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[CDAO-discuss] RES: next telecon for CDAO plans (Julie Thompson)
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From: Francisco P. <fra...@uc...> - 2009-10-31 11:23:27
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Hey guys, 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). 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 >>> cda...@li... >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://lists.sourceforge.net/lists/listinfo/cdao-discuss >>> or, via email, send a message with subject or body 'help' to >>> cda...@li... >>> >>> You can reach the person managing the list at >>> cda...@li... >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of CDAO-discuss digest..." >>> >>> >>> 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... >>> >>> ------------------------------ >>> >>> ----------------------------------------------------------------- >>> ------------- >>> Come build with us! The BlackBerry(R) Developer Conference in >>> SF, CA >>> is the only developer event you need to attend this year. >>> Jumpstart your >>> developing skills, take BlackBerry mobile applications to market >>> and stay >>> ahead of the curve. Join us from November 9 - 12, 2009. Register >> now! >>> http://p.sf.net/sfu/devconference >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> CDAO-discuss mailing list >>> CDA...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdao-discuss >>> >>> >>> 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 >> is the only developer event you need to attend this year. Jumpstart >> your >> developing skills, take BlackBerry mobile applications to market and >> stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference_______________________________________________ >> CDAO-discuss mailing list >> CDA...@li... >> https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ CDAO-discuss mailing list CDA...@li... https://lists.sourceforge.net/lists/listinfo/cdao-discuss |