Re: [mart-dev] BioMart output

On Tue, 27 Feb 2007, Ewan Birney wrote: On 27 Feb 2007, at 14:04, Arek Kasprzyk wrote: On 22 Feb 2007, at 15:48, Rosienne wrote: Hi, a few weeks ago I was attending an Open Door Workshop at the Sanger. I had occasion to speak to one of your team and mention a couple of problems we

Re: [mart-dev] BioMart output

On Tue, 27 Feb 2007, Arek Kasprzyk wrote: On 27 Feb 2007, at 14:25, Will Spooner wrote: snip WormMart has the same gene/transcript (CDS in WormBase's case) issues. I solve this by 'merging' the multiple transcript values into a single attribute in the gene_main table. See this example

Re: [mart-dev] Gramene datasets, error 502

Floris CRS4 Bioinformatics -- == Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. == -- --- William Spooner WormMart Developer

Re: [mart-dev] Java 6

Hi Syed, Do you have any timeline on the next BioMart release, and any details (other than java 1.6 support) on what it will contain? Thanks, Will On 9 Oct 2009, at 06:48, Syed Haider wrote: I just had a quick run on Fedora's default J 1.6, it doesnt work. This may well be Fedora's J

Re: [mart-dev] Biomart for restricted access datasets

to use basic authentication. This worked for 0.4 but it seemed quite slow though. Now with Biomart 0.7 the connection via the reverse proxy simply times out. Allan. -- William Spooner w...@eaglegenomics.com http://www.eaglegenomics.com

Re: [mart-dev] Adding canned queries to MartView

, Hinxton, Cambridge CB10 1SD, UK. == --- William Spooner Visiting Scientist [EMAIL PROTECTED]

Re: [mart-dev] Adding canned queries to MartView

, William Spooner wrote: on the martview -- == Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. == --- William Spooner Visiting Scientist [EMAIL PROTECTED]

Re: [mart-dev] data missing from results

email: [EMAIL PROTECTED] -- == Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. == --- William Spooner Visiting Scientist [EMAIL PROTECTED]

Re: [mart-dev] data missing from results

and Uniprot e.g exturl|http://www.ebi.ac.uk/msd-srv/atlas?id=%s added this on the requirements list for 0.8 release. cheers syed On Fri, 2008-03-28 at 16:18 +, William Spooner wrote: Hi Syed, The URLs are internal (relative) to www.wormbase.org, or dev.wormbase.org, or one of the wormbase

Re: [mart-dev] data missing from results

or not check is based on forward slash. and unfortunately we only support one entry for exturl from settings.conf. cheers syed On Fri, 2008-03-28 at 16:54 +, William Spooner wrote: OK - So I assume that 'http://www.ebi.ac.uk' is substituted with whatever is in 'exturl'? In which case I can

[mart-dev] Re: [Wormbase-help] wormmart bookmark

that the BioMart developers are working on a method to load such XML back into WormMart, initialising the query. I am cc'ing the mart-admin list to see if there is any further insight on progress. All the best, Will --- William Spooner Visiting Scientist [EMAIL PROTECTED]

Re: [mart-dev] gramene datasets on biomart.org

believe that this limitation will be addressed in the 0.7 BioMart release in may (syed - correct me if wrong)? For now you need to use gramene.org to get the correct links. Will --- William Spooner Visiting Scientist [EMAIL PROTECTED]

[mart-dev] Debugging martview via URL

.peptide FILTERS =wormbase_gene.default.filters.species_selection.Caenorhabditis elegans| wormbase_gene .default.filters.identity_status.LiveVISIBLEPANEL=resultspanel Thanks in advance, Will --- William Spooner Visiting Scientist [EMAIL PROTECTED]

Re: [mart-dev] 'like' filters

records containing that word, not just equal to it. cheers, Richard -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/ --- William Spooner Visiting Scientist [EMAIL PROTECTED]