All content

Search filter terms
Filter by category
Filter by type
Filter by tag
Filter by user
Filter by licence
Results per page:
Sort by:
Showing 12 results. Use the filters on the left and the search box below to refine the results.
User: Wassinki Licence: by-sa
Uploader

Workflow Mapping OligoNucleotides to an assembly (7)

Thumb
Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Created: 2009-02-13 | Last updated: 2009-02-13

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

Uploader

Blob Installing java certificates for services using SSL

Created: 2008-10-15 09:05:44 | Last updated: 2009-02-16 07:37:39

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This jar file, designed by sun microsystems, helps you to install certificates for java to access services using a secure socket. The complete documentation of this small java tool, including its source, can be found at: http://blogs.sun.com/andreas/entry/no_more_unable_to_find In this document, I will explain how to create a keystore holding the certificate required to access services provided by www.bioinformatics.nl . To install the certificate for www.bioinformatics.nl, do the follow...

File type: Java archive

Comments: 1 | Viewed: 1709 times | Downloaded: 1468 times

Tags:

Uploader

Workflow AppendToFile (2)

Thumb
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: User Wassinki

Uploader

Workflow Blat against ENSEMBLE Danio_rerio_Genome (1)

Thumb
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: User Wassinki

Uploader

Workflow Analysing workflows (3)

Thumb
This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

Created: 2009-05-06 | Last updated: 2009-05-06

Credits: User Wassinki User Pieter Neerincx User Katy Wolstencroft User Marco Roos

Uploader

Workflow BlatBlastCombi (2)

Thumb
This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: User Wassinki

Uploader

Workflow Blast against ENSEMBLE Danio_rerio_Genome (1)

Thumb
This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

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

Credits: User Wassinki

Uploader

Workflow Test SOAP/WSDL Service Availability (1)

Thumb
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...

Created: 2009-05-29

Credits: User Wassinki

Uploader

Workflow Test SoapLab Service Availability (1)

Thumb
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

Created: 2009-05-29 | Last updated: 2009-05-29

Credits: User Wassinki

Uploader

Blob Test Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:06:36 | Last updated: 2008-12-11 12:21:53

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small test set to quickly test the workflow. This test set can be run on almost any computer and takes 5 minutes approximately.

File type: XML

Comments: 0 | Viewed: 795 times | Downloaded: 45 times

Tags:

Results per page:
Sort by: