Hi Matthias, There are plenty of examples at http://www.myexperiment.org/ and I'm sure this will provide you with a good head start with any workflows you plan to develop.
Thanks Kieren Lythgow PhD student Mitochondrial Research Group Institute for Ageing & Health Newcastle University UK ________________________________________ From: Matthias Hoys [[email protected]] Sent: 14 July 2009 09:48 To: [email protected] Subject: [Taverna-users] New to Taverna - NCBI workflow Hello, First of all I'm pretty new to Taverna. I already downloaded and installed version 2 and played a bit with it. I even managed to get it working through our dreaded proxy server ;-) Now I've been thinking of using Taverna to semi-automate some data extractions from Genbank. This is what I would like to do: 1) input list = a list of GI or accession numbers 2) do a search in the NCBI nucleotide database for this list of GI numbers 3) retrieve the results in Genbank format 4) extract some data fields out of the Genbank records (for example: "product" or "info" fields 5) finally create a csv file with the following columns: GI number, "product" field, "info" field Is it difficult to do this with Taverna? I guess I will have to register the NCBI Entrez web services as activities, probably the ESearch and EFetch utilities? Has anyone created a workflow like this before? Thanks, Matthias _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ This e-mail and any attachments thereto may contain information which is confidential and/or protected by intellectual property rights and are intended for the sole use of the recipient(s) named above. Any use of the information contained herein (including, but not limited to, total or partial reproduction, communication or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received this e-mail in error, please notify the sender either by telephone or by e-mail and delete the material from any computer. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Devgen NV. Thank you for your cooperation. ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
