Pierre Rouze <pirou@psb.UGent.be> · Tue, 08 Jan 2008 09:54:29 +0100

Lieven Sterck wrote:

   Artemini is too mini : there is no way to create features besides 
CDS !!!  I need it myself (eg, to map repeats, NNN, introns, etc ...): 
what shall I do ?

> Hi Pierre,
>
> with 'edit' I mean the 'Modify This Record' button. Clicking on that will
> lead you to the 'edit page'.
>
> I don't see what you mention about the links, they all work with me!
> Also the workbench is working fine. I can see that you added the locus
> Esi0000_0035 on your workbench, I cannot edit ;-) it for the moment.
>
> more tomorrow.
> grtz,
> lieven
>
>
>   
>> lieven sterck wrote:
>>     
>>> Hi Pierre,
>>>
>>> the artemis interface is available. Therefore you have to go to the
>>> edit page and in the gene-structure section you will then find link(s)
>>> to artemini.
>>>
>>>       
>>     Sorry, but I spent already an hour with this Bogus, without seing
>> any "Edit" or whatever alike offered to me:
>>
>>     first page : Ostreoccus versus Ectocarpus : not too difficult this
>> one : I chose Ectocarpus
>>
>>     second page, already more difficult : Annotation, Browse (it would
>> have been my choice, but it is inactive..) Blast, Search & Wiki
>>        OK I got for search and got the first sequence in the list,
>> Esi0000_0035 by entering it in the Locus window..  Then I understood
>> that I add to choose either View or Workbench...  Workbench has no
>> effect but to put the gene on it !!! (is this button useful, really???)
>> Then View, with a nice navigation menu on the right... at least that's
>> what I thought : looking for your gene in detail whith the next one will
>> be here, sure .  No way !  No Edit or Artemini either..  In fact, it's
>> mosty shortcuts to things which I could have done before (search,
>> workbench) or infos already displayed on the screen... Exception :
>> Previous & New locus, but you end up with the very same stuff (for the
>> neighbour gene..), Blast: OK. Add to : same effect as the unuseful
>> workbench button ....
>>
>>     And nothing else !!!!
>>
>>     So, where damned is that "edit" page ???  It should be one pop-up in
>> the very first screen, immediately after you accessed a gene ! No one
>> complained about it ?
>>
>> For the protein alignment do you mean that you can not 'click' on a gene
>> in the alignment viewer?
>>
>>     I mean, clicking on the "green looking" Genbank entry name with is
>> displayed on the line "Protein ID: .." BELOW the  button "protein
>> alignment" : there is nothing coming up, when one (me at least) would
>> expect this to be an active link to the Genbank entry, allowing to check
>> what is this protein for real ... It's the same if you open the Blast
>> display by clicking "View Blast" : it's all dead info, no active link...
>>
>>     P.
>>     
>>> grtz,
>>> lieven
>>>
>>> Pierre Rouze wrote:
>>>       
>>>> Lieven Sterck wrote:
>>>>         
>>>>> Hi Pierre,
>>>>>
>>>>> it looks like you are accessing the wrong 'BOGAS'.
>>>>> Does the website you visit has an URL like
>>>>> .../sandbox/liste/BOGAS/trunk/.... ?? Then you are trying to login
>>>>> on the
>>>>> 'development version'!
>>>>>
>>>>> I think that you will have to change the URL to
>>>>> http://bioinformatics.psb.ugent.be/webtools/bogas/
>>>>>
>>>>>           
>>>>    OK, thanks !...
>>>>
>>>>    But I can't do much with your Bogas display .. sorry !  I need to
>>>> see SEVERAL genes next to each other and the exon frames and the
>>>> sequence nucleotide .. in other words, I need an Artemis(-like)
>>>> interface. I again can't see how to get it when you have accessed a
>>>> gene in Bogas ! Is there no way to get the annotated model of the
>>>> whole contig ??
>>>>
>>>>    Besides, I tried to get access to the automatic Blast results : I
>>>> can get the multiple alignment (nice!) but not to the proteins
>>>> entries in this alignment to understand wheere they come from
>>>> (several are apparently partial sequences..)
>>>>
>>>>    Pierre
>>>>
>>>>    P.
>>>>         
>>>>> then it should work!
>>>>>
>>>>> grtz,
>>>>> lieven
>>>>>
>>>>>
>>>>>           
>>>>>>  Hi Lieven,
>>>>>>
>>>>>>  I finally begun looking at Stefan Rensing "annotation" ... or at
>>>>>> least at
>>>>>> what I can see of it from your mails .. I can't indeed access Bogas
>>>>>> properly !
>>>>>>
>>>>>>  Here below is the message I get when searching for a locus (typing
>>>>>> one of
>>>>>> the problematic ones of Stefan from the Excel table tyou sent me a
>>>>>> while
>>>>>> ago..).
>>>>>>  I get the very same message when trying to access "annotation" ... I
>>>>>> don't know if you can explain what's wrong and help me by mail.
>>>>>>  Otherwise we will have to wait until in the lab, next tuesday.
>>>>>>
>>>>>>                 Error communicating with the database. Please
>>>>>> contact the
>>>>>> webmaster with the details if the error.
>>>>>>  url, genome, release, locus
>>>>>>
>>>>>>  DBD::mysql::st execute failed: Table 'bogas_ectsi_v2.history'
>>>>>> doesn't
>>>>>> exist at ../../src/perl/modules//BOGAS/DB/Rails.pm line 128.
>>>>>>     continue
>>>>>>  As far as I can judge from the Excel table, there is indeed a big
>>>>>> problem
>>>>>> with Stefan Rensing """annotation"" :  first, it seems that Stefan is
>>>>>> simply taking the gene models as they are, and Blast (or whatever
>>>>>> else)
>>>>>> them against some database of its own. This in itself is a problem :
>>>>>> I
>>>>>> have nothing against automatic pipelines, but they have to do more
>>>>>> than
>>>>>> that! Especially in the case of Ectocarpus where doing our very
>>>>>> best we
>>>>>> know that gene models can be wrong once in a while with fusion or
>>>>>> split,
>>>>>> even an automatic pipeline shall be made in such a way to point to
>>>>>> likely
>>>>>> wrong models in one way or another. Second to "annotate" a gene
>>>>>> product,
>>>>>> homology with a domain or a signature or a partial homology is not
>>>>>> enough! One/a pipeline should look for completeness of the product by
>>>>>> e.g. looking for the existence of all expected modules, or similarity
>>>>>> with close enough homologs allover the sequence (except termini, and
>>>>>> allowing gaps), and at least with adequate sequence length and at
>>>>>> least
>>>>>> return a warning if it not the case. I don't know what this
>>>>>> database is
>>>>>> made of, but I am pretty concerned in seeing an annotation like
>>>>>> "sigma54"
>>>>>> ... when we are annotating a eukaryotic organism !! (sigma factors
>>>>>> are
>>>>>> indeed prokaryotic transcription factors..).
>>>>>>
>>>>>>  So I will nevertheless look in detail at a few examples of Stefan
>>>>>> annotation, as soon as I can access Bogas properly, and write then a
>>>>>> draft mail that I would like both Mark &amp; Yves to agree upon to be
>>>>>> sent to Stefan.
>>>>>>
>>>>>>  best,
>>>>>>
>>>>>>  Pierre
>>>>>>  --
>>>>>> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
>>>>>> Pierre ROUZE                 Laboratoire Associe de l'INRA [France]
>>>>>> BioInformatics Team Leader      Department of Plant Systems Biology
>>>>>> Ghent
>>>>>> University, Technologie park 927, B-9052 GENT         BELGIUM
>>>>>> Flanders
>>>>>> Interuniversity Institute for Biotechnology            VIB Tel:32.933
>>>>>> 13694    Cell.Phone: 32.476 638 304     Fax:32.933 13809
>>>>>> pierre.rouze@psb.ugent.be    http://www.psb.ugent.be/bioinformatics
>>>>>> ___________________________________________________________________
>>>>>>
>>>>>>             
>>>>>
>>>>>           
>>>>         
>> --
>> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
>> Pierre ROUZE                 Laboratoire Associe de l'INRA [France]
>> BioInformatics Team Leader      Department of Plant Systems Biology
>> Ghent University, Technologie park 927, B-9052 GENT         BELGIUM
>> Flanders Interuniversity Institute for Biotechnology            VIB
>> Tel:32.933 13694    Cell.Phone: 32.476 638 304     Fax:32.933 13809
>> pierre.rouze@psb.ugent.be    http://www.psb.ugent.be/bioinformatics
>> ___________________________________________________________________
>>
>>     
>
>
>   

-- 
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Pierre ROUZE                 Laboratoire Associe de l'INRA [France]
BioInformatics Team Leader      Department of Plant Systems Biology
Ghent University, Technologie park 927, B-9052 GENT         BELGIUM
Flanders Interuniversity Institute for Biotechnology            VIB
Tel:32.933 13694    Cell.Phone: 32.476 638 304     Fax:32.933 13809
pierre.rouze@psb.ugent.be    http://www.psb.ugent.be/bioinformatics 
___________________________________________________________________

Subject:	Re: Stefan ... & BOGAS (2)
Date:	Tue, 08 Jan 2008 09:54:29 +0100
From:	Pierre Rouze <pirou@psb.UGent.be>
To:	Lieven Sterck <lieven.sterck@psb.ugent.be>
References:	<477F3B8A.4090704@psb.UGent.be> <19271.157.193.202.129.1199536388.squirrel@webmail.psb.ugent.be> <477FCB57.8020606@psb.UGent.be> <4781EF18.40908@psb.ugent.be> <47826356.9050303@psb.UGent.be> <51222.157.193.202.129.1199747946.squirrel@webmail.psb.ugent.be>