Re: [CDAO-discuss] RES: next telecon for CDAO plans (Julie Thompson)

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On Oct 31, 2009, at 8:12 AM, Francisco Prosdocimi wrote:

> I'm still here. Last week I was off to the Brazilian conference on  
> bioinformatics and I won the 2nd prize -- actually an honorable  
> mention -- on the databases-ontology section with our work (amongst  
> 36 posters in this area). The presentation was well received by the  
> evaluation committee and I'm looking forward to test CDAO soon using  
> actual data (and to add some phenetics missing concepts on it).

Congratulations!  We should put this on the CDAO web site.

Arlin

> Outstanding speakers were also present in this conference. Peer Bork  
> (from EBI-Heidelberg) have shown a very beautiful analysis of  
> metatranscriptomics in different levels of profoundness in the  
> Sargaços Sea using Venter's data (if I understood well). I had the  
> impression that we should think on how to represent metagenomics  
> data using CDAO... I guess it is gonna be useful...
>
> Nick Goldman (from EBI-Cambridge) presented an algorithm for  
> Evolutionary Multiple Alignments. He realized that gap-costs would  
> lead progressive multiple alignment tools to over-estimate the  
> number of deletion events; and minimize gaps (http://www.ebi.ac.uk/goldman-srv/prank/differences/ 
> ). So, he produced an algorithm producing a guide-tree that helps to  
> reduce this bias and claims to make a better "evolutionary"  
> alignment. He convinced me (and all the audience) about the utility  
> of his approach... but certainly Julie would be a better judge on  
> this subject. Please follow this at http://www.ebi.ac.uk/goldman-srv/prank/
> (He claims that even manual curated alignments, such as the ones on  
> BaliBASE would not be good positive controls to testing his  
> software... he really claims to make evolutionary-alignments that  
> would be invisible to the human eye... sure his methods need to be  
> checked carefully, but I think he found a real problem in standard  
> multiple alignment sequence techniques.)
>
> I will be glad to follow your discussions on Nov 2nd; if I  
> calculated well it doesn't match any of my classes. :)
>
> ps: I've found a prototype of MACSIMS alignment annotation from  
> Goldman's group too... but it is very application-specific and still  
> far away from CDAO semantics (http://www.ebi.ac.uk/goldman-srv/hsaml/example.html 
> )... he stayed some minutes seeing my poster but refused a verbal  
> explanation... "it is very clear" in the poster, he said...
>
> See you,
>
> -- 
> Prof. Francisco Prosdocimi, PhD
> -----------------------------
> Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia
> Universidade Católica de Brasília - UCB
> SGAN 916 Módulo B, Bloco C Sala 213
> 70.790-160 - Brasília / DF - Brasil
> Fone: +55 61 34487173
> http://biotec.icb.ufmg.br/chicopros
>
>
>
> -----Mensagem original-----
> De: Enrico Pontelli [mailto:epo...@cs...]
> Enviada: seg 26/10/2009 09:43
> Para: Arlin Stoltzfus
> Cc: cda...@li...
> Assunto: Re: [CDAO-discuss] next telecon for CDAO plans (Julie  
> Thompson)
>
> I am sure I can shuffle things and make myself available.
>
> Enrico
>
> On Oct 26, 2009, at 2:12 PM, Arlin Stoltzfus wrote:
>
>> Julie has asked about Monday, Nov. 2 at 2:30 pm (UTC -5).  This looks
>> promising from the doodle poll-- Vivek, Jim and I are available 1:30
>> and 3:30, so presumably we are available at 2:30 as well.  Enrico is
>> available at 1:30 but not 3:30 so there may be a snag there.  Enrico,
>> can you do 2:30 on Monday, Nov 2?
>>
>> Is anyone *unavailable* on Monday, Nov. 2 at 2:30 pm (UTC -5)?
>>
>> If not, I will go ahead with this date and time.
>>
>> Arlin
>>
>> On Oct 25, 2009, at 2:23 AM, Julie Thompson wrote:
>>
>>> Would monday 2nd nov, at 2.30 pm eastern be ok for everybody?
>>>
>>> Julie
>>>
>>> ----- Original Message -----
>>> From: cda...@li...
>>> Date: Saturday, October 24, 2009 14:02
>>> Subject: CDAO-discuss Digest, Vol 2, Issue 2
>>> To: cda...@li...
>>>
>>>> Send CDAO-discuss mailing list submissions to
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>>>>
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>>>> When replying, please edit your Subject line so it is more specific
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>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>>  1. Re: next telecon for CDAO plans (Arlin Stoltzfus)
>>>>  2. Re: next telecon for CDAO plans (Enrico Pontelli)
>>>>
>>>>
>>>> -----------------------------------------------------------------
>>>> -----
>>>>
>>>> Message: 1
>>>> Date: Fri, 23 Oct 2009 10:06:52 -0400
>>>> From: Arlin Stoltzfus <sto...@um...>
>>>> Subject: Re: [CDAO-discuss] next telecon for CDAO plans
>>>> To: cda...@li...
>>>> Message-ID: <C2D...@um...>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>>
>>>> We are at an impasse already.  There is no time when we can
>>>> get both
>>>> Enrico and Julie.
>>>>
>>>> Enrico, is there any way that you can free up Wednesday at
>>>> 8:30
>>>> mountain time (10:30 EDT)?
>>>>
>>>> Julie, can you free up Monday, Nov 2 at 1:30 pm Eastern?
>>>>
>>>> I forgot to add time-zone support to this poll, so its
>>>> misleading.
>>>> Let me clarify.  Strasbourg shifts its time (CET) on
>>>> October 25 from
>>>> UTC+2 to UTC+1, and we shift our Eastern time on November 1 from
>>>> UTC
>>>> -4 to UTC -5.
>>>>
>>>> So, Eastern and CET are 6 hours apart from now until *this*
>>>> Sunday,
>>>> and 6 hours apart after *next* Sunday, but in the interval next
>>>> week,
>>>> we will be 5 hours apart.
>>>>
>>>> Does that change anything?
>>>>
>>>> Arlin
>>>>
>>>> On Oct 21, 2009, at 11:43 AM, Arlin Stoltzfus wrote:
>>>>
>>>>> Dear CDAO developers--
>>>>>
>>>>> Its about time for another teleconference to check in on
>>>> progress
>>>>> and plans with CDAO.  Two timely issues to consider are
>>>> the VoCamp,
>>>>> and an opportunity for a short-term high-impact project.
>>>> The
>>>>> Phyloinformatics VoCamp (at the Biodiversity Info
>>>> Standards
>>>>> conference in Montpellier, France) is coming up in 3 weeks and
>>>> there
>>>>> are a variety of ways in which CDAO may be involved.
>>>> Probably we
>>>>> will be asked to give a CDAO boot camp to interested parties--
>>>> the
>>>>> better that is, the more people learn about CDAO.  In
>>>> regard to a
>>>>> short-term project, Enrico has the capacity to devote
>>>> graduate
>>>>> students to a project over the next 6 to 9 months, if we can
>>>> come up
>>>>> with something that is compelling and practicable.
>>>>>
>>>>> I have made a doodle poll here for time slots (in Eastern
>>>> Daylight
>>>>> Time) starting Friday and going 2 weeks ahead:
>>>>>
>>>>> http://www.doodle.com/n8wapcah489nah58
>>>>>
>>>>> Please indicate your availability as soon as possible.
>>>>>
>>>>> If there is a desire for some wiki space to develop ideas,
>>>> I'll ask
>>>>> for a volunteer to help me set this up at sourceforge.  Thanks,
>>>>>
>>>>> Arlin
>>>>> -------
>>>>> Arlin Stoltzfus (sto...@um...)
>>>>> Fellow, CARB; Adj. Assoc. Prof., UMBI; Research Biologist, NIST
>>>>> CARB, 9600 Gudelsky Drive, Rockville, MD
>>>>> tel: 240 314 6208; web: www.molevol.org
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Fri, 23 Oct 2009 08:17:45 -0600
>>>> From: "Enrico Pontelli" <epo...@cs...>
>>>> Subject: Re: [CDAO-discuss] next telecon for CDAO plans
>>>> To: "'Arlin Stoltzfus'" <sto...@um...>,
>>>> <cda...@li...>
>>>> Message-ID: <004301ca53eb$9a495e80$cedc1b80$@nmsu.edu>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>>
>>>> Unfortunately I will be in Pittsburgh until Wednesday night,
>>>> that's why the
>>>> start of my week is completely off. My Monday 2nd can be made
>>>> completelyavailable, and if really needed I can try to shuffle
>>>> meetings on Tuesday 3rd
>>>> (but only after 10:30 MST since I teach class before that).
>>>>
>>>>
>>>>
>>>> Enrico
>>>>
>>>>
>>>>
>>>> From: Arlin Stoltzfus [mailto:sto...@um...]
>>>> Sent: Friday, October 23, 2009 8:07 AM
>>>> To: cda...@li...
>>>> Subject: Re: [CDAO-discuss] next telecon for CDAO plans
>>>>
>>>>
>>>>
>>>> We are at an impasse already.  There is no time when we can
>>>> get both Enrico
>>>> and Julie.
>>>>
>>>>
>>>>
>>>> Enrico, is there any way that you can free up Wednesday at 8:30
>>>> mountaintime (10:30 EDT)?
>>>>
>>>>
>>>>
>>>> Julie, can you free up Monday, Nov 2 at 1:30 pm Eastern?
>>>>
>>>>
>>>>
>>>> I forgot to add time-zone support to this poll, so its
>>>> misleading.  Let me
>>>> clarify.  Strasbourg shifts its time (CET) on October 25
>>>> from UTC+2 to
>>>> UTC+1, and we shift our Eastern time on November 1 from UTC -4
>>>> to UTC -5.
>>>>
>>>>
>>>>
>>>> So, Eastern and CET are 6 hours apart from now until *this*
>>>> Sunday, and 6
>>>> hours apart after *next* Sunday, but in the interval next week,
>>>> we will be 5
>>>> hours apart.
>>>>
>>>>
>>>>
>>>> Does that change anything?
>>>>
>>>>
>>>>
>>>> Arlin
>>>>
>>>>
>>>>
>>>> On Oct 21, 2009, at 11:43 AM, Arlin Stoltzfus wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Dear CDAO developers--
>>>>
>>>>
>>>>
>>>> Its about time for another teleconference to check in on
>>>> progress and plans
>>>> with CDAO.  Two timely issues to consider are the VoCamp,
>>>> and an opportunity
>>>> for a short-term high-impact project.  The Phyloinformatics
>>>> VoCamp (at the
>>>> Biodiversity Info Standards conference in Montpellier, France)
>>>> is coming up
>>>> in 3 weeks and there are a variety of ways in which CDAO may be
>>>> involved.Probably we will be asked to give a CDAO boot camp to
>>>> interested parties--
>>>> the better that is, the more people learn about CDAO.  In
>>>> regard to a
>>>> short-term project, Enrico has the capacity to devote graduate
>>>> students to a
>>>> project over the next 6 to 9 months, if we can come up with
>>>> something that
>>>> is compelling and practicable.
>>>>
>>>>
>>>>
>>>> I have made a doodle poll here for time slots (in Eastern
>>>> Daylight Time)
>>>> starting Friday and going 2 weeks ahead:
>>>>
>>>>
>>>>
>>>> http://www.doodle.com/n8wapcah489nah58
>>>>
>>>>
>>>>
>>>> Please indicate your availability as soon as possible.
>>>>
>>>>
>>>>
>>>> If there is a desire for some wiki space to develop ideas, I'll
>>>> ask for a
>>>> volunteer to help me set this up at sourceforge.
>>>> Thanks,
>>>>
>>>>
>>>>
>>>> Arlin
>>>>
>>>> -------
>>>>
>>>> Arlin Stoltzfus (sto...@um...)
>>>>
>>>> Fellow, CARB; Adj. Assoc. Prof., UMBI; Research Biologist, NIST
>>>>
>>>> CARB, 9600 Gudelsky Drive, Rockville, MD
>>>>
>>>> tel: 240 314 6208; web: www.molevol.org
>>>> <http://www.molevol.org/>
>>>>
>>>>
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>>
>>>> ------------------------------
>>>>
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>>>>
>>>> End of CDAO-discuss Digest, Vol 2, Issue 2
>>>> ******************************************
>>>
>>> Dr. Julie D. Thompson
>>> Laboratoire de Bioinformatique et Génomique Intégratives,
>>> Institut de Génétique et de Biologie Moléculaire et Cellulaire
>>> (IGBMC),
>>> 1 rue Laurent Fries,
>>> 67404 Illkirch, France.
>>> Tel: (33) 388 65 34 97
>>> Fax: (33) 388 65 32 01
>>> http://www-igbmc.u-strasbg.fr
>>> ------------------------------------------------------------------------------
>>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
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>>> ahead of the curve. Join us from November 9 - 12, 2009. Register  
>>> now!
>>> http://p.sf.net/sfu/devconference_______________________________________________
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>>
>>
>> ------------------------------------------------------------------------------
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>> developing skills, take BlackBerry mobile applications to market and
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>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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>> https://lists.sourceforge.net/lists/listinfo/cdao-discuss
>
>
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> developing skills, take BlackBerry mobile applications to market and  
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> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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