September 2009 - beg-bogas@psb.ugent.be

[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"/ebi/extserv/bin/Dispatcher/bin/iprscan/converter.pl", line "422" checkIndex: index out of date?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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[Beg-bogas] saven met nieuwe GV versie
by Thomas Abeel 19 Sep '09

19 Sep '09

Hoi Lieven, Ik heb GenomeView op BOGAS geupgrade naar de nieuwste versie, maar BOGAS is er nog geen vriendjes mee. Saven met de nieuwste versie van GV lukt niet omdat de sequence zogezegd aangepast is. Het probleem is blijkbaar dat de sequence teruggestuurd wordt als uppercase en BOGAS dus denkt dat die aangepast is. GenomeView kan geen sequenties editen, dus eigenlijk is die check overbodig. Kan je de check in gv_ws.pl case-insensitive maken? Of verwijderen? Tot dat die check case-insensitive is of weg is, kan er niet gesaved worden. thanks, Thomas

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[Beg-bogas] test
by Lieven Sterck 16 Sep '09

16 Sep '09

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[Beg-bogas] (pas de sujet)
by Patrice LEROUGE 05 Sep '09

05 Sep '09

Dear colleague, I forgot my password, could you send me it agin? Sincerely Patrice LEROUGE

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[Beg-bogas] BRe: New BOGAS version online (fwd)
by Kenny Billiau 01 Sep '09

01 Sep '09

And yet another problem. ---------- Forwarded message ---------- Date: Tue, 01 Sep 2009 12:34:57 +0200 From: Marek Elias <melias(a)natur.cuni.cz> To: Kenny Billiau <kebil(a)psb.vib-ugent.be> Subject: Re: [Beg-bogas] New BOGAS version online Hi Kenny, one more thing - I am just trying to modify the locus Esi0281_0023 using GenomeView. The gene is very big with many exons, but if you try to modify the coordinates, they are no all diplayed in the respective vindow, because it seems it to be restricted to display some maximal number of lines and it is impossible to croll down. How then is it possible to modify the region of the gene outside this selection? Thanks, Marek Cituji Kenny Billiau <kebil(a)psb.vib-ugent.be>: > Hi, > > it's ok to bother me so much :) I'm here to fix those problems. > It's gonna take some longer to fix this one as it seems to work fine on > my test loci, but not outside the scope. > > I'll geet back to you as soon as it's fixed, > > Kenny > > On Mon, 31 Aug 2009, Marek Elias wrote: > > > Hi Kenny, > > > > I am sorry for bothering you again. Artemini still seems to have problems, > > now the response after my attempts to save chenged cooridnates is "Wrong > > params". I have no idea what this means. > > Thanks, > > Marek > > > > Cituji Kenny Billiau <kenny.billiau(a)ugent.be>: > > > > > Hi, > > > > > > ok, sorry for the inconvenience. The problem is sovled now :) > > > > > > I cannot really answer the question about splitting of genemodels. I'm > > > looking into it, but seem to experience problems with artemini myself. > > > I'll get back to you on that one as soon as I've fixed those problems. > > > > > > Kenny > > > > > > On Mon, 31 Aug 2009, Marek Elias wrote: > > > > > > > Hi Kenny, > > > > > I am still encountering troubles with he Artemeni tool, I have just > > > > > tried > to save new coordinates for the locus Esi0307_0011, but > > > > > after clicking on > "Save To Sever" there is no reaction. The model > > > > > in BOGAS does not chenge > and when I try to swith the Artemeni > > > > > window off a warning is diplayed > that the changes have not been > > > > > saved. Could you, please, look on this > problem? > > > > Thanks, > > > > marek > > > > > > Cituji Kenny Billiau <kenny.billiau(a)ugent.be>: > > > > > > Hi, > > > > > > > thx for letting us know :) > > > > > The artemini tool is working again. > > > > > > > wkr, > > > > > Kenny > > > > > > > On Sun, 30 Aug 2009, Marek Elias wrote: > > > > > > > > Hi Lieven, > > > > > > > please, ignore my previous message, a long time has simply > > > > > > > elapsed > > > > > > since I was using the BOGAS system last time, so I forgot how to > > > > > > actually modify gene models, but I have finally recalled. However, > > > > > > I > > > > > > nevertheless encounter an unexpected problem, while trying to > > > > > > modife > > > > > > the gene model of Esi0032_0099, the Artemini tool fails to start, > > > > > > > > > with > > > > > > the following error message: > > > > > > > "Message: Server returned HTTP response code: 500 for URL: > > > > > > http://bioinformatics..." > > > > > > > Could you, please, look on this. Thanks a lot! > > > > > > Marek > > > > > > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.vib-ugent.be>: > > > > > > > > Dear all, > > > > > > > > > we're pleased to announce that a new version of the BOGAS > > > > > > > > > > > > > > > portal has > > > > > > > been put online. > > > > > > > > > This version includes several fixes in protocols and > > > > > > > > > layout. > > > > > > Also a > > > > > > > 'true' genome browser has been incorporated (AnnoJ), the search > > > > > > > functionality has been upgraded, tiling array info is now > > > > > > > > > > > available, > > > > > > > a new annotation tool is provided (GenomeView), more > > > > > > > information > > > > is > > > > > > > included in the images (pop-up system), ... > > > > > > > > > Thanks all for your input and suggestions, > > > > > > > enjoy! > > > > > > > > > best regards, > > > > > > > lieven > > > > > > > > > PS. Remarks, questions, suggestions are off course still > > > > > > > > > > > > > > > welcome > > -- > ================================================================== > Kenny Billiau > Web Developer > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > kenny.billiau(a)ugent.be http://bioinformatics.psb.ugent.be > ================================================================== > "What we feel isn't important. The only question is what we do." > -- Rohl > >

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Re: [Beg-bogas] New BOGAS version online
by Kenny Billiau 01 Sep '09

01 Sep '09

Someone is having GV problems :/ ---------- Forwarded message ---------- Date: Tue, 01 Sep 2009 10:59:18 +0200 From: Marek Elias <melias(a)natur.cuni.cz> To: Kenny Billiau <kebil(a)psb.vib-ugent.be> Subject: Re: [Beg-bogas] New BOGAS version online Hi Kenny, I am sorry to say this, but I have anotehr problem:-). I learned yesterday how to use the new GenomeView tool to modify gene modes. I have succesfully used to change a few of them, but I was unable to do so with Esi0156_0032. It needs to be extended to incorporate also the downstream model Esi0156_0030, so I modified the coordinates, but the changes failed to be saved. Instead, "Status" of the model as indicated at the respective BOGAS page changed from "Active" to "dowload". What does this mean? Given this failure, I tried to modify the Esi0156_0030 model by extending it to cover Esi0156_0032, but the result was the same, again the chenge has not been saved and the status is now "download". Could you, please, check this? Thanks a lot. Please, let me know when Artemeni works again, I found that it is much easier to modify gene models with it than with GenomeView. With the latter, you need to add lines for additional exons and to inser each coordinate independently, whereas with Artemini I simply insert coordinates of all exons at once. Thanks again, Marek Cituji Kenny Billiau <kebil(a)psb.vib-ugent.be>: > Hi, > > it's ok to bother me so much :) I'm here to fix those problems. > It's gonna take some time longer to fix this one as it seems to work fine on > my test loci, but not outside that scope. > > I'll get back to you as soon as it's fixed, > > Kenny > > On Mon, 31 Aug 2009, Marek Elias wrote: > > > Hi Kenny, > > > > I am sorry for bothering you again. Artemini still seems to have problems, > > now the response after my attempts to save chenged cooridnates is "Wrong > > params". I have no idea what this means. > > Thanks, > > Marek > > > > Cituji Kenny Billiau <kenny.billiau(a)ugent.be>: > > > > > Hi, > > > > > > ok, sorry for the inconvenience. The problem is sovled now :) > > > > > > I cannot really answer the question about splitting of genemodels. I'm > > > looking into it, but seem to experience problems with artemini myself. > > > I'll get back to you on that one as soon as I've fixed those problems. > > > > > > Kenny > > > > > > On Mon, 31 Aug 2009, Marek Elias wrote: > > > > > > > Hi Kenny, > > > > > I am still encountering troubles with he Artemeni tool, I have just > > > > > tried > to save new coordinates for the locus Esi0307_0011, but > > > > > after clicking on > "Save To Sever" there is no reaction. The model > > > > > in BOGAS does not chenge > and when I try to swith the Artemeni > > > > > window off a warning is diplayed > that the changes have not been > > > > > saved. Could you, please, look on this > problem? > > > > Thanks, > > > > marek > > > > > > Cituji Kenny Billiau <kenny.billiau(a)ugent.be>: > > > > > > Hi, > > > > > > > thx for letting us know :) > > > > > The artemini tool is working again. > > > > > > > wkr, > > > > > Kenny > > > > > > > On Sun, 30 Aug 2009, Marek Elias wrote: > > > > > > > > Hi Lieven, > > > > > > > please, ignore my previous message, a long time has simply > > > > > > > elapsed > > > > > > since I was using the BOGAS system last time, so I forgot how to > > > > > > actually modify gene models, but I have finally recalled. However, > > > > > > I > > > > > > nevertheless encounter an unexpected problem, while trying to > > > > > > modife > > > > > > the gene model of Esi0032_0099, the Artemini tool fails to start, > > > > > > > > > with > > > > > > the following error message: > > > > > > > "Message: Server returned HTTP response code: 500 for URL: > > > > > > http://bioinformatics..." > > > > > > > Could you, please, look on this. Thanks a lot! > > > > > > Marek > > > > > > > > > Cituji Lieven Sterck <lieven.sterck(a)psb.vib-ugent.be>: > > > > > > > > Dear all, > > > > > > > > > we're pleased to announce that a new version of the BOGAS > > > > > > > > > > > > > > > portal has > > > > > > > been put online. > > > > > > > > > This version includes several fixes in protocols and > > > > > > > > > layout. > > > > > > Also a > > > > > > > 'true' genome browser has been incorporated (AnnoJ), the search > > > > > > > functionality has been upgraded, tiling array info is now > > > > > > > > > > > available, > > > > > > > a new annotation tool is provided (GenomeView), more > > > > > > > information > > > > is > > > > > > > included in the images (pop-up system), ... > > > > > > > > > Thanks all for your input and suggestions, > > > > > > > enjoy! > > > > > > > > > best regards, > > > > > > > lieven > > > > > > > > > PS. Remarks, questions, suggestions are off course still > > > > > > > > > > > > > > > welcome > > -- > ================================================================== > Kenny Billiau > Web Developer > Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > kenny.billiau(a)ugent.be http://bioinformatics.psb.ugent.be > ================================================================== > "What we feel isn't important. The only question is what we do." > -- Rohl > >

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