November 2007 - beg-bogas@psb.ugent.be

Re: [Beg-bogas] Getting started with BOGAS
by Thomas Abeel 15 Nov '07

15 Nov '07

Hello again, If you get the same error for both programs, it has probably something to do with the configuration of Java Web Start or your computer. From your error I have the impression that it has something to with you network connection. Please make sure that your firewall allows traffic from Java to load the required jar files. Can you get more information about the error? Artemini was tested both with Java 1.5 and 1.6, so the version should be no problem. kind regards, Thomas Claire Gachon schreef: > Hi Thomas, > thanks for your swift answer. > > 1) View alignment: I don't know what goes wrong, but I tried again > with Esi0009_0001 and Esi0009_0004: I just get this message > > 2) I have now tried Artemini, and it gives me the same kind of error > message as above > An error occurred while launching/running the application. > > Title: Artemini: Genome Visualization and Annotation > Vendor: VIB :: Plant Systems Biology :: Bioinformatics :: Thomas Abeel > Category: Download Error > > Unable to load resource: > http://bioinformatics.psb.ugent.be/webtools/artemini/artemini-2.11.jar > > > Could it be that somethign is wrong with my version of Java Web start? > > Claire > > At 15:07 15/11/2007, you wrote: >> Hello Claire, >> >>> _1) View alignment:_ when I click on the button, >>> Java web Start gets launched, "Checking for latest version" >>> then I get this message: >>> >>> Java Web start: Download Error >>> Unable to launch AlignView: a Sequence Alignment Viewer. >>> >>> Details: >>> An error occurred while launching/running the application. >>> >>> Title: AlignView: A Sequence Alignment Viewer >>> Vendor: VIB :: Plant Systems Biology :: Thomas Abeel >>> Category: Download Error >>> >>> Unable to load resource: >>> http://bioinformatics.psb.ugent.be/webtools/alignview/alignview-0.6.jar >> Which steps should I take to reproduce this error? I have just now >> tried to view the aligment for Esi0009_0001 and I encountered no >> problems. >> >> >>> _2) ESTs: >>> _EST is incompatible with the predicted model: is there any way to >>> retrieve easily ESTs sequences from the annotation page, in order to >>> check what is wrong with them (or the gene prediction? >>> Should I do it with Artemis (see below)? >>> >>> _3) Artemis_: >>> I have tried to install it on my computer (PC with Windows). So far >>> I have downloaded the file artemis.jar. My Java version is 1.5.0_08 >>> When I double-click on it, I get the following message: >>> Java Virtual Machine Launcher : Invalid or corrupt jar file >>> c:\Program files\artemis.jar >>> >>> Can you help? >> >> You should not download the artemis.jar file. The Artemis version >> within the BOGAS platform, called Artemini, is modified from the >> original Artemis program. This is again a Java Webstart Application. >> To launch Artemini for a locus, you can select 'Modify using >> Artemini' under the header 'Gene Structure' on the page that shows >> after you click the 'Modify This record' button. >> >> kind regards, >> Thomas

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[Fwd: Re: [Beg-bogas] Re: BOGAS]
by Lieven Sterck 15 Nov '07

15 Nov '07

---------------------------- Original Message ---------------------------- Subject: Re: [Beg-bogas] Re: BOGAS From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> Date: Thu, November 15, 2007 6:37 pm To: "Patrice Lerouge" <Patrice.Lerouge(a)univ-rouen.fr> -------------------------------------------------------------------------- Dear Patrice, what do you mean with 'access to data' ?? If you are able to login on the website, you should have access to all the data. kind regards, lieven > OK for entering in the website but it seems that I need a password for > having access to data. > Best regards > Patrice LEROUGE > > > > > A 11:09 14/11/2007 +0100, vous avez écrit : >>Hi, >> >>you have been invited to take part in the annotation of Ectoca= rpus. >>Please click on following link to activate your user account: >> >><3d'http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitatio>f4f58da406d3cccacae >>2a9ee547e5474 >> >>If the link doesn't work, try to go to http://bi= >>oinformatics.psb.ugent.be/webtools/bogas/users/enteric and enter >>f4f58da406d3cccacae2a9ee547e5474 >> >>with kind regards, >>t= he BOGAS team > _______________________________________________ > Beg-bogas mailing list > Beg-bogas(a)psb.ugent.be > https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas >

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[Beg-bogas] trpee kapot
by Thomas Abeel 15 Nov '07

15 Nov '07

Ik krijg voor elke locus van Trpee non-existant locus. groeten, Thomas

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[Beg-bogas] Re: BOGAS
by Patrice Lerouge 15 Nov '07

15 Nov '07

OK for entering in the website but it seems that I need a password for having access to data. Best regards Patrice LEROUGE A 11:09 14/11/2007 +0100, vous avez écrit : >Hi, > >you have been invited to take part in the annotation of Ectoca= rpus. >Please click on following link to activate your user account: > ><3d'http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitatio>f4f58da406d3cccacae >2a9ee547e5474 > >If the link doesn't work, try to go to http://bi= >oinformatics.psb.ugent.be/webtools/bogas/users/enteric and enter >f4f58da406d3cccacae2a9ee547e5474 > >with kind regards, >t= he BOGAS team

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[Beg-bogas] artemini service?? en DB schema
by Lieven Sterck 15 Nov '07

15 Nov '07

we need to implement stuff to allow users to merge models!! * do we need to allow people to change the tag (CDS, CDS_after,...) of a model? that would allow them to 'merge' models (because you can only merge models with the same kind of tag, and you need to be able to tag is as 'CDS' to be processed) * merged models will be inserted without a problem. but then the problem starts... ** then we need to make the overlapping models obsolete. (maybe use the locked table for this??) ** the query for the 'context' (and so) will need to be changed to deal with these obsolete models. L.

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[Beg-bogas] alignview
by Lieven Sterck 15 Nov '07

15 Nov '07

make text selectable and copyable in alignview. now aonly selectable i think. L.

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[Beg-bogas] Re: [Fwd: Re: Ectocarpus proteins]
by Lieven Sterck 15 Nov '07

15 Nov '07

Hi Marek, This is a not so easy issue (for us! not for you). the best option would be to select the model labeled 'CDS' and then insert your new coordinates. The other models you can ignore. grtz, lieven > Hi Lieven, > > thanks for the comments, it now seems that he problem with saving the > changes of gene models has been solved. I am sorry, however, to say > that I have just encountered another point requiring a discussion with > you. I found that some genes I am annotating are incorrectly predicted > as two or even three independent loci. How to correct these instances? > Should I merge somehow the models into one, which I subsequetly modify > bu inserting correct coordinates? If yes, how should I do it? Or > should I simply insert the correct coordinates into a field of one of > the partial "submodels" and ignore or delete the remaining? > Thanks, > Marek > > Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: > >> Hi Marek, >> >> I spotted the problem. You are talking about locus Esi0425_0013, no? >> I can see that you made an edit in the DB, but the problem is that there >> seems to be a double save. If you check in the history the last-1 date >> you'll see your edit. >> >> We are sorting this out as quickly as possible. >> >> best regards, >> lieven >> >> >>> Dear Lieven, >>> >>> thanks for the change in artemini, this is exactly what I think will >>> make the annotation much more straightforward. I checked the system >>> with one gene (correcting coordinates of one exon). I saved the >>> modified coordinates using "Save to server" command in "File" menu >>> option, but the model has not changed in the database yet. Are you >>> reviewing opur annotations before incorporating them into the >>> database? Or what is going on? >>> Thanks. Cheers, >>> >>> Marek >>> >>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>> >>>> Dear Marek, >>>> >>>> we made some adjustments to the artemini functionality and as a result >>>> the >>>> coordinates you see in the artemini window are now the same as in the >>>> webpage (= they are in reference to the whole scaffold). >>>> You can just copy and paste your coordinates into the artemini, save >>>> it >>>> and they will be entered into the DB. >>>> >>>> I hope this can satisfy your needs. If not, please do let me know, so >>>> we >>>> can think of better solution. >>>> >>>> thanks and best regards, >>>> lieven >>>> >>>> >>>> ---------------------------- Original Message >>>> ---------------------------- >>>> Subject: Re: Ectocarpus proteins >>>> From: "Lieven Sterck" <lieven.sterck(a)psb.ugent.be> >>>> Date: Thu, November 8, 2007 11:17 pm >>>> To: melias(a)natur.cuni.cz >>>> Cc: cock(a)sb-roscoff.fr >>>> beg-bogas(a)psb.ugent.be >>>> -------------------------------------------------------------------------- >>>> >>>> Dear Marek, >>>> >>>> You can find a manual on how to use the artemis tool on the Sanger >>>> Institute website. >>>> May I inquire if you find the artemis tool itself not user-friendly or >>>> rather the way it is incoporated in the portal? >>>> >>>> The coordinates in the artemini view differ indeed from the ones on >>>> the >>>> webpage. this is because the sequence you get to see in the artemini >>>> view >>>> is only a subpart of the whole scaffold (this in order to let the >>>> procedure go faster). The coordinates you see in artemini are in >>>> reference >>>> to the subpart while you have (and also on the webpage) them in >>>> reference >>>> of the whole scaffold. >>>> >>>> In theory it is possible to make the coordinates 'box' editable. but, >>>> ... >>>> i'm a little bit reluctant to do this due to bad experience with this >>>> approach in previous projects. We noticied it is very easy to include >>>> mistakes this way (aspecially for non experienced annotators). That is >>>> why >>>> we include the artemini system in this version (where some basic >>>> checks >>>> on >>>> the structure are performed and you have the visual check of the >>>> structure). >>>> But I also completely understand your point that for more experienced >>>> users this might not be ideal... >>>> What we also can do is to add a function in the artemini to 'transfer' >>>> the >>>> coordinates you enter (in reference of the whole scaffold) onto the >>>> subpart in artemini. That way you could just paste your coordinates >>>> into >>>> the coordinate box of artemini, push the 'transfer' button and they >>>> will >>>> be adjusted onto the subpart. You can then also profit from the visual >>>> check. When you then save your modifications they will be entered to >>>> the >>>> DB. >>>> Do you think this might be more useful? or does it still sounds to >>>> much >>>> of >>>> a hastle? >>>> >>>> best and thanks for the feedback, >>>> lieven >>>> >>>> >>>>> Dear Lieven, >>>>> >>>>> thanks for the link, I have successfully downloaded the protein >>>>> database. I would like to start making corrections of the gene models >>>>> I >>>> foud to be incorrectly predicted ion the rpesent annotation. Is there >>>> any >>>> manual how to work with the Artemini tool? I found it not be too >>>> user-friendly. For instance, I do not understand why the exon >>>> coordinates indicated by Artemini differs from the actual coordinates >>>> on >>>> supercontigs? Just take the gene Esi0425_0013. The present >>>>> coordinates, with an incorrect first exon, are as follows: >>>>> >>>>> 47430..47455,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>> >>>>> I would like to change the first exon so that the coordinates are >>>>> like >>>> this: >>>>> >>>>> 45460..45476,47682..47802,48669..48716,49305..49400,50478..50556,51041..51197,53081..53171 >>>>> >>>>> The coordinates given for this gene in Artemini are as follows: >>>>> >>>>> 3555..3580,3807..3927,4794..4841,5430..5525,6603..6681,7166..7322,9206..9296 >>>>> >>>>> Why there is the difference? I have to say that I would highly >>>>> appreciate if it is possible to edit gene models just by typing the >>>> correct coordinates of exons I found by comparing my CDS models with >>>> the >>>> contig sequence. Is this possible? >>>>> Thank you and best regards, >>>>> >>>>> Marek E. >>>>> >>>>> >>>>> >>>>> Cituji Lieven Sterck <lieven.sterck(a)psb.ugent.be>: >>>>> >>>>>> Dear Marek, >>>>>> the download is available from this address: >>>>>> https://bioinformatics.psb.ugent.be/gdb/ectocarpus >>>>>> (login/passw : psbguest/ectocarpus) >>>>>> Apologises that I haven't informed you earlier, it is quite hectic >>>>>> for >>>> the >>>>>> moment. >>>>>> please let me know if this doesn't work. >>>>>> best regards, >>>>>> lieven >>>>>>> Dear Lieven, >>>>>>> you mentioned that from this week's Monday the whole predicted >>>> proteome of Ectocarpus should be available for download. I tried to >>>> find >>>> a >>>> link to the file at BOGAS web page but haven't found any. Could you, >>>> please, let me know, where to go for the downloading? >>>>>>> Thanks, best regards, >>>>>>> Marek Elias >>>>>>> Cituji lieven sterck <lieven.sterck(a)psb.ugent.be>: >>>>>>>> Dear Marek, >>>>>>>> From monday on you will be able to download all predicted >>>>>>>> protein/genes >>>>>>>> in batch. >>>>>>>> sorry for the delay. >>>>>>>> regards, >>>>>>>> lieven >>>>>>>> Kenny Billiau wrote: >>>>>>>>> -------- Original Message -------- >>>>>>>>> Subject: Re: password to the Ectocarpus genome portal >>>>>>>>> Date: Fri, 02 Nov 2007 15:49:39 +0100 >>>>>>>>> From: melias(a)natur.cuni.cz >>>>>>>>> To: Kenny Billiau <kenny.billiau(a)psb.ugent.be> >>>>>>>>> References: >>>>>>>>> <20071102114032.ry1oc3gmmjcckc8s(a)www.natur.cuni.cz> >>>>>>>>> <472B0B6C.8060706(a)psb.ugent.be> >>>>>>>>> Hi Kenny, >>>>>>>>> thanks for the advice with getting the access to the Ectocarpus >>>> portal. I have created an accounted and started to work. Is it >>>> possible to download the set of predicted protein sequences? It >>>> would suit me better to do some local stand-alone searches (BLAST, >>>>>>>>> HMMER) than to use only your web BLAST server. Thanks again, >>>>>>>>> Marek >>>>>>>>> Cituji Kenny Billiau <kenny.billiau(a)psb.ugent.be>: >>>>>>>>>> Hi, >>>>>>>>>> I've sent you an invitation mail so you can choose your own >>>> login/password. You can use this login to access the ectocarpus >>>> wiki >>>>>>>>>> as >>>>>>>>>> well, >>>>>>>>>> Kenny >>>>>>>>>> melias(a)natur.cuni.cz wrote: >>>>>>>>>>> Dear Dr. Billiau, >>>>>>>>>>> I am a member of the Ectocarpus genome consortium. Mark Cock >>>>>>>>>>> sent >>>>>>>>>>> us a message announcing the Ectocarpus genome annotation >>>>>>>>>>> portal and redirected us to you for obtaining a password to >>>>>>>>>>> the >>>> portal. I have one to the BLAST page at the Ghent web site >>>> (user: ectocarpus, password: sillysilly) but it does not work >>>> for the portal at >>>>>>>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/. May be >>>>>>>>>>> this >>>> is not the right link to the portal, so please, let me know how can >>>> I >>>> access the portal so taht I can start annotating. Thank >>>> you in advance and best regards, >>>>>>>>>>> Marek Elias >>>>>>>>>>> Department of Botany >>>>>>>>>>> Faculty of Science >>>>>>>>>>> Charles University >>>>>>>>>>> Benatska 2 >>>>>>>>>>> 128 01 Praha 2 >>>>>>>>>>> Czech Republic >>>>>>>>>> -- >>>>>>>>>> ================================================================== >>>> 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)psb.ugent.be >>>>>>>>>> http://bioinformatics.psb.ugent.be >>>> ================================================================== >>>>>>>> -- >>>>>>>> ============================================================== >>>>>>>> Lieven >>>> Sterck Predoctoral fellow 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.ugent.be >>>>>>>> Website: http://bioinformatics.psb.ugent.be >>>>>>>> -------------------------------------------------------------- >>>>>>>> Algal >>>> Genetics Group >>>>>>>> UMR 7139 CNRS-UPMC >>>>>>>> VÃÂÃÂ©gÃÂÃÂ©taux Marins et BiomolÃÂÃÂ©cules (Marine >>>>>>>> Plants and >>>>>>>> Biomolecules) >>>> Station Biologique Place Georges Teissier, BP74 >>>>>>>> 29682 Roscoff Cedex, France >>>>>>>> Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >>>>>>>> ============================================================== >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >> >> > >

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[Beg-bogas] Re: BOGAS
by Pierre-Olivier de Franco 14 Nov '07

14 Nov '07

hi ! it's an "invalid invitation code " .... I wait for your help bests, Pierre-olivier de franco beg-bogas(a)psb.ugent.be a écrit : > Hi, > > you have been invited to take part in the annotation of Ectocarpus. > Please click on following link to activate your user account: > > 9b4c622d040c7057be6 c98b16d344e1f > <http://bioinformatics.psb.ugent.be/webtools/bogas/users/invitationcode/9b4c…> > > If the link doesn't work, try to go to > http://bioinformatics.psb.ugent.be/webtools/bogas/users/enteric and > enter 9b4c622d040c7057be6c98b16d344e1f > > with kind regards, > the BOGAS team -- ------------------------- Pierre - Olivier de FRANCO, PhD student Functional Genomics Group,UMR 7139 CNRS-UPMC "Marine Plants and Biomolecules" ------------------------------- Station Biologique Place Georges Teissier BP74 29682 Roscoff Cedex Email : defranco(a)sb-roscoff.fr Tel: +33 2 98 29 23 23 poste 403 Fax: +33 2 98 29 23 24 -----------------------------------

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[Beg-bogas] artemini is aant freaken :-(
by lieven sterck 14 Nov '07

14 Nov '07

kheb den indruk dat hij in de war slaagt met het bijvoegen van Ns ?? L. -- ============================================================== Lieven Sterck Predoctoral fellow 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.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

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[Beg-bogas] genome annotation
by Pierre-Olivier de Franco 14 Nov '07

14 Nov '07

Hi, I am Pierre-olivier de Franco, I am PhD student in the Station Biologique of Roscoff. I am on the list of annotators of the Ectocarpus genome and I would like to have access to the annotation website. Bests Pierre-Olivier de Franco Mark Cock a écrit : > Hi PO, > > You are on the list of annotators already so there is no problem. Just > send a mail to: > > beg-bogas(a)psb.ugent.be > > and ask them for a password. > > You should have had the other information but here it is again just in > case. > > Let me know if you have a probelm. > > Mark > > > Pierre-Olivier de Franco wrote: >> Hi Mark, >> >> I have generated a lot of data on Glutathione S transferase genes in >> the Ectocarpus genome and EST databases ( 20 genes) and I can >> provide the gene annotation, localization, structure, duplications >> events... >> I wonder if I could have access to the genome annotation platform to >> known what else could be interesting to investigate. I do not think >> that I will annotate enough genes to be on the final paper but I am >> writing one on "glutathione transferase family in E.sil" and I would >> compare my own annotation with the automatic one. >> >> Can you provide me an acces to the annotation website, or give me the >> person to contact. >> >> sorry for the english ... I tried :-D >> thanks >> PO >> > > -- ------------------------- Pierre - Olivier de FRANCO, PhD student Functional Genomics Group,UMR 7139 CNRS-UPMC "Marine Plants and Biomolecules" ------------------------------- Station Biologique Place Georges Teissier BP74 29682 Roscoff Cedex Email : defranco(a)sb-roscoff.fr Tel: +33 2 98 29 23 23 poste 403 Fax: +33 2 98 29 23 24 -----------------------------------

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