Hello Kieren, I found a nice example workflow on myexperiment.com but it's written for Taverna 1. I now downloaded and installed Taverna 1.7.1 but on startup it seems to hang on "Populating service list" (proxy settings are filled in). Any idea what this could mean?
Thanks, Matthias -----Original Message----- From: Kieren Lythgow [mailto:[email protected]] Sent: Tuesday, July 14, 2009 1:36 PM To: [email protected] Subject: Re: [Taverna-users] New to Taverna - NCBI workflow 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. 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