Log in
Register
Give us Feedback
InviteWorkflow Entry: Fetch PDB flatfile from RCSB server
| Citations (0) | Version History | Reviews (1) | Comments (4) |
 Version 1
(of 1)
|
Version created on:
25/01/08 @ 11:52:38
by:
Katy Wolstencroft
|
Revision comments 
Last edited on: 05/03/08 @ 16:11:13 by: Katy Wolstencroft
Title: Fetch PDB flatfile from RCSB server
Type: Taverna 1
Preview
(Click on the image to get the full size)
Download Scalable Diagram (SVG)
Description
Given aPDB identifier such as '1crn', this workflow fetches the PDB format flatfile from the RCSB
Download
Run
Run this Workflow in the Taverna Workbench...
Option 1:
Launch in TavernaNote: 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/133/download?version=1
[ More Info ]
Workflow Components
Workflow Type
Log in to add Tags
Shared with Groups (1)
Current:
5.0 / 5
(1 rating)
Log in to rate and see breakdown of ratings
Statistics
None
Earliest Version:
[1] - Fetch PDB flatfile from RCSB server
This Workflow only has one version.
Reviews
(1)
View
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Linked Data
Non-Information Resource URI: http://www.myexperiment.org/workflows/133
Alternative Formats
Copyright © 2007 - 2011 The University of Manchester and University of Southampton
Log in to make a comment
It would be good to have some sort of md5 check - because when you use batch downloads, sometimes you can have network problems and not be aware of it.
Also, you can save the date of the download and the version of pdb database, to make the experiment easier to reproduce.
Also, it could give an error message when the pdb protein doesnt' exists (e.g. un-existing ids, keywords, etc..)
I agree with Giovanni on the error message / early failure. Still, something like this workflow should be immediately available at startup of Taverna. The novice Taverna user should not need to despair over not finding such basic routines. Same for sequences.
No idea if this already worked for Taverna 1.7 but for 2.x I am definitely missing an example value for the input port, i.e. 1crn.