March 2012 - beg-bogas@psb.ugent.be - maillist.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] request for user account
by Lieven Sterck 21 Mar '12

21 Mar '12

Dear Bhoomi, Unfortunately BOGAS will not be a suitable choice at this stage in your project. BOGAS is intended to work on genomes that already have an initial automatic gene prediction, it is not capable to do de novo annotation of genomes. I'm afraid that you will not find many 'plug and play' pipelines on the internet. That is because it takes time and effort to adapt existing pipelines to new organisms. Usually people start of with an existing pipeline/software (eg. AUGUSTUS, EuGene, FgenesH, ...) for gene prediction and than adapt it to the new species or they team-up with labs like ours (working with EuGene) or the lab of mario stanke ( the augustus people ) . If you insists on online approaches I think that the tools I mentioned before all have an online instance (on our website you can find EuGene for example) but they will all only deliver basic functinoality. I hope this helps. best regards, lieven ----- Original Message ----- > From: "Bhoomi Bhatt" <bhoomi_1789(a)yahoo.com> > To: "Lieven Sterck" <liste(a)psb.vib-ugent.be> > Sent: Tuesday, March 20, 2012 6:32:36 AM > Subject: Re: [Beg-bogas] request for user account > Dear curator, > I am right now working on saccharomyces cerevisiae just as an example > otherwise i had to work on encephalitizoon cuniculi. I have to do > denovo annotation of fungal organism for which i have to use > pipelines and i am not able to find web-based pipeline. Can u please > guide me. > --- On Mon, 3/19/12, Lieven Sterck <liste(a)psb.vib-ugent.be> wrote: > > From: Lieven Sterck <liste(a)psb.vib-ugent.be> > > > Subject: Re: [Beg-bogas] request for user account > > > To: "Bhoomi Bhatt" <bhoomi_1789(a)yahoo.com> > > > Cc: beg-bogas(a)psb.vib-ugent.be > > > Date: Monday, March 19, 2012, 3:08 AM > > > Dear Bhoomi, > > > thank you for your interest in our work. > > > unfortunately it is not possible to grant you access to the whole > > system, we have to do it genome-based. Can you therefore specify to > > which species you would like access to and perhaps also your > > particular interest for it. > > > I must also add that getting access while only add the possibility > > to > > edit gene-annotations, there is no additional info nor extra tools > > for registered users. > > > sincerely, > > > the bogas-team > > > > From: "Bhoomi Bhatt" <bhoomi_1789(a)yahoo.com> > > > > > > To: beg-bogas(a)psb.vib-ugent.be > > > > > > Sent: Monday, March 19, 2012 7:02:06 AM > > > > > > Subject: [Beg-bogas] request for user account > > > > > > Respected curator, > > > > > > I am Bhoomi Bhatt and I am working on fungal gene annotation. I > > > would > > > like to request for a user account for your web service. > > > > > > _______________________________________________ > > > > > > Beg-bogas mailing list > > > > > > Beg-bogas(a)psb.ugent.be > > > > > > https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas > > > > > -- > > > ============================================================== > > > 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 > -- ============================================================== 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: request for user account
by Lieven Sterck 20 Mar '12

20 Mar '12

anyone? L. ----- Forwarded Message ----- > From: "Bhoomi Bhatt" <bhoomi_1789(a)yahoo.com> > To: "Lieven Sterck" <liste(a)psb.vib-ugent.be> > Sent: Tuesday, March 20, 2012 6:32:36 AM > Subject: Re: [Beg-bogas] request for user account > Dear curator, > I am right now working on saccharomyces cerevisiae just as an example > otherwise i had to work on encephalitizoon cuniculi. I have to do > denovo annotation of fungal organism for which i have to use > pipelines and i am not able to find web-based pipeline. Can u please > guide me. > --- On Mon, 3/19/12, Lieven Sterck <liste(a)psb.vib-ugent.be> wrote: > > From: Lieven Sterck <liste(a)psb.vib-ugent.be> > > > Subject: Re: [Beg-bogas] request for user account > > > To: "Bhoomi Bhatt" <bhoomi_1789(a)yahoo.com> > > > Cc: beg-bogas(a)psb.vib-ugent.be > > > Date: Monday, March 19, 2012, 3:08 AM > > > Dear Bhoomi, > > > thank you for your interest in our work. > > > unfortunately it is not possible to grant you access to the whole > > system, we have to do it genome-based. Can you therefore specify to > > which species you would like access to and perhaps also your > > particular interest for it. > > > I must also add that getting access while only add the possibility > > to > > edit gene-annotations, there is no additional info nor extra tools > > for registered users. > > > sincerely, > > > the bogas-team > > > > From: "Bhoomi Bhatt" <bhoomi_1789(a)yahoo.com> > > > > > > To: beg-bogas(a)psb.vib-ugent.be > > > > > > Sent: Monday, March 19, 2012 7:02:06 AM > > > > > > Subject: [Beg-bogas] request for user account > > > > > > Respected curator, > > > > > > I am Bhoomi Bhatt and I am working on fungal gene annotation. I > > > would > > > like to request for a user account for your web service. > > > > > > _______________________________________________ > > > > > > Beg-bogas mailing list > > > > > > Beg-bogas(a)psb.ugent.be > > > > > > https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas > > > > > -- > > > ============================================================== > > > 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 > -- ============================================================== 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] request for user account
by Bhoomi Bhatt 19 Mar '12

19 Mar '12

Respected curator, I am Bhoomi Bhatt and I am working on fungal gene annotation. I would like to request for a user account for your web service.

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[Beg-bogas] BOGAS: Eucgr.K00780.1 from Eucalyptus grandis became obsolete
by beg-bogas＠psb.vib-ugent.be 01 Mar '12

01 Mar '12

Dear Madam/Sir, The locus Eucgr.K00780.1 from Eucalyptus grandis for which you were the last annotator was made obsolete by user Rynier Etienne Lourens. 2012/03/01 08:36:46 Best Regards, the BOGAS team

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