Thanks Paul, I managed to load your first example workflow into my Taverna 1.7.1 installation. After putting some stuff in comment in the mygrid.properties config file, the program starts fine now. Let's play a bit :-)
Matthias -----Original Message----- From: Paul Fisher [mailto:[email protected]] Sent: Tuesday, July 14, 2009 2:51 PM To: [email protected] Subject: Re: [Taverna-users] New to Taverna - NCBI workflow Hi, Kieren is correct. One example I can think of is: http://www.myexperiment.org/workflows/25 And if you note the author.... ;) Another workflow that may be of use is http://www.myexperiment.org/workflows/172 In this workflow, I take the output of an NCBI search, and use xpath queries to get results from the NCBI xml file returned. You can chop and change the workflow as you see fit. At the moment it takes a kegg pathway description and finds publications for it. Not very useful for what you want, but can act as an example of how to use the NCBI services. regards, Paul. Kieren Lythgow wrote: > 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! 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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. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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/
