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

[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 21 Oct '09

21 Oct '09

2009/10/21 14:48:37 An error occured connecting to the database server Error message below: No config found for genome 'Bathy' and release '666666'! at CheckAndStartBOGASupdate_dev.pl line 61

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 21 Oct '09

21 Oct '09

2009/10/21 14:45:01 An error occured connecting to the database server Error message below: No config found for genome 'Bathy' and release '666666'! at CheckAndStartBOGASupdate_dev.pl line 61

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 21 Oct '09

21 Oct '09

2009/10/21 14:44:37 An error occured connecting to the database server Error message below: No config found for genome 'Bathy' and release '666666'! at CheckAndStartBOGASupdate_dev.pl line 61

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 21 Oct '09

21 Oct '09

2009/10/21 14:40:56 An error occured connecting to the database server Error message below: No config found for genome 'Bathy' and release '666666'! at CheckAndStartBOGASupdate_dev.pl line 61

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Re: [Beg-bogas] BOGAS - Bathycoccus Annotation
by Dr. M. A. Huynen 12 Oct '09

12 Oct '09

Dear Stephane Yuo have given me access to your genomes. I however would like to have access to Bathycoccus, which is not among the species in the list of species on the web page. Can you give me access to Bathycoccus? thanks, Martijn Martijn A. Huynen, Ph.D. Center for Molecular and Biomolecular Informatics Nijmegen Centre for Molecular Life Sciences Radboud University Nijmegen Medical Centre CMBI 260 Radboud University Nijmegen Medical Centre Box 9101 6500 HB Nijmegen Netherlands M.Huynen(a)cmbi.ru.nl tel. +31-(0)24-3619543 fax. +31-(0)24-3619395 On Fri, 9 Oct 2009, beg-bogas(a)psb.vib-ugent.be wrote: > Date: Fri, 9 Oct 2009 22:36:20 +0200 (CEST) > From: beg-bogas(a)psb.vib-ugent.be > To: huynen(a)cmbi.ru.nl > Subject: [UTF-8] BOGAS - Bathycoccus Annotation > > Dear, > > please find your invitation code to access the bathycoccus 454 data and > its annotation. > > d16ca12ba4ba8fa09cce6af6dfb5d689 > > by clicking on this link you will be directed to a page to register, > choose your login and password etc. > > Best regards > Stephane >

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Re: [Beg-bogas] BOGAS - Bathycoccus Annotation
by Dr. M. A. Huynen 12 Oct '09

12 Oct '09

thanks Stephane ! Martijn A. Huynen, Ph.D. Center for Molecular and Biomolecular Informatics Nijmegen Centre for Molecular Life Sciences Radboud University Nijmegen Medical Centre CMBI 260 Radboud University Nijmegen Medical Centre Box 9101 6500 HB Nijmegen Netherlands M.Huynen(a)cmbi.ru.nl tel. +31-(0)24-3619543 fax. +31-(0)24-3619395 On Fri, 9 Oct 2009, beg-bogas(a)psb.vib-ugent.be wrote: > Date: Fri, 9 Oct 2009 22:36:20 +0200 (CEST) > From: beg-bogas(a)psb.vib-ugent.be > To: huynen(a)cmbi.ru.nl > Subject: [UTF-8] BOGAS - Bathycoccus Annotation > > Dear, > > please find your invitation code to access the bathycoccus 454 data and > its annotation. > > d16ca12ba4ba8fa09cce6af6dfb5d689 > > by clicking on this link you will be directed to a page to register, > choose your login and password etc. > > Best regards > Stephane >

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[Beg-bogas] problem with bathycoccus
by Lieven Sterck 29 Sep '09

29 Sep '09

dear, there seems to be some problem with the bogas_Bathy DB => some genes are assigned to contigs that are not present in the contigs table (nor in the blastDBs)! possible typo : chrom017-28 in stead of chrom028-17? best, L. PS. @ developers: can we not add these constraints/links in the DB (all contig_id from gene table should be in contigs table). -- ============================================================== 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 ============================================================== "You tried your best and you failed miserably. The lesson is: never try!" - H. Simpson

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[Beg-bogas] problem with bathycoccus
by Lieven Sterck 29 Sep '09

29 Sep '09

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[Beg-bogas] Error in InterProScan job iprscan-20090928-0946134603
by EBI InterProScan Server 28 Sep '09

28 Sep '09

failed to create XML output To help us solve the problem, please copy and paste this error and email it to the administrator <a href="mailto:?subject=Error in InterProScan job iprscan-20090928-0946134603"></a>. Sorry about the inconvenience and thank you for using InterProScan. <pre>"/ebi/extserv/bin/Dispatcher/bin/iprscan/converter.pl", line "422" checkIndex: index out of date? at /ebi/extserv/bin/Dispatcher/bin/iprscan/converter.pl line 422. </pre>

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[Beg-bogas] GenomeView for BOGAS upgraded to 1.9998
by Thomas Abeel 19 Sep '09

19 Sep '09

Hi all, I've updated the version available in BOGAS to 1.9998. I've also tied BOGAS to the official release to that whenever I make a new release BOGAS is automatically updated as well. What's new since the last version that was in BOGAS (1.90), although this is not all relevant for BOGAS: # hover windows for short reads # limit number of undo's that are stored for memory efficieny. # display of pairing information # more configuration options # improved handling of command line arguments to load sources # clear cache option # fixed bug in feature editing not properly updating some panels # simplified editing of features to be more user friendly # fixed a bunch of bugs in JAnnot # halved memory of Sequence # improvements to fasta parser # Session (re)store (#2560880) # Split pile-up coverage graph in forward and reverse coverage # Improvements to short read representation to keep it more responsive(#2849434) # Fixed navigation bug where all key navigation would be done twice (#2851257) # Implemented pop-up screen that shows the actual read coverage when hovering over the pile-up graph (#2839254) # Improved search and added overlap search # Improved gene structure track # Improved feature track # Improved multiple alignment track: faster, less memory and better visualized # Improved keyboard navigation # New navigation panel, inspired by Argo2 # Multi-threaded track loading # Removed BioMoby support # Removed chromosome view # Major GUI reorganization to accommodate removed and added features # Fixed a bunch of bugs and glitches # Added basic support for Distributed Annotation Servers (DAS) # Added short read support # Added support for authentication and SSL # Added caching to URLSource which makes it more efficient to retrieve data from the network cheers, Thomas

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