About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
NCBI BLAST (SOAP)

Workflow Entry: NCBI BLAST (SOAP)

Created at: 29/11/10 @ 20:46:58 Last updated: 29/11/10 @ 20:47:00

Version 1 (of 1)

Version created on: 29/11/10 @ 20:46:58 by: Hamish McWilliam | Revision comments Expand

Title: NCBI BLAST (SOAP)

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/1689/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (5)

Name	Description
Email	Your e-mail address. For example: email@example.org.
Program	NCBI BLAST program to use for search. For example: blastp.
Databases	List of databases to search. For example: uniprotkb_swissprot.
Sequence	Query sequence. Either sequence data in any common format, or an entry identifier in DB:ID format. For example: uniprot:wap_rat.
Sequence_type	Query sequence type. Either protein or nucleotide.

Processors (9)

Name	Type	Description
run	arbitrarywsdl	Submit an analysis job See the Service entry for this web service.
parametersXML	local
parametersXML1	local
parametersXML2	local
getResult	arbitrarywsdl	Get a job result formatted using a particular renderer See the Service entry for this web service.
parametersXML3	local
parametersXML4	local
Job_status_poll	workflow
Byte___to_String	local

Beanshells (1)

Name	Description	Inputs	Outputs
Is_Running		job_status	is_running

Outputs (3)

Name	Description
JobId
Job_status
Result

Links (16)

Source	Sink
Databases	parametersXML1:database
Email	parametersXML:email
Program	parametersXML1:program
Sequence	parametersXML1:sequence
Sequence_type	parametersXML1:stype
Byte___to_String:string	Result
Job_status_poll:Job_Status	Job_status
getResult:parameters	parametersXML4:input
parametersXML1:output	parametersXML:parameters
parametersXML2:jobId	Job_status_poll:JobId
parametersXML2:jobId	parametersXML3:jobId
parametersXML3:output	getResult:parameters
parametersXML4:output	Byte___to_String:bytes
parametersXML2:jobId	JobId
parametersXML:output	run:parameters
run:parameters	parametersXML2:input

Coordinations (1)

Controller	Target
Job_status_poll	getResult

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (2)

(Workflows/Files)

Information Tags (7)

Original Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (1)

(Workflows/Files)

NCBI BLAST (SOAP)

Information Favourited By (0)

No one

Information Statistics

107 viewings

299 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - NCBI BLAST (SOAP)

Created on: Monday 29 November 2010 @ 20:46:58 (GMT)

Created by: Hamish McWilliam

Revision comments:

None

This Workflow only has one version.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (7)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Original Uploader

Katy Wolstencroft

EBI_NCBI_BLAST (v1)

Created: 17/01/11 @ 12:51:58 | Last updated: 17/01/11 @ 12:52:03

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow performs an NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

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

Viewed: 75 times | Downloaded: 34 times

Tags (13):