Viewed: 11 times | Downloaded: 5 times

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Workflow Avg and StdDev IST 600 (1)

Created: 21/09/11 @ 07:51:07 | Last updated: 21/09/11 @ 07:51:04

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A workflow to calculate and name the average and standard deviation of a list of numbers. Changes made to the original workflow are: an inout and output, a concatenation to list the average and standard deviation outputs, a string constant to name the list, and a concatenation to string the name znd the calculations.

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Workflow Fertilzer Use Ist 600 (1)

Created: 21/09/11 @ 08:52:43 | Last updated: 21/09/11 @ 08:52:41

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilzerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment.org/files/568/download/FertilizerUse.xls. Based on the water use workflow by David Withers

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Workflow Broccoli production comparisons in NY and ... (1)

Created: 21/09/11 @ 15:23:11 | Last updated: 21/09/11 @ 15:23:08

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilzerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment.org/files/568/download/FertilizerUse.xls. Based on the water use workflow by David Withers

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Viewed: 11 times | Downloaded: 5 times

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Workflow Simple protein distance phylogeny workflow (1)

Created: 22/09/11 @ 16:47:46 | Last updated: 22/09/11 @ 16:47:49

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs a multiple alignment and makes a phylogeny using a distance method on a set of protein sequences  

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Workflow Algebra 1 - IST 600 (1)

Created: 28/09/11 @ 07:00:03 | Last updated: 28/09/11 @ 07:00:00

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A kepler workflow to solve the following problem: If x=3, solve for x: |(x+5)/(x-5)|

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Workflow Get 7 day weather information for selected... (1)

Created: 14/09/11 @ 05:46:28 | Last updated: 14/09/11 @ 05:46:25

Credits: User Gstalloch User Franck Tanoh

Attributions: Workflow Get weather information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value is my home town. To find out any supported city run the 'Get cities by country name' workflow

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Workflow Hipster Geek -IST 600 (1)

Created: 28/09/11 @ 06:54:14 | Last updated: 28/09/11 @ 06:54:11

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A kepler workflow that concatenates 5 strings of random Hipster Geek from http://hipsteripsum.me/ into a word-wrapped paragraph.

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Viewed: 14 times | Downloaded: 6 times

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Workflow Algebra 2 - IST 600 (1)

Created: 28/09/11 @ 07:16:30 | Last updated: 28/09/11 @ 07:16:33

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A work flow that answers the following equation: If x=3, solve for x: |(x-5)/(x+5)| + |(x+5)/(x-5)|

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Viewed: 11 times | Downloaded: 10 times

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Workflow Convert a URL to an image - IST 600 (1)

Created: 28/09/11 @ 07:26:22 | Last updated: 28/09/11 @ 07:26:26

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow converts the Lackadaisy Cats comic to an image in Kepler.

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Viewed: 14 times | Downloaded: 11 times

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Workflow Elevation plot v.2 (2)

Created: 06/10/11 @ 03:54:30 | Last updated: 06/10/11 @ 16:32:18

Credits: User Chrisser

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Functionally identical to the original. I tried to upload a version with annotation, but somehow the notes didn't make it to myExperiment. From the prior verion: This workflow accepts city and country names as user-supplied input. These value are supplied to the GetWeather webservice (http://www.webservicex.net/globalweather.asmx?WSDL), which returns an XML record of location and weather info for each recognized city. (See the uploaded photo "weather example") The XML returned fr...

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

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Workflow Mapping Service (2)

Created: 06/10/11 @ 04:44:03 | Last updated: 06/10/11 @ 05:01:20

Credits: User tpacurtis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This service generates a google map of a group of place names and coordinates. The workflow will accept both coordinates and place names. This workflow takes place names/coordinates from both a spreadsheet, as well as on-the-fly input of a list of coordinates or place names (please note, if no supplemental data is desired, an empty link will allow the workflow to function). The Mapping Service workflow was created to assist in generating a map of where a series of interviews took p...

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

Viewed: 32 times | Downloaded: 7 times

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Workflow A Comparison of China and US populations (2)

Created: 28/11/11 @ 16:51:34 | Last updated: 28/11/11 @ 17:12:37

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow is a comparison of China's population with the United States. It also compared the population of males and females from ages 0 - 4 to illustrate any gender gaps that may be occurring in the birth rates. The graphs are produced through the google chart API service. The data is from world population spreadsheets obtained from Gapminder.org.

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Viewed: 13 times | Downloaded: 9 times

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Workflow Connect flare events with proton events on... (4)

Created: 15/11/11 @ 13:57:35 | Last updated: 15/05/12 @ 13:09:09

Credits: User Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow uses flares listed in the goes_sxf_flare list, checks wether this flare is connected to Earth via the Parker spiral, and looks for proton events at earth listed in the goes_proton_event list. The flare listing and the proton listing is combinded into a VOTable output.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Run a Workflow on Taverna Server (local t2... (1)

Created: 20/02/12 @ 11:38:53

Credits: User Anja Le Blanc

Attributions: Workflow Run a Workflow on Taverna Server

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Uses a local t2flow file to submit and run this workflow on the taverna server. You need a user name and password to execute this workflow. Input to the workflow which runs remotely will be requested interactively.

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Workflow Find workflow ancestors (2)

Created: 08/05/12 @ 11:15:30 | Last updated: 09/07/12 @ 10:56:06

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution 3.0 Unported License

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Given a t2flow file (Taverna 2 workflow), extract ancestor workflow UUIDs and search myExperiment for matching workflow entries. Note that this will also match the workflow itself and nested workflows, but does not match against other workflows having the same ancestors (but newer UUIDs).

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Workflow Run sextractor using a votable (2)

Created: 26/07/12 @ 11:23:30 | Last updated: 07/09/12 @ 12:25:41

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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It runs sextractor and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Sextractor is called by an bash script as 'sex'. Sextractor is called for every row in the votable. Columns where the configuration file and the image file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain refer...

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Workflow Create votable from sextractor results (2)

Created: 26/07/12 @ 11:39:53 | Last updated: 21/08/12 @ 08:20:36

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow creates a votable from the results provided by sextractor (votables). It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running sextractor and such files accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

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Workflow Ajusting galaxy paramenters using sextractor (5)

Created: 26/07/12 @ 12:02:48 | Last updated: 07/09/12 @ 12:29:00

Credits: User Julian Garrido

Attributions: Workflow Create configuration files from a template and a votable Workflow Run sextractor using a votable Workflow Create votable from sextractor results Workflow Add columns to a votable resulting from executing sextractor.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow creates configuration files for sextractor, it runs sextractor using this configuration files, it adds sextractor results to the input votable and adds new calculated columns. This task requires a votable as input, a template, a vocabulary and the specification of the column names that contain some required files (configuration files, image files, ...). These files must be accesible from taverna. Sextractor is called by an bash script as 'sex'. Every row in the votable cotains ...

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Workflow Run galfit using a votable (2)

Created: 26/07/12 @ 12:20:52 | Last updated: 07/09/12 @ 12:39:42

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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It runs galfit and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Galfit is called by a bash script as 'galfit'. Galfit is called for every row in the votable. Columns where the result file name and the configuration file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain references to o...

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

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Workflow Create votable from galfit results (4)

Created: 26/07/12 @ 12:27:41 | Last updated: 07/09/12 @ 12:47:12

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/).

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Workflow Create galfit configuration files with par... (1)

Created: 26/07/12 @ 12:41:51 | Last updated: 26/07/12 @ 12:44:09

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow creates galfit configuration files using a partition criteria. The resulting configuration files are different depending on whether the galaxy has o doesn't have a bar. They are created (one for every row in the votable) using a template whose keys are replaced by data from a votable. Keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file. This workflow uses astrotaverna ...

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Workflow Adjusting galaxy parameters using galfit (4)

Created: 26/07/12 @ 12:56:18 | Last updated: 07/09/12 @ 12:57:59

Credits: User Julian Garrido

Attributions: Workflow Create configuration files from a template and a votable Workflow Run galfit using a votable Workflow Create votable from galfit results Workflow Create votable from different galfit paramenter adjustments Workflow Create galfit configuration files with partition criteria using votable

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow creates galfit configuration files using data from a votable, it runs galfit, its results is added to the votable, it creates new config files for galfit using the previous results, it runs galfit a second time considering galaxies that have and do not have bars in order to adjust the objective parameters and it finally includes the results into the votable. It requires the specification of the columns that contain file names (these files should be accesibles from taverna). If t...

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Workflow Create votable from different galfit param... (2)

Created: 21/08/12 @ 09:15:17 | Last updated: 07/09/12 @ 12:56:08

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/). The galfit files may come from adjusting 'disk, bulb, ba...

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Workflow Add columns to a votable resulting from ex... (1)

Created: 30/08/12 @ 09:33:55

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Addcolumns that are needed to run galfit and ellipse. it requires columns coming from sextractor and the astrotaverna plugin.

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Workflow Build plots from galfit and ellipse results (2)

Created: 30/08/12 @ 09:51:58 | Last updated: 07/09/12 @ 13:33:55

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Build plots from galfit and ellipse results (http://www.myexperiment.org/workflows/3068.html, http://www.myexperiment.org/workflows/3052.html).

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Workflow NCBI Protein Clustal Omega Alignment (1)

Created: 31/08/12 @ 19:18:55

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

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Viewed: 7 times | Downloaded: 0 times

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Workflow Detect ellipse failures and get votable wi... (1)

Created: 07/09/12 @ 13:26:05

Credits: User Julian Garrido

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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It detects if ellipse has failed by checking if the resulting data file exists. It adds a column (validellipse) that contains 1 if ellipse didn't fail and 0 if ellipse failed. It returns a votable that contains all the data with the new column and a votable that contains only the rows where ellipse didn't failed. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

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Viewed: 11 times | Downloaded: 3 times

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htm
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Workflow Measuring Cellular Respiration in Animals (1)

Created: 31/10/12 @ 10:42:24

Credits: User Dhefley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 This is an incomplete workflow of an experiment designed to measure the cellular respiration of different animals under different conditions.

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Viewed: 8 times | Downloaded: 0 times

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Pack Pathway to Phenotype using Text Mining


Created: 10/08/09 @ 13:01:47 | Last updated: 11/08/09 @ 14:51:31

This pack contains a list of workflows and result files obtained from the analysis of candidate pathways believed to play a role in resistance to African Trypanosomiasis in the mouse model organism.

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Pack Natural product likeness filter


Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

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