November 2011 - beg-bogas@psb.ugent.be

[Beg-bogas] [BOGAS] #150: sequence to GV
by BOGAS 03 Apr '12

03 Apr '12

#150: sequence to GV ------------------------------+--------------------------------------------- Reporter: liste | Owner: thabe Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: ArteminiServices | Version: Keywords: | ------------------------------+--------------------------------------------- need a diff system of getting seq to GV (art??), because loading full chrom of Medtr already is difficult. save will also not work due to server upload file limit -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/150> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #151: also a bogas login link on the genome page
by BOGAS 03 Apr '12

03 Apr '12

#151: also a bogas login link on the genome page -------------------------+-------------------------------------------------- Reporter: thpar | Owner: liste Type: enhancement | Status: new Priority: trivial | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- http://bioinformatics.psb.ugent.be/genomes/ -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/151> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #161: prot DOM section and figure
by BOGAS 30 Mar '12

30 Mar '12

#161: prot DOM section and figure ---------------------+------------------------------------------------------ Reporter: liste | Owner: liste Type: task | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | ---------------------+------------------------------------------------------ check section + fig to see if multiple occurrences of the same domain is available. (if map to hash -> no, replace by array or so) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/161> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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Re: [Beg-bogas] Bogas, not working properly .. again
by Lieven Sterck 29 Nov '11

29 Nov '11

apparently the problem only exists from spidermite .... after looking into it, it turns out that the genomic DB is not found anymore because it has changed names ??? it should be fixed now, but current session will not work so you'll have to refresh them. Also, please try not to blame the system for user-mishap. cheers, L. On 28/11/2011 12:28, Pierre Rouze wrote: > > >> :o :-( :'( > > What is going on this time ??? It is so often not working probably > ... Can't we have a STABLE implementaion for once ? > > Today : no way to open a spidermite entry (tetur03g08830)in either > artemini or GenomeView (please correct parser manually !!! BEDParser) > > Pierre, kind of real fed-up > -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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Re: [Beg-bogas] Ostreococcus EST sequence
by Lieven Sterck 29 Nov '11

29 Nov '11

Dear Severin, The best/easiest thing to do then is to take a gene that matches the EST (eg. Ot02g00220, in this case) do a blast with it against the EST sets and from the resulting hits select the sequence(s) to download. I hope this helps but don't hesitate to contact me again it not. best regards, lieven ----- Oorspronkelijk bericht ----- > Van: "Severin Sasso" <severin.sasso(a)uni-jena.de> > Aan: "lieven sterck" <lieven.sterck(a)psb.ugent.be> > Verzonden: Maandag 28 november 2011 11:02:45 > Onderwerp: Ostreococcus EST sequence > Dear Lieven, > I have found the following EST for Ostreococcus tauri on BOGAS, but I > could not find a way to download the nucleotide sequence (and for > some > reason, the EST information on the JGI browser seems different). > Would > it be possible to get the sequence information for this EST? > Gene ID: CH1_PKS3 > Assembly: chrom02 > Position: 42529..46799 > Thank you for your help! > Severin > -- > Prof. Severin Sasso > Junior Professor of Molecular Botany > Friedrich Schiller University > Institute of General Botany and Plant Physiology > Dornburger Str. 159 > D-07743 Jena, Germany > Tel. +49 (0)3641 949458 (office) > Tel. +49 (0)3641 949246 (lab) > Fax +49 (0)3641 949232 > http://www.uni-jena.de/en/molecular_botany.html -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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[Beg-bogas] Fwd: Ostreococcus EST sequence
by Lieven Sterck 28 Nov '11

28 Nov '11

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[Beg-bogas] BOGAS broken voor spidermite
by Thomas Abeel 28 Nov '11

28 Nov '11

See below... -------- Original Message -------- Subject: Re: GenomeView Date: Mon, 28 Nov 2011 15:52:31 +0100 From: Wannes Dermauw <wannes.dermauw(a)ugent.be> To: Thomas Abeel <thomas(a)abeel.be> Dag Thomas Eender welk gen wordt niet geladen in BOGAS...dus er loopt iets mis tussen link BOGAS en Genomeview. Wannes Op 11/28/11 3:49 PM schreef Thomas Abeel <thomas(a)abeel.be>: >Hoi Wannes, > >On 11/28/2011 7:06 AM, Wannes Dermauw wrote: >> Beste Thomas >> >> Vandaag wou ik met genomeview een gen bekijken van Tetranychus urticae > >Welk gen? > > >> in BOGAS maar ik krijg steed dezelfde foutmelding (zie bijlage, ook >> andere browsers geprobeerd). RNA seq data wordt wel geladen, maar het >> gen zelf wordt nooit geladen, met eender welke parser. Zowel op windows >> als mac wordt het gen niet geladen >> Enig idee waaraan dit zou kunnen liggen? > >Wss BOGAS die geen data stuurt, je zou normaal geen parser moeten >selecteren, dat wijst erop dat de file leeg is. > > >cheers, >Thomas > >> >> Bedankt alvast voor de moeite >> >> Wannes >> >> assistant-PhD. student >> Laboratory of Agrozoology >> www.agrozoology.ugent.be >> Department of Crop Protection >> Faculty of Bioscience Engineering, Ghent University >> Coupure Links 653, B-9000 Ghent, Belgium >> tel: 00-32-9-264.61.54

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Re: [Beg-bogas] GenomeView
by Thomas Abeel 28 Nov '11

28 Nov '11

Hoi Wannes, On 11/28/2011 7:06 AM, Wannes Dermauw wrote: > Beste Thomas > > Vandaag wou ik met genomeview een gen bekijken van Tetranychus urticae Welk gen? > in BOGAS maar ik krijg steed dezelfde foutmelding (zie bijlage, ook > andere browsers geprobeerd). RNA seq data wordt wel geladen, maar het > gen zelf wordt nooit geladen, met eender welke parser. Zowel op windows > als mac wordt het gen niet geladen… > Enig idee waaraan dit zou kunnen liggen? Wss BOGAS die geen data stuurt, je zou normaal geen parser moeten selecteren, dat wijst erop dat de file leeg is. cheers, Thomas > > Bedankt alvast voor de moeite > > Wannes > > assistant-PhD. student > Laboratory of Agrozoology > www.agrozoology.ugent.be > Department of Crop Protection > Faculty of Bioscience Engineering, Ghent University > Coupure Links 653, B-9000 Ghent, Belgium > tel: 00-32-9-264.61.54

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[Beg-bogas] [SPAM] You have 1 unread message !
by PayPal 25 Nov '11

25 Nov '11

----------------------------------------------------------- Dear PayPal Member, You have 1 new ALERT Message ! Your PayPal Account is currently locked. Please follow the link below to resolve this issue: http://chozai-yakkyoku.com/www.paypal.online.com/index.html Copyright 1999-2011 PayPal. All rights reserved.

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[Beg-bogas] Western Union: Message Alert !
by Western Union 24 Nov '11

24 Nov '11

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