All content

DNA sequence analysis pilot (1)

• Download

  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)  

Created: 2009-07-10 | Last updated: 2009-11-30

Credits: Angela Luijf Glatard

Using CQL to query protein sequence data (1)

• Download

To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

Created: 2009-05-07

Credits: Stian Soiland-Reyes

Attributions: Using CQL to query protein sequence data

DOI Record Generator (1)

• Download

This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file.

Created: 2009-04-29

Credits: Andrea Wiggins

Attributions: Data Set Metadata Generator

Run XMPP cloud services. (2)

• Download

Basic workflow indicating how a XMPP service can be called with XML input and output. Source code for the activity is available from: github.com/egonw/xws-taverna/tree/master That page explains you how to install the plugin you must install on top of Taverna 2.0. The workflow will not work otherwise.

Created: 2009-04-25 | Last updated: 2010-03-22

Credits: Egon Willighagen

Workflow Pattern - Structured Discriminato... (1)

• Download

This workflow is an alternative GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored for the same data group. Other tokens on the place "begin" can be processed recurrently if they belong to another data group. Please note that the transitions "C" and "ignore" have different priorities (not shown in the graph) that make the net determ...

Created: 2009-01-20

Credits: Andreas Hoheisel

Workflow Pattern - Structured Loop (C) (2)

• Download

This workflow is a GWorkflowDL representation of a structured loop that counts from 0 to 99.   This workflow is equivalent to the following pseudo code: for ( i:=0; i Please remark that this demonstration workflow does not invoke any external services at all.

Created: 2008-12-09

Credits: Andreas Hoheisel

Attributions: Workflow Pattern - Structured Loop (B)

Download pathways for external references ... (2)

• Download

Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2008-11-14

Credits: Thomaskelder

Attributions: CloneItemsInList

AppendToFile (2)

• Download

Processor to add content to a (existing)  file. The content is added to the end of the file. The inputs: Filename: the file name of a file, if the file does not exists, a new file is added Content: the string to append NewLine [default = true]: if true, a newline is added to the end of the line (useful if you want to add a record each time)   The processor supports Multi-Threading since version 2.

Created: 2008-11-11 | Last updated: 2008-11-11

Credits: Wassinki

Blat against ENSEMBLE Danio_rerio_Genome (1)

• Download

The blat workflow invokes the blat services provided at www.bioinformatics.nl (author Pieter Neerincx). As input, it takes a database name (for example, Danio_rerio_Genome for Zebra Fish) and one or more sequences in Fasta format. The output will be a tab separated output of the blat. An eValue string constant is added to filter on the e-Value. Note, the e-Value is not exactly the same as the blast e-Value. To run this workflow, a certificate to access www.bioinformatics.nl needs to instal...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

View Download Add New Item

WikiPathways workflows

Created: 2008-09-16 11:43:57 | Last updated: 2009-02-03 12:47:00

5 items in this pack

Comments: 0 | Viewed: 227 times | Downloaded: 54 times

Data Set Metadata Generator (1)

• Download

This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

Created: 2008-08-19 | Last updated: 2008-08-19

Credits: Andrea Wiggins

Retrieve Protein Sequence (1)

• Download

Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

Created: 2008-07-30 | Last updated: 2009-12-03

Credits: Katy Wolstencroft

Fasta_string_to_fasta_list (1)

• Download

Split a string containing a set of sequences in fasta format into a list for fasta formated sequences.

Created: 2008-06-06

Credits: Hamish McWilliam

EBI_FASTA (1)

• Download

Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement FASTA services (REST or SOAP) should be used instead.  

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Fetch today's xkcd comic (1)

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.  I just uploaded this example so I can play around with the myexperiment api.

Created: 2008-05-05 | Last updated: 2008-05-05

Credits: Alan Williams

Attributions: Fetch today's xkcd comic

Unique tags (2)

• Download

This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".

Created: 2008-03-11 | Last updated: 2008-03-11

Credits: Don Cruickshank

Attributions: Viking boat

Fetch PDB flatfile from RCSB server (1)

• Download

Given aPDB identifier such as '1crn', this workflow fetches the PDB format flatfile from the RCSB

Created: 2008-01-25 | Last updated: 2008-03-05

Credits: Katy Wolstencroft

Retrieve SNPs from regions around known genes (1)

• Download

Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

Created: 2007-11-07

Example of a conditional execution workflow (2)

• Download

If the input is true the workflow returns the temperature in Celsius, if false the temperature in Fahrenheit is returned.

Created: 2007-10-03 | Last updated: 2008-01-27

BLASTP with simplified results returned (2)

• Download

This workflow Performs a blastp search on protein sequence, extracts sequence id within the blast report and retrives the corresponding seuqences.

Created: 2007-10-03 | Last updated: 2008-03-06

Parse UniProt text file (2)

• Download

This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers. Example input for this workflow is: O35613

Created: 2007-10-03 | Last updated: 2009-12-03

Remove null values (2)

• Download

This workflow removes any null values from a list of strings

Created: 2007-10-03 | Last updated: 2007-11-13

DOI2PMID (2)

• Download

Converts Digital Object Identifiers into their corresponding PubMed identifiers, if they exist.

Created: 2007-10-03

NCBI Gi to Kegg Pathways (1)

• Download

User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways

find events in xray and radio (7)

• Download

instruments: hessiEC, phoenix2 attention: hessi name has changed!

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: Anja Le Blanc