- beg-bogas@psb.ugent.be - maillist.psb.ugent.be

[Beg-bogas] request on Ectocarpus and view in Artemini
by Thierry Tonon 23 Jun '10

23 Jun '10

To whom it may concer, I was working this morning on the Ectocarpus genome through the public database and try do view the locus Esi0080_0017 in Artemini. Unfortunately, Java opens, the sequence is loading, but after, I have an error message "Fatal error!" "The Application encountered and unforeseen error......Message: complement (114421..114550)" I hope you will be able to fix the problem very soon. Thank you very much in advance to consider my request. Yours sincerely. Thierry. -- Thierry Tonon Abiotic Stress and Functional Genomics of Seaweeds UMR 7139 CNRS-UPMC Station Biologique Place Georges Teissier 29682 Roscoff cedex France Tel.: +33 (0)2 98 29 23 30 Fax: +33 (0)2 98 29 23 85 Emails: tonon(a)sb-roscoff.fr thitonon(a)gmail.com http://www.sb-roscoff.fr/UMR7139/

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Re: [Beg-bogas] BOGAS - Bathycoccus Annotation
by Rodrigo De la Iglesia 22 Jun '10

22 Jun '10

Dear Stephan: Hope you are doing well. I change my computer and I forgot my login/password to access to the bathycoccus genome. Could you please give me that information?+ best regards. Rodrigo 2010/3/29 <beg-bogas(a)psb.vib-ugent.be> > Dear, > > please find your invitation code to access the bathycoccus 454 data and its > annotation. > > > http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitationcode/766b… > > by clicking on this link you will be directed to a page to register, choose > your login and password etc. > If the link doesn't work, try to go to _url and enter > 766b6fd897514d6db8ff29ea9b66a982 > > Best regards > Stephane > > > -- Rodrigo De la Iglesia, PhD Profesor Asistente Laboratorio de Microbiología Marina Facultad de Ciencias Biológicas P. Universidad Católica de Chile Alameda 340, Casilla 114-D 56-2-6862845 (rdelaigl(a)bio.puc.cl)

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[Beg-bogas] [BOGAS] #164: add link to previous release
by BOGAS 17 Jun '10

17 Jun '10

#164: add link to previous release -------------------------+-------------------------------------------------- Reporter: strom | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- Have a link and search option to go to the previous release of an annotation. This means that we have 2 databases for a same genome project. What should be shown is a non-editable, non-browsable snapshot from the previous release (structure, blast hits, domains etc) in a new window. Also, with a search one should be able to seach (not default) in the previous release (using keywords or locus ID) and find the corresponding locus in the current release. In the transition period between 2 releases this might be quite useful. -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/164> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] User account request
by 滝尾進 03 Jun '10

03 Jun '10

Dear Sirs, I am studying red algal retrotransposons. From the publication by Nature, I found that Ectocarpus genome webpage is available. Then, I visited to the webpage of Ectocarpus (http://bioinformatics.psb.ugent.be/webtools/bogas/ ), but could not open the page. Please let me know the procedures for getting the user account. Sincerely yours, S. Takio ********************************************** Dr. Susumu TAKIO Center for Marine Environment Studies Kumamoto University Kurokami 2-39-1 Kumamoto 860-8555 Japan TEL & FAX: (81)96-342-3443 mail: stakio(a)gpo.kumamoto-u.ac.jp **********************************************

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[Beg-bogas] [BOGAS] #163: make EST stuff more efficient
by BOGAS 15 May '10

15 May '10

#163: make EST stuff more efficient -------------------------+-------------------------------------------------- Reporter: liste | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- see if cannot make est routines/tables more efficient. eg. feasible to calculate 'model-fit' on the fly (+no need to store that info -> est table remains fixed) => OK for graphics prob: how to get model-fir info to text part of page?? + checking fit should be quick -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/163> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #162: remove 'redundancy' in prot-aln table
by BOGAS 06 May '10

06 May '10

#162: remove 'redundancy' in prot-aln table -------------------------+-------------------------------------------------- Reporter: liste | Owner: liste Type: enhancement | Status: new Priority: minor | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- if the alignment of best10 == one of the others (= only prot eg from same species) don't remake/store the aln again, just put pointer to other aln. (=> modif in graphics.pm needed) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/162> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] Esi0340_0006
by Cecile Herve 15 Apr '10

15 Apr '10

Dear colleague, I'm currently working on the annotation of the multigenic C5-epimerase family from the Ectocarpus siliculosus genome. I have a problem with one gene: it looks like I can't get access to the genomic sequence of Esi0340_0006 as Artemini doesn't want to open properly (it gives a fatal error message each time). I don't know if you can fix this or if you know another way I can get the genomic sequence for this particular gene? With many thanks, Sincerely, Cécile -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Cécile Hervé UMR7139 Marine Plants and Biomolecules Station Biologique de Roscoff Place Georges Teissier BP74 29682 Roscoff FRANCE Tel. +33(0) 298 292 323 (ask n°403) Fax. +33(0) 298 292 324

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[Beg-bogas] new version BOGAS
by Lieven Sterck 06 Apr '10

06 Apr '10

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[Beg-bogas] [BOGAS] #160: blast-hits and seq in AnnoJ
by BOGAS 30 Mar '10

30 Mar '10

#160: blast-hits and seq in AnnoJ -------------------------+-------------------------------------------------- Reporter: liste | Owner: liste Type: enhancement | Status: new Priority: minor | Milestone: BOGAS_v4 Component: AnnoJ | Version: Keywords: | -------------------------+-------------------------------------------------- see if we can present blast-hits and hte actual seq in annoJ-BOGAS (without putting seq in DB) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/160> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #159: make locus_id stuff case insensitive
by BOGAS 30 Mar '10

30 Mar '10

#159: make locus_id stuff case insensitive -------------------------+-------------------------------------------------- Reporter: liste | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- thx to mibel, we spotted a 'bug' in handeling the locus_ids when capitals are (not) used, some of the pics are wrong because they do 'eq' in stead of regEx. -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/159> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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