October 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

1 1

[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

1 3

[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

1 1

Re: [Beg-bogas] BOGAS - Eucalyptus grandis Annotation
by Erich Bornberg 27 Oct '11

27 Oct '11

Thanks for your email. I am currently out of office but will try to catch up with emails from Oct. 30th onwards. EB

1 0

[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 27 Oct '11

27 Oct '11

2011/10/27 20:33:06 An error occured connecting to the database server Error message below: DBI connect('bogas_mipuc:psbsql04:3306','bogas',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 0 at /www/group/biocomp/extra/bioinformatics_prod/webtools/sandbox/liste/BOGAS/trunk/src/perl/modules/BOGAS/DB.pm line 260

1 0

[Beg-bogas] [BOGAS] #179: opsplitsen CACHE directory
by BOGAS 26 Oct '11

26 Oct '11

#179: opsplitsen CACHE directory -------------------------+-------------------------------------------------- Reporter: brhel | Owner: liste Type: enhancement | Status: new Priority: minor | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- momenteel wordt alles opgeslagen in één directory -> opsplitsen per genoom(versie) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/179> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

1 0

[Beg-bogas] [BOGAS] #178: annotation summary table
by BOGAS 24 Oct '11

24 Oct '11

#178: annotation summary table -------------------------+-------------------------------------------------- Reporter: brhel | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- Het zu handig zijn om op de 'overview' pagina een tabel te hebben met de standaard annotatie statistieken: - aantal (multi-exon) genen - aantal introns - aantal EST-gevalideerde genen - aantal homology-supported genen - ... Natuurlijk zou deze tabel af en toe moeten geupdate worden -> via een cron-job elke week ofzo (indien er gewerkt is aan deze annotatie in die week; gemakkelijk te checken via de modification_date ) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/178> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

1 0

[Beg-bogas] [BOGAS] #177: EST assignment -> UTR assignment problem
by BOGAS 24 Oct '11

24 Oct '11

#177: EST assignment -> UTR assignment problem ---------------------+------------------------------------------------------ Reporter: brhel | Owner: liste Type: defect | Status: new Priority: major | Milestone: Component: Website | Version: Keywords: | ---------------------+------------------------------------------------------ De volgende situatie doet zich voor: - een EST wordt toegekend aan een gen - de structuur van de EST komt niet overeen met het gen - de EST wordt wel gebruikt om de 'outer UTR' border van het gen te bepalen -> de EST staat nu op 'Y' ipv op 'N' -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/177> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

1 0

[Beg-bogas] Returned mail: see transcript for details
by Mail Delivery Subsystem 21 Oct '11

21 Oct '11

The original message was received at Fri, 21 Oct 2011 01:06:59 +0200 from localhost.localdomain [127.0.0.1] ----- The following addresses had permanent fatal errors ----- <dunan(a)lrsv.ups-tlse.fr> (reason: 550 5.1.1 <dunan(a)lrsv.ups-tlse.fr>: Recipient address rejected: User unknown in local recipient table) ----- Transcript of session follows ----- ... while talking to polext1.scsv.ups-tlse.fr.: >>> DATA <<< 550 5.1.1 <dunan(a)lrsv.ups-tlse.fr>: Recipient address rejected: User unknown in local recipient table 550 5.1.1 <dunan(a)lrsv.ups-tlse.fr>... User unknown <<< 554 5.5.1 Error: no valid recipients

1 0

[Beg-bogas] [BOGAS] #176: change gene type
by BOGAS 17 Oct '11

17 Oct '11

#176: change gene type -------------------------+-------------------------------------------------- Reporter: brhel | Owner: Liste Type: enhancement | Status: new Priority: minor | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- It would be easy to allow rapid changes from 'mRNA' to 'pseudo' and vice versa. However, now I have to do these changes manually through psbsql04 -> For someone without access, it is not possible to do this! -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/176> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

1 0