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

[Beg-bogas] Populus gene density data
by Vining, Kelly 02 Dec '11

02 Dec '11

Hello, I see you have a chromosome graphic showing poplar gene density on the Bogas home page. Could you please tell me where I might be able to download/plot this gene density data to generate my own graphic? What tool did you use to generate this graphic? Thanks for any help. Kind regards, Kelly Vining Faculty Research Associate 352 Richardson Hall Oregon State University Corvallis, OR 97331 (541) 737-2843

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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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[Beg-bogas] [BOGAS] #182: go to search page
by BOGAS 23 Nov '11

23 Nov '11

#182: go to search page -------------------------+-------------------------------------------------- Reporter: strom | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- when a search from the main pages (a wrong ID or a name was given) failed, the return to search link should not bring the user back to the main page but to the full search page... to suggest the user to formulate a better search. -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/182> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #181: web interface
by BOGAS 23 Nov '11

23 Nov '11

#181: web interface -------------------------+-------------------------------------------------- Reporter: strom | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- to avoid confusion. hide/show "private" items depending on public access or moderated access. E.g. the WIKI is not public, but the link is there still visible. If not logged in, it should not show on the public site. -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/181> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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