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From: Francisco P. <fra...@uc...> - 2009-11-20 16:32:28
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Bonjour a tous! :) I'm curious to know about what was going on in France. I wish I was there. I filled the doodle dates... sorry, but this is gonna be the last week of the semester and I'm a bit busy. But there is still a lot of dates/times to have the meeting. I prefer the meeting via Skype... I have had problems using it but I'll solve them surely. 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 81305488 http://biotec.icb.ufmg.br/chicopros -----Mensagem original----- De: Arlin Stoltzfus [mailto:sto...@um...] Enviada: sex 20/11/2009 03:07 Para: cda...@li... Assunto: [CDAO-discuss] scheduling for next meeting; regular monthly meetings Hello all. I'm just about back to normal after returning from France on Saturday. I'd like to have a CDAO teleconference this month. Our web site is out of date, and we have some opportunities opening up that I would like to discuss. In fact, I would like to have a teleconference every month. We discussed this last time (Nov 2) but there were not enough people to make a decision. Also last time, Julie and Francisco had trouble connecting with Skype-- thats another issue that we need to address. So, can you please help me with the following three things, each of which will take a few minutes: 1. Take the doodle poll to choose the next telecon: http://www.doodle.com/khuwm9t83d8qmeaz 2. Reply to this message with your choices for the best time for a regular monthly meeting (just arrange the options with > and = to indicate preference, e.g., M = F > T = W = Th) * best day of the week: M T W Th F * best week of the month: 1 2 3 4 * best time of the day (Eastern US): 8:00, 10:00, 12:00, 14:00 3. In a separate reply, share your ideas for how to make a monthly meeting both effective and accessible. We have been holding teleconferences using a system where each person has to pay to call in. Some people are using Skype to avoid the costs, but this introduces other issues. What other possibilities are there? The purpose of our meetings is to make decisions, share information, and build cohesion over priorities and responsibility. Are there other ways to do this? 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 |
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From: Arlin S. <sto...@um...> - 2009-11-20 15:07:37
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Hello all. I'm just about back to normal after returning from France on Saturday. I'd like to have a CDAO teleconference this month. Our web site is out of date, and we have some opportunities opening up that I would like to discuss. In fact, I would like to have a teleconference every month. We discussed this last time (Nov 2) but there were not enough people to make a decision. Also last time, Julie and Francisco had trouble connecting with Skype-- thats another issue that we need to address. So, can you please help me with the following three things, each of which will take a few minutes: 1. Take the doodle poll to choose the next telecon: http://www.doodle.com/khuwm9t83d8qmeaz 2. Reply to this message with your choices for the best time for a regular monthly meeting (just arrange the options with > and = to indicate preference, e.g., M = F > T = W = Th) * best day of the week: M T W Th F * best week of the month: 1 2 3 4 * best time of the day (Eastern US): 8:00, 10:00, 12:00, 14:00 3. In a separate reply, share your ideas for how to make a monthly meeting both effective and accessible. We have been holding teleconferences using a system where each person has to pay to call in. Some people are using Skype to avoid the costs, but this introduces other issues. What other possibilities are there? The purpose of our meetings is to make decisions, share information, and build cohesion over priorities and responsibility. Are there other ways to do this? 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 |
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From: Arlin S. <sto...@um...> - 2009-11-02 20:55:03
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Dear CDAO list members-- The telecon today was attended by Enrico, Vivek and I. Some people in other countries wanted to join, but faced technical or other barriers. Suggestions are welcome for how to use technology to bring CDAO developers together effectively and (relatively) inexpensively. Some of us can't use skype because our employers prevent it. Vivek has developed a proof-of-concept for "nexplorer3", which is to be an ontology-aware version of nexplorer. It will take an RDF file with a CDAO tree, and is able to query that with SPARQL and display it. Vivek says he was able to display a 2000-OTU tree from the Tree-o- Life project. We look forward to hearing more from Vivek on this project as it proceeds. See http://exon.niaid.nih.gov/nexplorer/. We decided on several "to do" items: * Enrico -- collect images and develop a 10 to 15 min CDAO "boot camp" presentation (for VoCamp) * Brandon -- put the latest version of CDAO on sourceforge. The version from August is not there yet! * Arlin -- fix the web site to make sure users get the right version of CDAO * Vivek -- make a crude diagram of the architecture of a portal with nexplorer3 for curation, display and annotation I encourage those of you who were not at the meeting to offer your help. 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 |
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From: Julie T. <ju...@ig...> - 2009-11-02 19:43:07
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There seems to be some confusion. I thought 2.30pm UTC -5, was 8.30pm french time, but nobody is online. sorry about that...Julie----- Original Message -----From: cda...@li...Date: Monday, November 2, 2009 19:22Subject: CDAO-discuss Digest, Vol 3, Issue 1To: 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 (Julie Thompson) > (Enrico Pontelli)> 2. Next Telecon for CDAO Plans (Enrico Pontelli)> 3. Re: next telecon for CDAO plans (Julie Thompson) > (Jim Balhoff)> 4. Re: RES: next telecon for CDAO plans (Julie Thompson)> (Arlin Stoltzfus)> > > -----------------------------------------------------------------> -----> > Message: 1> Date: Mon, 2 Nov 2009 08:49:09 -0700> From: "Enrico Pontelli" <epo...@cs...>> Subject: Re: [CDAO-discuss] next telecon for CDAO plans (Julie> Thompson)> To: "'Arlin Stoltzfus'" <sto...@um...>,> <cda...@li...>> Message-ID: <008401ca5bd4$0789b4a0$169d1de0$@nmsu.edu>> Content-Type: text/plain; charset="iso-8859-1"> > I believe we reached an agreement on a conference call for today > at 2:30pm.> Could please someone clarify time zone of reference (I had difficulty> understanding the UTC-5). > > Enrico> > > -----Original Message-----> From: Arlin Stoltzfus [mailto:sto...@um...] > Sent: Monday, October 26, 2009 2:12 PM> To: cda...@li...> Subject: Re: [CDAO-discuss] next telecon for CDAO plans (Julie > Thompson)> 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 G?nomique Int?gratives,> > Institut de G?n?tique et de Biologie Mol?culaire 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> > > > > ------------------------------> > Message: 2> Date: Mon, 2 Nov 2009 08:55:28 -0700> From: "Enrico Pontelli" <epo...@cs...>> Subject: [CDAO-discuss] Next Telecon for CDAO Plans> To: <cda...@li...>> Message-ID: <009b01ca5bd4$e8d9c260$ba8d4720$@nmsu.edu>> Content-Type: text/plain; charset="us-ascii"> > We will have a telecon to discuss next objectives and short-term > goals for> CDAO development. The telecon is on today at 2:30pm > eastern time (12:30> Mountain, 1:30 Central). The contact number is:> > > > Toll-free Tel: 1-866-705-2554> Toll Tel: 1-913-227-1201> Participant Passcode: 736420> > > > As Arlin mentioned a few days back, the two short term > objectives are> > 1. CDAO in the VoCamp> > 2. MIAPA-like support and > other short term projects> > > > Enrico> > > > =========================================================================> > Department of Computer > Science Voice: +1> (575) 646-6239> > New Mexico State > University Fax:> +1 (575) 646-1002> > Box 30001, MSC > CS > > Las Cruces, NM 88003> > > > -------------- next part --------------> An HTML attachment was scrubbed...> > ------------------------------> > Message: 3> Date: Mon, 2 Nov 2009 12:45:13 -0500> From: Jim Balhoff <ba...@ne...>> Subject: Re: [CDAO-discuss] next telecon for CDAO plans (Julie> Thompson)> To: Arlin Stoltzfus <sto...@um...>> Cc: cda...@li...> Message-ID: <0C2...@ne...>> Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes> > FYI - I don't think I'll be able to call in today, but I mainly > just > wanted to stay in the loop on CDAO. I'll take a look at any > minutes > that are posted.> > Thanks,> Jim> > > ____________________________________________> James P. Balhoff, Ph.D.> National Evolutionary Synthesis Center> 2024 West Main St., Suite A200> Durham, NC 27705> USA> > > > > ------------------------------> > Message: 4> Date: Mon, 2 Nov 2009 13:21:57 -0500> From: Arlin Stoltzfus <sto...@um...>> Subject: Re: [CDAO-discuss] RES: next telecon for CDAO plans (Julie> Thompson)> To: cda...@li...> Message-ID: <9DE...@um...>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes> > 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 > > Sarga?os 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 P?s-Gradua??o em Ci?ncias Gen?micas e Biotecnologia> > Universidade Cat?lica de Bras?lia - UCB> > SGAN 916 M?dulo B, Bloco C Sala 213> > 70.790-160 - Bras?lia / 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: <C2D225D4-62F6-48FF-9559-> 441...@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 G?nomique Int?gratives,> >>> Institut de G?n?tique et de Biologie Mol?culaire 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> >> > > > > ------------------------------> > -----------------------------------------------------------------> -------------> 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 3, Issue 1> ******************************************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 97Fax: (33) 388 65 32 01http://www-igbmc.u-strasbg.fr |
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From: Arlin S. <sto...@um...> - 2009-11-02 18:22:12
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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 >>>> 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 > |
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From: Jim B. <ba...@ne...> - 2009-11-02 17:45:28
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FYI - I don't think I'll be able to call in today, but I mainly just wanted to stay in the loop on CDAO. I'll take a look at any minutes that are posted. Thanks, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
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From: Enrico P. <epo...@cs...> - 2009-11-02 15:56:22
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We will have a telecon to discuss next objectives and short-term goals for CDAO development. The telecon is on today at 2:30pm eastern time (12:30 Mountain, 1:30 Central). The contact number is: Toll-free Tel: 1-866-705-2554 Toll Tel: 1-913-227-1201 Participant Passcode: 736420 As Arlin mentioned a few days back, the two short term objectives are 1. CDAO in the VoCamp 2. MIAPA-like support and other short term projects Enrico ========================================================================= Department of Computer Science Voice: +1 (575) 646-6239 New Mexico State University Fax: +1 (575) 646-1002 Box 30001, MSC CS Las Cruces, NM 88003 |
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From: Enrico P. <epo...@cs...> - 2009-11-02 15:50:13
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I believe we reached an agreement on a conference call for today at 2:30pm. Could please someone clarify time zone of reference (I had difficulty understanding the UTC-5). Enrico -----Original Message----- From: Arlin Stoltzfus [mailto:sto...@um...] Sent: Monday, October 26, 2009 2:12 PM To: cda...@li... Subject: Re: [CDAO-discuss] next telecon for CDAO plans (Julie Thompson) 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 |
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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 |
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From: Enrico P. <epo...@cs...> - 2009-10-30 21:48:05
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Wow. Enrico From: Arlin Stoltzfus [mailto:sto...@um...] Sent: Wednesday, October 28, 2009 9:00 AM To: cda...@li... Subject: [CDAO-discuss] CDAO exposure I'm not sure how many people are using CDAO, but there seem to be a lot of people looking at the paper-- its been viewed 661 times, according to the latest news from the publisher: Begin forwarded message: From: Tom Hill <tom...@la...> Date: October 20, 2009 11:02:27 PM EDT To: sto...@um... Subject: Your article in Evolutionary Bioinformatics Reply-To: tom...@la... Dear Dr Stoltzfus, A quick update on the status of your paper, Initial Implementation of a Comparative Data Analysis Ontology, which was published 15 weeks ago. Since publication your paper has been viewed 661 times. |
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From: Arlin S. <sto...@um...> - 2009-10-28 15:00:10
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I'm not sure how many people are using CDAO, but there seem to be a lot of people looking at the paper-- its been viewed 661 times, according to the latest news from the publisher: Begin forwarded message: > From: Tom Hill <tom...@la...> > Date: October 20, 2009 11:02:27 PM EDT > To: sto...@um... > Subject: Your article in Evolutionary Bioinformatics > Reply-To: tom...@la... > > Dear Dr Stoltzfus, > > A quick update on the status of your paper, Initial Implementation > of a Comparative Data Analysis Ontology, which was published 15 > weeks ago. > > Since publication your paper has been viewed 661 times. > |
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From: Hilmar L. <hl...@ne...> - 2009-10-28 00:23:54
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On Oct 26, 2009, at 1:12 PM, Arlin Stoltzfus wrote: > Is anyone *unavailable* on Monday, Nov. 2 at 2:30 pm (UTC -5)? I am on another conf call at that time, but as I said to Arlin before that shouldn't hold anything up. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Arlin S. <sto...@um...> - 2009-10-27 18:53:53
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OK, the CDAO telecon will be next Monday, i.e., Monday, Nov. 2 at 2:30 pm (UTC -5) Please mark you calendars. I would like to discuss 2 things: 1. a CDAO training presentation for the VoCamp participants 2. potential for building MIAPA-like support as a short-term, high- impact project Please let me know if you have other items to put on the agenda. Regarding #1 above, if you have any CDAO posters or presentations, lets find a way to recycle and reuse that material to make a presentation. Arlin On Oct 26, 2009, at 5:43 PM, Enrico Pontelli wrote: > 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 > |
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From: Enrico P. <epo...@cs...> - 2009-10-26 21:43:17
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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 |
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From: Arlin S. <sto...@um...> - 2009-10-26 21:03:48
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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 |
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From: Julie T. <ju...@ig...> - 2009-10-25 06:49:55
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Would monday 2nd nov, at 2.30 pm eastern be ok for everybody?Julie----- Original Message -----From: cda...@li...Date: Saturday, October 24, 2009 14:02Subject: CDAO-discuss Digest, Vol 2, Issue 2To: 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 97Fax: (33) 388 65 32 01http://www-igbmc.u-strasbg.fr |
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From: Enrico P. <epo...@cs...> - 2009-10-23 14:18:38
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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 completely available, 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 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 <http://www.molevol.org/> |
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From: Arlin S. <sto...@um...> - 2009-10-23 14:07:11
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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 |
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From: Arlin S. <sto...@um...> - 2009-10-21 15:43:46
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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 |
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From: Arlin S. <sto...@um...> - 2009-09-11 18:16:12
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On Sep 11, 2009, at 11:34 AM, Alan Ruttenberg wrote: > On Tue, Sep 8, 2009 at 3:51 PM, Arlin Stoltzfus > <sto...@um...> wrote: >> On Sep 2, 2009, at 3:31 PM, Alan Ruttenberg wrote: >> >>> BTW, looked up and found CDAO. I think I've discussed this with >>> Hilmar >>> in the past. >>> >>> There's overlap with interest that is pushing IAO development. >>> Perhaps >>> you or one of your collaborators are interested in participating? >> >> Yes, many of the concepts in our ontology [CDAO] are information >> artefacts, though >> this is not explicit. I consider "phyogenetic tree" to be an >> information >> artefact (I can explain why if its not clear), > > I think it's clear, but it certainly couldn't hurt to say how you view > this explicitly. I think that phyogenetic tree is more specifically a > "model", (and I have an idea about how to define model) in a similar > way that a gene regulatory network is a model. See > http://icbo.buffalo.edu/Presentations/Ruttenberg.pdf 91-93 . Not on > slides, but talking point, was that the thing that distinguishes this > sort of model from a data structure is that all the parts in the model > are explicitly mapped to some sort of entity/statement about entities > in "first order reality" (see Werner Ceuster's slide in that file #63 > - yellow is first order. Have to track down the defs of 1st,2nd,3rd he > has) Thanks for your response, Alan. I'm going to cc this to the cdao- discuss mailing list. Others might be interested in trying to sort out the upper-level status of "tree" and other troublesome concepts. The case with "tree" is a wee bit more complicated than "model" as defined. Phylogeneticists often speak of an "unrooted tree" for the case where they have inferred the connectivity but not the direction of branches. To the extent that branches map to the process of evolution, and evolution is in "first-order reality" (i'm not sure, because I don't what first-order reality is), the mapping must be less than a direct mapping to first-order reality, because evolution is always directional, whereas branches of phylogenetic trees may lack direction. In this way, a tree is more like a data structure. "Metabolic pathways" (which are, in some ways, similar to "phylogenetic trees") have the opposite problem-- their directionality is often over-specified relative to chemical reality, in which the flow of matter can go against the direction of a "pathway". There might be other problems as well. My perspective has been to avoid such issues on the grounds that I find upper-level ontologies are speculative and lack substantive implications for querying over domain knowledge. Entire books have been written on such things as what a "gene" is. In earlier versions of the SO, a mRNA was "part_of" a gene, in spite of the fact that everyone learns in high school that mRNAs are made or RNA while genes are made of DNA (this error was removed in later versions of SO). In other words, expert domain knowledge of genetics does not include knowing exactly what a gene is, and domain knowledge of genomics does not include knowing what a sequence is (or, at least, not in a frame- independent way-- and that might be part of the problem). My view is that no one really knows what a tree is, and so we don't have to know this either. Arlin |
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From: Arlin S. <sto...@um...> - 2009-09-10 20:55:50
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Dear all-- I would like to discuss possible goals and milestones for opening up CDAO development so that it becomes more of a community project. There are two parts of this-- building the infrastructure to support a community project, and cultivating a community of stakeholder- participants. The community of stakeholders might be small or modest in size, and presumably would consist mainly of developer-scientists involved in projects to manage data resources or provide services. Right now our community of stakeholders consists of ourselves and a few people associated with nexml and phyloWS who are experimenting with using CDAO to anchor annotations. Here is the technology that we have to support our community: * public web site (www.evolutionaryontology.org) * public code repository (sourceforge) * public email list (this list) The main thing we are missing right now is * documentation We identified this need at the meeting, and I seem to recall that Julie offered to do something about this. Is there anything else we need in terms of technology? In terms of community engagement, we could begin by being more responsive to our nexml and phenoscape stakeholders. In the spring they were asking for our help, but i didn't find the time to do it then-- and as a result, we missed an opportunity to engage them. I sent out a mass email in August to ask for people to voice their concerns and suggest ideas, but I got no responses. Moving forward, it might be beneficial to have: - a regular newsfeed or other way to reach stakeholders with updates (could be done via the email list) - monthly teleconferences advertised online, so that anyone can call in to join us To engage the community more pro-actively, we might want to create an online course, hold a workshop, or target a project for CDAO compatibility. Other ideas? Arlin |
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From: Arlin S. <sto...@um...> - 2009-09-10 17:15:37
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Dear phyloinformatics folk-- As part of a push to open up CDAO development and be more responsive, the development team has set up a public email list (cda...@li... ). If you would like to become involved, please subscribe to the list by filling in the blanks on this page: https://lists.sourceforge.net/lists/listinfo/cdao-discuss Thanks, and sorry for the cross-postings. 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 |
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From: Arlin S. <sto...@um...> - 2009-09-10 13:54:51
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Welcome to our new public list! At the July-August developer meeting in New Mexico, we discussed four priorities: 1. Funding. This discussion should go on the private list ( cda...@go... ). 2. Opening up the development model, and making CDAO a community project. There are two parts of this-- technology support and community engagement. We need the infrastructure to support a community project, and we need to cultivate a community of stakeholder- participants. I'm going to start a separate thread for this. 3. Setting up some kind of portal to showcase interop resources. The portal would provide services such as format conversion. 4. Finding ways to train students and others so that they can be productive quickly. Because we don't have specific funding, we have to make this project work by combining many smaller efforts. But each new person working on the project requires time to get familiar with the concepts and approaches of phylogenetics and ontology. I'm going to start a separate thread for #2 and #3. 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 |
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From: Arlin S. <sto...@um...> - 2009-09-09 19:48:34
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NESCent Phyloinformatics VoCamp OPEN CALL FOR PARTICIPATION Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the National Evolutionary Synthesis Center (NESCent: http://nescent.org) is sponsoring a "Phyloinformatics VoCamp". We invite scientists from diverse sub-disciplines to apply for this event, as explained below. The application deadline is September 18, 2009. More information about motivation, plans, and preliminary ideas is available online at http://bit.ly/VoCamp_Proposal. Feel free to disseminate this notice to colleagues who may be interested.* A VoCamp (http://vocamp.org) is an intense, hands-on, working meeting with face-to-face interactions between a diverse group of people focused on vocabulary and ontology design, development and application. The Phyloinformatics VoCamp will include ontology and vocabulary developers from relevant efforts, experts on knowledge representation and reasoning, and users and developers of integrative applications that use these ontologies. This event will partially overlap with the Biodiversity Information Standards (TDWG: http://tdwg.org) Annual Conference in Montpellier, France, November 9-13, 2009. The VoCamp is an activity of the TDWG Interest Group on Phylogenetics Standards (http://wiki.tdwg.org/Phylogenetics) and is partly supported by TDWG and the Université Montpellier. GOALS AND ACTIVITIES -------------------- The objective of the event is to connect previously disparate ontology development efforts, stakeholder communities, and interoperability initiatives with shared objectives. Aside from sharing knowledge, expertise, and best practices, our goal is to build-out existing ontology resources in a hands-on manner in terms of ontological rigor, semantic richness, and modularity that supports effective reuse. We also plan to have programming expertise and activities present at the event, such as for necessary large-scale transformations, and especially for proof-of-concept applications that directly apply the ontologies being developed. On a long-term basis, we anticipate that the event, if successful, will give rise to similarly structured follow-up events organized by the participating stakeholder communities, such as TDWG, SONet (http://sonet.ecoinformatics.org), and OBO (http://www.obofoundry.org). ORGANIZATION ------------ The VoCamp will be 4 days in duration during November 7-11, 2009 and is co-located with the TDWG annual conference (http://www.tdwg.org/conference2009) in Montpellier, France. The first two days (Nov 7-8) will be dedicated entirely to VoCamp and the remainder of the event (Nov 10-11) will overlap with TDWG 'workshops days'. Participants will have the opportunity, and are encouraged, to interact with TDWG participants and attend conference sessions outside of the VoCamp. The specific vocabulary development targets will be selected by the participants partly in advance through a dedicated area on a wiki, a mailing list, and one or more conference calls, and partly on-site through an Open Space activity. The exact agenda for the event will be developed similarly, but will be largely devoted to ontology and vocabulary development time. At the event itself, participants will self-organize into small subgroups focused on particular targets. The VoCamp will conclude with a wrap-up session, and a report presented to the TDWG conference audience. We also anticipate that several "boot camps" will be needed to ensure a productive event for all participants, for example on ontology design and engineering, reasoning, and infrastructure for collaborative development of ontologies. We welcome comments and suggestions for issues in ontology development that are not explicitly addressed here or in our proposal but that could be addressed at the event. Please email the organizers at vo...@ne... with any suggestions. HOW TO APPLY ------------ The application consists of your cv and your responses to 6 questions about your experience, skills, objectives, support, and commitment to open software development. To apply, please fill out the online form at http://bit.ly/VoCamp_Form by September 18, and submit your CV to the organizers at vo...@ne.... NESCent will provide funds in support of expenses, including travel, accommodation, registration, and meals. Pending the final amount of funds available and the support requested by the participants, sponsorship may need to be capped. Logistical and travel details will be communicated to accepted and confirmed participants. We specifically encourage applications from members of under- represented groups, specifically women and minorities, and from graduate students and post-docs. If you have questions or are unsure whether to apply, please contact an organizer or write to vo...@ne... . Please understand that funding and space for this event are limited. We also need to balance a critical mass of expertise in specific areas with broad participation. Therefore, not all qualified applicants can be guaranteed acceptance. Yours, The Organizing Committee Arlin Stoltzfus, Chair (University of Maryland Biotechnology Institute) Nico Cellinese (University of Florida) Karen Cranston (Field Museum of Natural History) Hilmar Lapp (NESCent) Sheldon McKay (Cold Spring Harbor Laboratory, iPlant Collaborative) Enrico Pontelli (New Mexico State University) * This announcement is being sent to the following lists: evoldir, TDWG, SSB, nexml, phylows, CDAO, SONet, GBIF, Ecolog, TAXACOM. |