Hi, You should be able to load this workflow into Taverna 2 also. Taverna 2 has inbuilt functionality to convert T1 workflows to T2.
However, my recent experience with T2.1 found that it is VERY strict with iteration strategies, as a result I had to 'modify' some of my earlier workflows. Happy hacking! Paul. Matthias Hoys wrote: > 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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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/ > ------------------------------------------------------------------------------ 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/
