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Arek Kasprzyk | 1 May 2012 15:34
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Re: [BioMart Users] incorrect links for Ensembl Genomes genes

Hi Dan,

The hyperlinks on the 08 portal appear to be correct but not In the 07version. In 07 the Ensembl Genomes are dependent on the global variable 'exturl' that points to Ensembl site.  I guess the way to fix it would be to manually edit the links on your side and make them independent from the 'exturl'. We would then pick up the change on our 07 portal.


a

On Fri, Apr 20, 2012 at 10:39 AM, Dan Staines <dstaines <at> ebi.ac.uk> wrote:


On 04/20/2012 03:25 PM, Arek Kasprzyk wrote:
Hi Dan,
the portals are being updated right now, so hopefully this should get
'smuggled in' as well

superb, thanks!


--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/



--
Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead
www.biomart.org
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Danny | 3 May 2012 16:19
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[BioMart Users] retrieving sequences


 Hi everyone. I need to retrieve the sequences of all transcripts and 3'UTRs from the EPO mammals, preferibly in one single fasta file. What's the way? Thanks a lot.
                                                                                Danny
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Celine Noirot | 3 May 2012 09:27
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[BioMart Users] Sort of filters is not keep

Hi,
I'm doing the configuration a martform with mart editor, I sorted
filter as I want  but after saving it and reopen the sort is not keep
like shown in joined image (depth and length are before Name). And in
frontend it's always printed at the end of the form (contig form).
Do you know this trouble ? How can I fix it ?
Regards
Céline

--

-- 

Céline Noirot
Plateforme Bioinfo Genotoul- Unité BIA
INRA, 24 Chemin de Borde Rouge - Auzeville
CS 52627
31326 Castanet Tolosan cedex
Tel. 05 61 28 57 24
http://bioinfo.genotoul.fr

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George Gutman | 2 May 2012 08:30
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[BioMart Users] Where to address questions

I'm trying to download collections of protein coding regions from various
genomes and am having trouble.  Where can I address my questions?  Do I
need to be a member of this list to post here?

     George Gutman
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Arek Kasprzyk | 3 May 2012 18:55
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Re: [BioMart Users] Where to address questions

Dear George,

please feel free to post here and we'll try to help you. Please give us more details on your problem, the portal that you are using etc


a

On Wed, May 2, 2012 at 2:30 AM, George Gutman <gagutman <at> uci.edu> wrote:
I'm trying to download collections of protein coding regions from various
genomes and am having trouble.  Where can I address my questions?  Do I
need to be a member of this list to post here?

    George Gutman
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Arek Kasprzyk | 3 May 2012 18:57
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Re: [BioMart Users] retrieving sequences

Hi Danny,

did you try a sequence retrieval tool from BioPortal?


a


On Thu, May 3, 2012 at 10:19 AM, Danny <dannyjmh <at> gmail.com> wrote:

 Hi everyone. I need to retrieve the sequences of all transcripts and 3'UTRs from the EPO mammals, preferibly in one single fasta file. What's the way? Thanks a lot.
                                                                                Danny

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Arek Kasprzyk | 3 May 2012 18:59
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Re: [BioMart Users] Sort of filters is not keep

Hi Celine,

would you be able to provide a few screen shots to help us understand the problem?

cheers,
a

On Thu, May 3, 2012 at 3:27 AM, Celine Noirot <Celine.Noirot <at> toulouse.inra.fr> wrote:
Hi,
I'm doing the configuration a martform with mart editor, I sorted
filter as I want  but after saving it and reopen the sort is not keep
like shown in joined image (depth and length are before Name). And in
frontend it's always printed at the end of the form (contig form).
Do you know this trouble ? How can I fix it ?
Regards
Céline

--

Céline Noirot
Plateforme Bioinfo Genotoul- Unité BIA
INRA, 24 Chemin de Borde Rouge - Auzeville
CS 52627
31326 Castanet Tolosan cedex
Tel. 05 61 28 57 24
http://bioinfo.genotoul.fr

_______________________________________________
Users mailing list
Users <at> biomart.org
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Prateek Kumar | 3 May 2012 18:59
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[BioMart Users] Mark some attributes as checked by default

Hi 


I am trying to use biomart 0.8 rc 6 martconfigurator to set some attributes as checked by default, I tried to set the property "default" to true but its not one of the changeable properties. Can I do this by making setting some internal modification (rather than through the configurator)? I know this should be possible because the same source when viewed as "Analysis" portal internally has all attributes checked.

Thanks
Prateek
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Gert Hulselmans | 2 May 2012 16:55
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[BioMart Users] Biomart v0.8 - last svn: "Filters" and "Attributes" list empty when using OpenID login.

Hi,

I am using Biomart v0.8 - last svn.

When I add a group and a user for usage with OpenID and
try to login to my BioMart server (webinterface), I can select
one of my datasets, but the "Filters" and Attributes" list stay
empty.

The BioMart server works fine for the anonymous user
(full list of options below "Filters" and "Attributes").

Can this be fixed?

- Gert Hulselmans
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Estrella, Heather | 3 May 2012 19:07
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Re: [BioMart Users] Sort of filters is not keep

Hi Celine, 

I think I've run into a similar problem with some of the ordering in Martconfigurator when a drag/drop the
attributes or filters within Martconfigurator.  It's a sporadic problem. What I found works when I run
into the problem is to right click and use the "move up" and "move down" options to do the ordering rather
than drag/drop with the mouse. Most of the time though drag/drop with the mouse works OK.

Sometimes restarting martconfigurator helps too.

Heather

-----Original Message-----
From: users-bounces <at> biomart.org [mailto:users-bounces <at> biomart.org] On Behalf Of Celine Noirot
Sent: Thursday, May 03, 2012 12:28 AM
To: users <at> biomart.org
Subject: [BioMart Users] Sort of filters is not keep

Hi,
I'm doing the configuration a martform with mart editor, I sorted
filter as I want  but after saving it and reopen the sort is not keep
like shown in joined image (depth and length are before Name). And in
frontend it's always printed at the end of the form (contig form).
Do you know this trouble ? How can I fix it ?
Regards
Céline

-- 

Céline Noirot
Plateforme Bioinfo Genotoul- Unité BIA
INRA, 24 Chemin de Borde Rouge - Auzeville
CS 52627
31326 Castanet Tolosan cedex
Tel. 05 61 28 57 24
http://bioinfo.genotoul.fr

_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users
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Gmane