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

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

1 0

[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

1 0

[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.

2 1

[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

1 0

[Beg-bogas] Message diffusion : Authorization reject
by SYMPA 28 Feb '12

28 Feb '12

Your message for list 'fmg' (attached below) was rejected. You are not allowed to send this message for the following reason : Message diffusion in the list is restricted to list subscribers. For further information, please contact fmg-request(a)kendy.up.ac.za

1 0

[Beg-bogas] bogas
by Christophe Plomion 24 Jan '12

24 Jan '12

dear colleague can I get a username to connect at http://bioinformatics.psb.ugent.be/webtools/bogas/ <http://bioinformatics.psb.ugent.be/webtools/bogas/%29%C2%A0> thanks christophe Le 23/01/2012 19:24, Zander Myburg a écrit : > Dear EUCAGEN members and genome paper collaborators, > This is a quick update on the status of the DOE-JGI /E. grandis > /genome project and the associated genome paper. There has been some > important developments that will affect the genome analysis, the > schedule of the genome paper and the content of companion papers. > ** > *UPDATED ANNOTATION (V1.1)* > The JGI has produced a new filtered annotation set (V1.1) of the > initial 8X mapped /Eucalyptus grandis BRASUZ1/ genome assembly. This > version (1.1) is a subset of the initial annotation (1.0) and was > released together with Phytozome 8.0 (Jan 16, 2012). V1.1 was produced > by filtering (out) 8620 low-confidence gene models from the original > v1.0 annotation using criteria described on Phytozome > http://www.phytozome.net/eucalyptus.php. Most of the removed gene > models are short, incomplete models with little or no EST support and > most form singletons in the Phytozome gene cluster database (i.e. they > do not cluster with any other known proteins). In short, we consider > this subset (36,376 primary protein coding loci) a high confidence > subset and will report it as such in the main genome paper. Some > contributors have already indicated that they have expression evidence > for some removed gene models, or that they can find full length > versions of the gene models using their own gene predictions. It is > therefore likely that some legitimate gene models are included in the > filtered set, which is why V1.0 will still be available in Phytozome > (browser track and searchable). My opinion is that the filtered set is > an important part of the genome biology of Eucalyptus - we see many > pseudogenes and it is possible that the genome is undergoing gene loss > after whole-genome duplication and high rates of tandem duplication. > The V1.1 annotation files are available for download at > ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Egrandis/annotation/. The > low confidence, filtered set is also available for download there. > We have decided to report gene numbers for the initial V1.0 annotation > in the main genome paper and to report the V1.1 subset as a "high > confidence" subset. This means that collaborators working on companion > papers can keep V1.0 models in figures and tables, and then provide > summary data for the high confidence models in their papers and > supplementary materials as needed. We would like people to rather > highlight the high confidence subset rather than the low confidence > filtered set. > *GENOME PAPER DRAFT* > I am at JGI this week working with Jerry Tuskan on the first full > draft of the main genome paper. By the end of the week, we will have a > much better idea of which contributed analyses, figures and tables can > be included. Some of the analyses done for the genome paper (e.g. > whole-genome duplication analysis) will have to be rerun with V1.1. We > will contact people directly for updated results. In some cases we > also need both a short and a detailed version of the methods used to > produce the contributed results (for the Online Methods and > Supplementary Notes sections of the paper). We will contact people > directly for that. Please be ready to provide updated results (v1.1 > numbers) and methods for the genome paper draft. At this stage we are > looking at producing a final draft by end of March/early April and > will circulate the first draft to core collaborators as soon as possible. > *COMPANION PAPERS* > We have a list of draft companion paper abstracts that we will use to > motivate a special issue of New Phytologist. If anybody wants to > submit additional abstracts for consideration, those can be emailed to > me by the end of this week. An updated list of submitted abstracts > will be uploaded to the Eucalyptus Genome Wiki on > BOGAS (http://bioinformatics.psb.ugent.be/webtools/bogas/) > <http://bioinformatics.psb.ugent.be/webtools/bogas/%29%A0> At this > stage, we would like companion papers to be in final draft by mid > April. Papers that do not get included in the New Phytologist special > issue can be submitted in other relevant journals such as BMG Genomics > and Tree Genetics and Genomes. > *E. CAMALDULENSIS GENOME* > KASUZA DNA Research Institute in Japan has decided to release the E. > camaldulensis genome sequence data which they have produced via the > genome database on Kazusa DNA Inst website, > http://www.kazusa.or.jp/eucaly/. Details of the database construction > will be published on the Japanese Society for Plant Cell and Molecular > Biology website http://www.jspcmb.jp/english/pbcontents/index.html. We > are delighted about this development. The E. camaldulensis genome > data, together with the E. globulus genome data produced by JGI and by > collaborators in Australia will be very valuable for comparative > genomics among these three representatives of the main sections of the > subgenus Synphyomyrtus including most of the commercially grown > eucalypts. We encourage collaborators to make use of the E. > camaldulensis genome resource. > I hope that you find this information useful. Please email me if you > have any questions or suggestions for the main genome paper or > companion papers. > Kind regards > Zander Myburg > ** > > > >>> > *From: * "David M. Goodstein" <dmgoodstein(a)lbl.gov> > *To:* <phytozome-user(a)lists.lbl.gov> > *Date: * 2012/01/17 01:51 PM > *Subject: * Announcing the release of Phytozome v8.0 > > Highlights include: > > *JGI Genomes:* > -preliminary assembly and annotation of */Panicum virgatum/* > (switchgrass) and */Phaseolus vulgaris/* (common bean) > -assembly and annotation of the arabidopsis comparator */Capsella > rubella/* > -Updated annotations of /*Aquilegia coerulea*, *Eucalyptus grandis*/, > and */Volvox carteri/* > * > * > *External Genomes:* > *-*updated annotations of /*Brachypodium distachyon*/, /*Oryza > sativa*/ (rice), /*Zea mays* /(maize) > -addition of */Linum usitatissimum/ *(flax), /*Brassica rapa*/ (napa > cabbage), */Malus domestica/ *(apple). > > > regards, > > The JGI Phytozome Team > > > > > > > > > > > >

1 0

[Beg-bogas] [BOGAS] #184: genome / annotation stats summary table
by BOGAS 19 Jan '12

19 Jan '12

#184: genome / annotation stats summary table -------------------------+-------------------------------------------------- Reporter: brhel | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- A table describing some genome / annotation statistics. This table should be updated using a script (and not after each gene update, as it might hog resources on large genomes). I will come up with a Proposal involving a script to generate the stats + a MySQL table structure to store this data. -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/184> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

1 0

[Beg-bogas] 1 New Mail Message
by UGent Webmail Service 12 Jan '12

12 Jan '12

1 0

[Beg-bogas] [BOGAS] #183: webserver cache
by BOGAS 23 Dec '11

23 Dec '11

#183: webserver cache ---------------------+------------------------------------------------------ Reporter: strom | Owner: liste Type: defect | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | ---------------------+------------------------------------------------------ Keeping images etc in the cache of the web server is nice to speed-up the visualization. But some time every 12-24h, this cache should be purged... updating data on bogas, to then see that nothing changes is frustrating/misleading for all... Can't we put an expiration date on files in the cache? -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/183> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

1 0

[Beg-bogas] problems blasting in the ectocarpus website
by Andres Ritter 23 Dec '11

23 Dec '11

Dear Mr(s), I can not blast into the ectocarpus genome any more. Is this normal? Greetings, -- *Andrés RITTER* Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Portugal 49 Santiago - Chile Casilla114-D

2 1