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From: Francisco P. <fra...@uc...> - 2010-01-20 03:00:46
|
Dear CDAO members, We are now updating our web-page from http://evolutionaryontology.org into a wiki version. The idea is having an open environment on which everybody can make contributions and post suggestions/discussions/information. I was setting up wiki pages hosted both at NESCent and Sourceforge. I would like to ask you please to take a quick look on both and let me know which of them you think will be better for our project (please note: draft version). -- CDAO@NESCent https://www.nescent.org/sites/cdao/Main_Page -- CDAO@sourceforge https://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page Visually they look pretty much the same, i. e., they are wiki pages. ;) But there are some petites differences that one might argue about: -- User-adding: ** SourceForge allow easy new member adding for the ones having a sourceforge account (https://sourceforge.net/apps/trac/sourceforge/ticket/4381) ** NESCent helpdesk tickets shall be open to ask for new user additions -- The right place in multidisciplinary research field: ** NESCent hosting may be more appropriated for a domain-specific academic ontology on evolutionary biology ** SourceForge hosting may be more appropriated for an open-source computational project -- Visualization ** SourceForge page is not full-screen since they leave a SF banner at the top I can't see other differences and I would take SourceForge for user-adding simplicity. Please let me know whether you can see any other advantages on hosting it here or there -- or even anywhere else. Regards, -- Prof. Francisco Prosdocimi, PhD ---------------------------------- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília - UCB SGAN 916 Módulo B, Bloco B Sala 006 70.790-160 - Brasília / DF - Brasil Fone: +55 61 34487173 http://biotec.icb.ufmg.br/chicopros |
From: Arlin S. <sto...@um...> - 2010-01-11 17:37:57
|
Dear all-- I'm sorry again for disseminating incorrect information about the teleconference. The notes from the teleconference are below. These notes-- along with the 2009 annual report on the CDAO project that will be released soon-- will appear on a public wiki that we hope to have set up later this month (Francisco has been working on this and it just needs a final test). If you have questions or comments, let me know. 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 ------- = January 11, 2010, teleconference = The teleconference included Arlin, Vivek and Sam Donnelly (pPOD), and lasted an hour from 12:15 to 1:15. Julie missed the conference due to the erroneous connection information. Francisco is traveling and was not able to attend. Alan Ruttenberg hopes to attend some time soon, but was unavailable today. I'm not sure what happened to Brandon. We briefly reviewed the activities of the year. In 2009, CDAO-related activities included * representation of concept alignment between CDAO and MAO (Developer meeting, July) * representation of token cases of evolutionary transitions (Developer meeting, July) * limited release of version 2 (November) * publication of 1 paper and 1 book chapter * presentation of CDAO 4 times at conferences (in posters or talks) * opening up the development process ** public list with at least 15 legitimate members, traffic of about 10 posts per month ** open teleconferences starting in November * use of CDAO in 4 demonstration projects (no production uses yet) This was followed by some thoughts about strategic opportunities involving pPOD (Sam) and Nexplorer3 (Vivek). Sam is interested in looking for ways to build bridges with the pPOD project. Nexplorer3 is very promising and might provide a powerful demonstration of the potential of ontology-based interfaces to data. Specifically, Nexplorer3 shaping up to be a graphical-plus-SPARQL interface to a repository of character-data-and-trees data sets (e.g., like TreeBase or Nexplorer). The NIAID group is devoting part of Vivek's time plus a Java programmer plus part of a web designer to this project. They have developed translation tools to generate CDAO- encoded data from Pandit and TreeBase (via the NEXUS translations available on the old Nexplorer web site). This is a demonstration project with a deadline in March. It might be a good use of our time to help Vivek in every possible way to make this a success, so that his supervisor will continue to devote resources to this project. |
From: Enrico P. <epo...@cs...> - 2010-01-11 15:36:10
|
I got in too late, but I also got error with the access code when I try to get in Enrico From: Julie Thompson [mailto:ju...@ig...] Sent: Monday, January 11, 2010 8:07 AM To: cda...@li... Subject: Re: [CDAO-discuss] CDAO-discuss Digest, Vol 5, Issue 2 sorry - but conference centre says my access code is not valid: I'm using 375259 Julie ----- Original Message ----- From: cda...@li... Date: Monday, January 11, 2010 15:42 Subject: CDAO-discuss Digest, Vol 5, 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: CDAO teleconference Monday, January > 11, 10:00 am EST (GMT > -5) (Arlin Stoltzfus) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Mon, 11 Jan 2010 09:22:50 -0500 > From: Arlin Stoltzfus <sto...@um...> > Subject: Re: [CDAO-discuss] CDAO teleconference Monday, January 11, > 10:00 am EST (GMT -5) > To: cda...@li... > Message-ID: <48C...@um...> > Content-Type: text/plain; charset="us-ascii" > > Dear all-- > > The teleconference is coming up in 40 minutes. The > agenda is to > review 2009 and start thinking about 2010 goals. Below is > an > incomplete document to serve as a guide. > > For those of you who have access to the project admin group, the > wiki > version of this is online at: > > http://groups.google.com/group/cdao-manage/web/review-of- > project-for-2009 > > Francisco is working on a way for us to have wiki content > that > everyone can edit. > > 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 > > On Jan 8, 2010, at 12:32 PM, Arlin Stoltzfus wrote: > > > Dear all-- > > > > Happy new year. Last month we decided to start > holding a regular > > telecon on the second Monday of every month. Below are > the details on > > the teleconference. > > > > date: Monday, January 8, 2009 > > time: 10:00 am Eastern (GMT -5) > > dial-in number (long-distance charges apply): 1-213-289-0500 > > participant access code: 375259 > > > > All developers and users (actual and potential) of CDAO are > invited to > > participate. However, note that this involves a long- > distance call > > that will be charged to your phone. > > > > The CDAO Project: 2009 annual report > > Brief review of 2009 > > Development and evaluation of CDAO content > > The recurring theme this year was how to integrate with > other > ontologies. Here is a quick synopsis of changes in the two > versions > that came out this year: > 2009-Jul version: added an alignment with MAO (July, 2009) > 2009-Nov version: ? > > Note that we have started to separate the namespace versioning > from > the version of the OWL code. A new CVS version is created > every time > someone checks in a new change in CVS. However, this is > not > necessarily a new namespace. Rather than give the > namespaces numbers > like "1.0" and "2.0", which sound like CVS versions, we decided > to > call them > > CDAO currently contains concepts pertaining to trees, > character > matrices, "OTUs", evolutionary changes ("transitions"), and a > few > miscellaneous things. The upper-level relations of these > concepts > have not been established. There are a handful of concepts > that were > added by a single developer in 2008 that were never vetted and > should > be considered tentative. Evaluation, so far, has not gone > beyond the > initial reasoning tests applied by Prosdocimi et al (2009). > Community of active developers and users > > The original development team consisted of 5 individuals from > 3 > institutions (the authors of Prosdocimi, et al., 2009). In > 2009 we > attempted to reach out to a broader community, with limited > success. > We re-named the private Google group from cdao-dev to cdao-admin > and > created a public list at sourceforge. The cdao- > ad...@go... > list is for the project leaders to discuss funding and > personnel > issues, while cda...@li... is a public > list > available for anyone who wishes to get involved. > > In October we proposed to have regular, open teleconferences on > a > monthly basis. The first open teleconference took place > November 2, > 2009, and included only 3 participants. Another took place > Dec 1, > 2009. Scheduling is difficult across 9 time zones, and > there have > been difficulties with making the connection for users who wish > to > avoid long-distance charges. > > In spite of these moves toward openness, the group of active > persons > has not changed significantly. A few new people joined the > open > sourceforge list, but these people have not contributed to the > code or > joined the teleconferences. Vivek Gopalan and Peter > Midford have > contributed to electronic discussions about CDAO, and we hope > that > they will contribute more actively in the future. > Publication and communication to a broader community > > Information relating to the CDAO project has been communicated > in a > published paper, in various electronic communications, and by > means of > 2 web sites. The paper by Prosdocimi, et al. (2009) is the > first peer- > reviewed technical publication from the group. At the same > time, we > published a second review paper. According to the > publisher, the > paper was viewed 661 times by October 20. > > The main source of basic information on the CDAO project, and > the URI > home for the ontology, is at evolutionaryontology.org. The > source > code repository is at SourceForge. There is also a Google > group for > administrators of the project, but this is private so it is not > a > means of disseminating project information. > > Posters: > Evolution, 2009 (Hilmar) > Brazilian bioinformatics, 2009 > Projects and use-cases > > 1. Data interop hackathon at NESCent. > > https://www.nescent.org/wg_evoinfo/Semantic_API_for_CDAO_Subgroup > 2. SPARQL query and visualization of trees. > > Vivek has developed a proof-of-concept for "nexplorer3", which > is to > be an ontology-aware version of nexplorer. It will take an > RDF > filewith 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/ > . > > > > 3. VoCamp. > > https://www.evoio.org/wiki/Integrating_Ontologies > > 4. Triple Store. > > Enrico described it like this: "With some leftover funds, I > have > assembled a team composed of Brandon, 2 > other graduate students, and myself. The goal is to create a > basic > portal which will allow > access to CDAO (e.g., documentation, ontology files, etc) > translation services (we are working on refining NEXUS, adding > MEGA > and PHYLIP, and eventually Nexml) > import TreeBase > maintain everything as a triple-store in RDF > eventually we would like to add a user interface for annotations > and > manipulations (Nexplorer style)" > Funding > > Two project leaders (Pontelli, Stoltzfus) were involved in the > VoCamp > planning that effectively provided some money for a CDAO-based > project > at the VoCamp. > > Enrico was able to spend some leftover money on a CDAO-based > project > (see above). > > Other than that, there was no dedicated funding for CDAO > work. One > proposal is pending: Cellinese, Cranston, Lapp, McKay, Pontelli, > and > Stoltzfus submitted an NSF INTEROP proposal to fund a data > interoperability network. Part of this money would go to > technical > support for the community, and could be used for work on CDAO > and > other technologies that underly interop solutions. The > proposal is in > review currently. > > Recognition > Francisco got an award for his CDAO poster at the Brazilian > Bioinfo > conference. > > Strategic planning for 2010 > > Development and evaluation of CDAO content > > Higher-level relations of concepts (e.g., how does an OTU relate > to a > "tree"?). Arlin started a document to serve as a point of > reference > for this discussion. > > Community of active developers and users > > What do we plan to do to expand and energize the community > of > developers and users. > > Publication and communication to a broader community > > What do we plan to do to disseminate project results to the community? > > Projects and use-cases > > What projects do we plan to undertake? > Funding > > What funding will we seek? > > NESCent? > > CREST proposal (Pontelli) > > Stoltzfus, Pontelli and Gupta plan to submit a revised NIH > proposal in > February seeking major support for CDAO in the context of a > project to > develop workflow systems. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: nexplorer3.png > Type: image/png > Size: 137582 bytes > Desc: not available > > ------------------------------ > > ----------------------------------------------------------------- > ------------- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution > fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > > ------------------------------ > > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > > End of CDAO-discuss Digest, Vol 5, 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 |
From: Julie T. <ju...@ig...> - 2010-01-11 15:25:03
|
sorry - but conference centre says my access code is not valid: I'm using 375259Julie----- Original Message -----From: cda...@li...Date: Monday, January 11, 2010 15:42Subject: CDAO-discuss Digest, Vol 5, 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: CDAO teleconference Monday, January > 11, 10:00 am EST (GMT> -5) (Arlin Stoltzfus)> > > -----------------------------------------------------------------> -----> > Message: 1> Date: Mon, 11 Jan 2010 09:22:50 -0500> From: Arlin Stoltzfus <sto...@um...>> Subject: Re: [CDAO-discuss] CDAO teleconference Monday, January 11,> 10:00 am EST (GMT -5)> To: cda...@li...> Message-ID: <48C...@um...>> Content-Type: text/plain; charset="us-ascii"> > Dear all--> > The teleconference is coming up in 40 minutes. The > agenda is to > review 2009 and start thinking about 2010 goals. Below is > an > incomplete document to serve as a guide.> > For those of you who have access to the project admin group, the > wiki > version of this is online at:> > http://groups.google.com/group/cdao-manage/web/review-of-> project-for-2009> > Francisco is working on a way for us to have wiki content > that > everyone can edit.> > 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> > On Jan 8, 2010, at 12:32 PM, Arlin Stoltzfus wrote:> > > Dear all--> >> > Happy new year. Last month we decided to start > holding a regular> > telecon on the second Monday of every month. Below are > the details on> > the teleconference.> >> > date: Monday, January 8, 2009> > time: 10:00 am Eastern (GMT -5)> > dial-in number (long-distance charges apply): 1-213-289-0500> > participant access code: 375259> >> > All developers and users (actual and potential) of CDAO are > invited to> > participate. However, note that this involves a long-> distance call> > that will be charged to your phone.> >> > The CDAO Project: 2009 annual report> > Brief review of 2009> > Development and evaluation of CDAO content> > The recurring theme this year was how to integrate with > other > ontologies. Here is a quick synopsis of changes in the two > versions > that came out this year:> 2009-Jul version: added an alignment with MAO (July, 2009)> 2009-Nov version: ?> > Note that we have started to separate the namespace versioning > from > the version of the OWL code. A new CVS version is created > every time > someone checks in a new change in CVS. However, this is > not > necessarily a new namespace. Rather than give the > namespaces numbers > like "1.0" and "2.0", which sound like CVS versions, we decided > to > call them> > CDAO currently contains concepts pertaining to trees, > character > matrices, "OTUs", evolutionary changes ("transitions"), and a > few > miscellaneous things. The upper-level relations of these > concepts > have not been established. There are a handful of concepts > that were > added by a single developer in 2008 that were never vetted and > should > be considered tentative. Evaluation, so far, has not gone > beyond the > initial reasoning tests applied by Prosdocimi et al (2009).> Community of active developers and users> > The original development team consisted of 5 individuals from > 3 > institutions (the authors of Prosdocimi, et al., 2009). In > 2009 we > attempted to reach out to a broader community, with limited > success. > We re-named the private Google group from cdao-dev to cdao-admin > and > created a public list at sourceforge. The cdao-> ad...@go... > list is for the project leaders to discuss funding and > personnel > issues, while cda...@li... is a public > list > available for anyone who wishes to get involved.> > In October we proposed to have regular, open teleconferences on > a > monthly basis. The first open teleconference took place > November 2, > 2009, and included only 3 participants. Another took place > Dec 1, > 2009. Scheduling is difficult across 9 time zones, and > there have > been difficulties with making the connection for users who wish > to > avoid long-distance charges.> > In spite of these moves toward openness, the group of active > persons > has not changed significantly. A few new people joined the > open > sourceforge list, but these people have not contributed to the > code or > joined the teleconferences. Vivek Gopalan and Peter > Midford have > contributed to electronic discussions about CDAO, and we hope > that > they will contribute more actively in the future.> Publication and communication to a broader community> > Information relating to the CDAO project has been communicated > in a > published paper, in various electronic communications, and by > means of > 2 web sites. The paper by Prosdocimi, et al. (2009) is the > first peer- > reviewed technical publication from the group. At the same > time, we > published a second review paper. According to the > publisher, the > paper was viewed 661 times by October 20.> > The main source of basic information on the CDAO project, and > the URI > home for the ontology, is at evolutionaryontology.org. The > source > code repository is at SourceForge. There is also a Google > group for > administrators of the project, but this is private so it is not > a > means of disseminating project information.> > Posters:> Evolution, 2009 (Hilmar)> Brazilian bioinformatics, 2009> Projects and use-cases> > 1. Data interop hackathon at NESCent.> > https://www.nescent.org/wg_evoinfo/Semantic_API_for_CDAO_Subgroup> 2. SPARQL query and visualization of trees.> > Vivek has developed a proof-of-concept for "nexplorer3", which > is to > be an ontology-aware version of nexplorer. It will take an > RDF > filewith 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/ > .> > > > 3. VoCamp.> > https://www.evoio.org/wiki/Integrating_Ontologies> > 4. Triple Store.> > Enrico described it like this: "With some leftover funds, I > have > assembled a team composed of Brandon, 2> other graduate students, and myself. The goal is to create a > basic > portal which will allow> access to CDAO (e.g., documentation, ontology files, etc)> translation services (we are working on refining NEXUS, adding > MEGA > and PHYLIP, and eventually Nexml)> import TreeBase> maintain everything as a triple-store in RDF> eventually we would like to add a user interface for annotations > and > manipulations (Nexplorer style)"> Funding> > Two project leaders (Pontelli, Stoltzfus) were involved in the > VoCamp > planning that effectively provided some money for a CDAO-based > project > at the VoCamp.> > Enrico was able to spend some leftover money on a CDAO-based > project > (see above).> > Other than that, there was no dedicated funding for CDAO > work. One > proposal is pending: Cellinese, Cranston, Lapp, McKay, Pontelli, > and > Stoltzfus submitted an NSF INTEROP proposal to fund a data > interoperability network. Part of this money would go to > technical > support for the community, and could be used for work on CDAO > and > other technologies that underly interop solutions. The > proposal is in > review currently.> > Recognition> Francisco got an award for his CDAO poster at the Brazilian > Bioinfo > conference.> > Strategic planning for 2010> > Development and evaluation of CDAO content> > Higher-level relations of concepts (e.g., how does an OTU relate > to a > "tree"?). Arlin started a document to serve as a point of > reference > for this discussion.> > Community of active developers and users> > What do we plan to do to expand and energize the community > of > developers and users.> > Publication and communication to a broader community> > What do we plan to do to disseminate project results to the community?> > Projects and use-cases> > What projects do we plan to undertake?> Funding> > What funding will we seek?> > NESCent?> > CREST proposal (Pontelli)> > Stoltzfus, Pontelli and Gupta plan to submit a revised NIH > proposal in > February seeking major support for CDAO in the context of a > project to > develop workflow systems.> > > -------------- next part --------------> An HTML attachment was scrubbed...> -------------- next part --------------> A non-text attachment was scrubbed...> Name: nexplorer3.png> Type: image/png> Size: 137582 bytes> Desc: not available> > ------------------------------> > -----------------------------------------------------------------> -------------> This SF.Net email is sponsored by the Verizon Developer Community> Take advantage of Verizon's best-in-class app development support> A streamlined, 14 day to market process makes app distribution > fast and easy> Join now and get one step closer to millions of Verizon customers> http://p.sf.net/sfu/verizon-dev2dev > > ------------------------------> > _______________________________________________> CDAO-discuss mailing list> CDA...@li...> https://lists.sourceforge.net/lists/listinfo/cdao-discuss> > > End of CDAO-discuss Digest, Vol 5, 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 |
From: Arlin S. <sto...@um...> - 2010-01-11 15:06:17
|
I'm sorry-- the information that I sent was the expired number for a past conference. Please use this number: dial-in number (long-distance charges apply): 1 (605) 475-4333 participant access code: 375259 We'll start a few minutes late-- 10:15 am Eastern (GMT -5)-- to allow people to adjust to this 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 On Jan 11, 2010, at 9:22 AM, Arlin Stoltzfus wrote: > Dear all-- > > The teleconference is coming up in 40 minutes. The agenda is to > review 2009 and start thinking about 2010 goals. Below is an > incomplete document to serve as a guide. > > For those of you who have access to the project admin group, the > wiki version of this is online at: > > http://groups.google.com/group/cdao-manage/web/review-of-project-for-2009 > > Francisco is working on a way for us to have wiki content that > everyone can edit. > > 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 > > On Jan 8, 2010, at 12:32 PM, Arlin Stoltzfus wrote: > >> Dear all-- >> >> Happy new year. Last month we decided to start holding a regular >> telecon on the second Monday of every month. Below are the details >> on >> the teleconference. >> >> date: Monday, January 8, 2009 >> time: 10:00 am Eastern (GMT -5) >> dial-in number (long-distance charges apply): 1-213-289-0500 >> participant access code: 375259 >> >> All developers and users (actual and potential) of CDAO are invited >> to >> participate. However, note that this involves a long-distance call >> that will be charged to your phone. >> > > The CDAO Project: 2009 annual report > > Brief review of 2009Development and evaluation of CDAO content > The recurring theme this year was how to integrate with other > ontologies. Here is a quick synopsis of changes in the two versions > that came out this year: > 2009-Jul version: added an alignment with MAO (July, 2009) > 2009-Nov version: ? > > Note that we have started to separate the namespace versioning from > the version of the OWL code. A new CVS version is created every > time someone checks in a new change in CVS. However, this is not > necessarily a new namespace. Rather than give the namespaces > numbers like "1.0" and "2.0", which sound like CVS versions, we > decided to call them > > CDAO currently contains concepts pertaining to trees, character > matrices, "OTUs", evolutionary changes ("transitions"), and a few > miscellaneous things. The upper-level relations of these concepts > have not been established. There are a handful of concepts that > were added by a single developer in 2008 that were never vetted and > should be considered tentative. Evaluation, so far, has not gone > beyond the initial reasoning tests applied by Prosdocimi et al (2009). > Community of active developers and users > The original development team consisted of 5 individuals from 3 > institutions (the authors of Prosdocimi, et al., 2009). In 2009 we > attempted to reach out to a broader community, with limited > success. We re-named the private Google group from cdao-dev to cdao- > admin and created a public list at sourceforge. The cda...@go... > list is for the project leaders to discuss funding and personnel > issues, while cda...@li... is a public list > available for anyone who wishes to get involved. > > In October we proposed to have regular, open teleconferences on a > monthly basis. The first open teleconference took place November 2, > 2009, and included only 3 participants. Another took place Dec 1, > 2009. Scheduling is difficult across 9 time zones, and there have > been difficulties with making the connection for users who wish to > avoid long-distance charges. > > In spite of these moves toward openness, the group of active persons > has not changed significantly. A few new people joined the open > sourceforge list, but these people have not contributed to the code > or joined the teleconferences. Vivek Gopalan and Peter Midford have > contributed to electronic discussions about CDAO, and we hope that > they will contribute more actively in the future. > Publication and communication to a broader community > Information relating to the CDAO project has been communicated in a > published paper, in various electronic communications, and by means > of 2 web sites. The paper by Prosdocimi, et al. (2009) is the first > peer-reviewed technical publication from the group. At the same > time, we published a second review paper. According to the > publisher, the paper was viewed 661 times by October 20. > > The main source of basic information on the CDAO project, and the > URI home for the ontology, is at evolutionaryontology.org. The > source code repository is at SourceForge. There is also a Google > group for administrators of the project, but this is private so it > is not a means of disseminating project information. > > Posters: > • Evolution, 2009 (Hilmar) > • Brazilian bioinformatics, 2009 > Projects and use-cases1. Data interop hackathon at NESCent. > https://www.nescent.org/wg_evoinfo/Semantic_API_for_CDAO_Subgroup > 2. SPARQL query and visualization of trees. > Vivek has developed a proof-of-concept for "nexplorer3", which is to > be an ontology-aware version of nexplorer. It will take an RDF > filewith 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/ > . > > <nexplorer3.png> > > 3. VoCamp. > https://www.evoio.org/wiki/Integrating_Ontologies > > 4. Triple Store. > Enrico described it like this: "With some leftover funds, I have > assembled a team composed of Brandon, 2 > other graduate students, and myself. The goal is to create a basic > portal which will allow > • access to CDAO (e.g., documentation, ontology files, etc) > • translation services (we are working on refining NEXUS, adding > MEGA and PHYLIP, and eventually Nexml) > • import TreeBase > • maintain everything as a triple-store in RDF > • eventually we would like to add a user interface for annotations > and manipulations (Nexplorer style)" > Funding > Two project leaders (Pontelli, Stoltzfus) were involved in the > VoCamp planning that effectively provided some money for a CDAO- > based project at the VoCamp. > > Enrico was able to spend some leftover money on a CDAO-based project > (see above). > > Other than that, there was no dedicated funding for CDAO work. One > proposal is pending: Cellinese, Cranston, Lapp, McKay, Pontelli, and > Stoltzfus submitted an NSF INTEROP proposal to fund a data > interoperability network. Part of this money would go to technical > support for the community, and could be used for work on CDAO and > other technologies that underly interop solutions. The proposal is > in review currently. > > Recognition > Francisco got an award for his CDAO poster at the Brazilian Bioinfo > conference. > > Strategic planning for 2010 > Development and evaluation of CDAO content > Higher-level relations of concepts (e.g., how does an OTU relate to > a "tree"?). Arlin started a document to serve as a point of > reference for this discussion. > > Community of active developers and users > What do we plan to do to expand and energize the community of > developers and users. > > Publication and communication to a broader community > What do we plan to do to disseminate project results to the community? > > Projects and use-cases > What projects do we plan to undertake? > Funding > What funding will we seek? > > NESCent? > > CREST proposal (Pontelli) > > Stoltzfus, Pontelli and Gupta plan to submit a revised NIH proposal > in February seeking major support for CDAO in the context of a > project to develop workflow systems. > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Arlin S. <sto...@um...> - 2010-01-11 14:23:09
|
Dear all-- The teleconference is coming up in 40 minutes. The agenda is to review 2009 and start thinking about 2010 goals. Below is an incomplete document to serve as a guide. For those of you who have access to the project admin group, the wiki version of this is online at: http://groups.google.com/group/cdao-manage/web/review-of-project-for-2009 Francisco is working on a way for us to have wiki content that everyone can edit. 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 On Jan 8, 2010, at 12:32 PM, Arlin Stoltzfus wrote: > Dear all-- > > Happy new year. Last month we decided to start holding a regular > telecon on the second Monday of every month. Below are the details on > the teleconference. > > date: Monday, January 8, 2009 > time: 10:00 am Eastern (GMT -5) > dial-in number (long-distance charges apply): 1-213-289-0500 > participant access code: 375259 > > All developers and users (actual and potential) of CDAO are invited to > participate. However, note that this involves a long-distance call > that will be charged to your phone. > The CDAO Project: 2009 annual report Brief review of 2009 Development and evaluation of CDAO content The recurring theme this year was how to integrate with other ontologies. Here is a quick synopsis of changes in the two versions that came out this year: 2009-Jul version: added an alignment with MAO (July, 2009) 2009-Nov version: ? Note that we have started to separate the namespace versioning from the version of the OWL code. A new CVS version is created every time someone checks in a new change in CVS. However, this is not necessarily a new namespace. Rather than give the namespaces numbers like "1.0" and "2.0", which sound like CVS versions, we decided to call them CDAO currently contains concepts pertaining to trees, character matrices, "OTUs", evolutionary changes ("transitions"), and a few miscellaneous things. The upper-level relations of these concepts have not been established. There are a handful of concepts that were added by a single developer in 2008 that were never vetted and should be considered tentative. Evaluation, so far, has not gone beyond the initial reasoning tests applied by Prosdocimi et al (2009). Community of active developers and users The original development team consisted of 5 individuals from 3 institutions (the authors of Prosdocimi, et al., 2009). In 2009 we attempted to reach out to a broader community, with limited success. We re-named the private Google group from cdao-dev to cdao-admin and created a public list at sourceforge. The cda...@go... list is for the project leaders to discuss funding and personnel issues, while cda...@li... is a public list available for anyone who wishes to get involved. In October we proposed to have regular, open teleconferences on a monthly basis. The first open teleconference took place November 2, 2009, and included only 3 participants. Another took place Dec 1, 2009. Scheduling is difficult across 9 time zones, and there have been difficulties with making the connection for users who wish to avoid long-distance charges. In spite of these moves toward openness, the group of active persons has not changed significantly. A few new people joined the open sourceforge list, but these people have not contributed to the code or joined the teleconferences. Vivek Gopalan and Peter Midford have contributed to electronic discussions about CDAO, and we hope that they will contribute more actively in the future. Publication and communication to a broader community Information relating to the CDAO project has been communicated in a published paper, in various electronic communications, and by means of 2 web sites. The paper by Prosdocimi, et al. (2009) is the first peer- reviewed technical publication from the group. At the same time, we published a second review paper. According to the publisher, the paper was viewed 661 times by October 20. The main source of basic information on the CDAO project, and the URI home for the ontology, is at evolutionaryontology.org. The source code repository is at SourceForge. There is also a Google group for administrators of the project, but this is private so it is not a means of disseminating project information. Posters: Evolution, 2009 (Hilmar) Brazilian bioinformatics, 2009 Projects and use-cases 1. Data interop hackathon at NESCent. https://www.nescent.org/wg_evoinfo/Semantic_API_for_CDAO_Subgroup 2. SPARQL query and visualization of trees. Vivek has developed a proof-of-concept for "nexplorer3", which is to be an ontology-aware version of nexplorer. It will take an RDF filewith 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/ . 3. VoCamp. https://www.evoio.org/wiki/Integrating_Ontologies 4. Triple Store. Enrico described it like this: "With some leftover funds, I have assembled a team composed of Brandon, 2 other graduate students, and myself. The goal is to create a basic portal which will allow access to CDAO (e.g., documentation, ontology files, etc) translation services (we are working on refining NEXUS, adding MEGA and PHYLIP, and eventually Nexml) import TreeBase maintain everything as a triple-store in RDF eventually we would like to add a user interface for annotations and manipulations (Nexplorer style)" Funding Two project leaders (Pontelli, Stoltzfus) were involved in the VoCamp planning that effectively provided some money for a CDAO-based project at the VoCamp. Enrico was able to spend some leftover money on a CDAO-based project (see above). Other than that, there was no dedicated funding for CDAO work. One proposal is pending: Cellinese, Cranston, Lapp, McKay, Pontelli, and Stoltzfus submitted an NSF INTEROP proposal to fund a data interoperability network. Part of this money would go to technical support for the community, and could be used for work on CDAO and other technologies that underly interop solutions. The proposal is in review currently. Recognition Francisco got an award for his CDAO poster at the Brazilian Bioinfo conference. Strategic planning for 2010 Development and evaluation of CDAO content Higher-level relations of concepts (e.g., how does an OTU relate to a "tree"?). Arlin started a document to serve as a point of reference for this discussion. Community of active developers and users What do we plan to do to expand and energize the community of developers and users. Publication and communication to a broader community What do we plan to do to disseminate project results to the community? Projects and use-cases What projects do we plan to undertake? Funding What funding will we seek? NESCent? CREST proposal (Pontelli) Stoltzfus, Pontelli and Gupta plan to submit a revised NIH proposal in February seeking major support for CDAO in the context of a project to develop workflow systems. |
From: Arlin S. <sto...@um...> - 2010-01-08 17:32:52
|
Dear all-- Happy new year. Last month we decided to start holding a regular telecon on the second Monday of every month. Below are the details on the teleconference. date: Monday, January 8, 2009 time: 10:00 am Eastern (GMT -5) dial-in number (long-distance charges apply): 1-213-289-0500 participant access code: 375259 All developers and users (actual and potential) of CDAO are invited to participate. However, note that this involves a long-distance call that will be charged to your phone. I'll send out an agenda later. Probably we will review the accomplishments of 2009 (2 workshop projects and 2 demo projects used CDAO in a significant way) and discuss goals for 2010. For now, I just wanted to put everyone on notice, including those of you in France who are about to go home for the weekend. 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 |
From: Jim B. <ba...@ne...> - 2009-12-09 22:58:59
|
On Dec 9, 2009, at 5:50 PM, Hilmar Lapp wrote: > I understand that there's no direct way to get those triples out, that's OK. But using an appropriate ontology (CDAO?), I would want to be able to use a reasoner that infers from a phenotype being associated with a state that the taxon that has the state is then also, by some relationship, related with the phenotype. > > I understand that that's not what the XSLT is doing - rather it hard-codes that logic I suppose. But if we can use a reasoner and an ontology that declares the semantics of matrix, state, TU, and character, we would supposedly not need to hard-code that but simply run the reasoner to infer the taxon-phenotype relationship from the state-phenotype relationship. > > Am I off-track here? I think you could provide a relation chain via the ontology you're using which would let the reasoner make that direct link. >> We need a way to embed what the actual link between the taxon and the state/phenotype is (because now we have multiple options). > > I see. So the relationship between state and phenotype does now no longer unambiguously determine the inferable relationship between taxon and phenotype. Is that what you are saying? Yes, we currently provide a specific link between the phenotype and the state. But I think that link is the same regardless of which link we want to exist between the taxon and the phenotype. Also, for a given state and phenotype, we want to link different taxa to that using different relations. (For everyone who may have no idea of the context - we want to distinguish different intents when a phenotype is associated with a higher level taxon and meant to apply to all subtaxa, vs. another weaker association that doesn't down-propagate in that way). - Jim |
From: Hilmar L. <hl...@ne...> - 2009-12-09 22:51:05
|
On Dec 9, 2009, at 5:32 PM, Jim Balhoff wrote: > On Dec 9, 2009, at 4:31 AM, Rutger Vos wrote: > >>> In the meantime, can we stick the phenotype in NeXML as its own >>> "think" that gets an ID, and then relate it to the state *and* the >>> taxon using the ID and the applicable relationships? (I'm also >>> copying >>> the NeXML list here in case they can help with answering that.) >> >> States are defined per column (character) and are linked per cell to >> the applicable taxon, so this should be possible if the phenotype >> definition is an annotation of a state. > > I guess Hilmar is asking for pure RDFa way to end up with a triple > linking an OTU to a state. I don't think this is possible - it > requires some NeXML-aware application code, be it XSLT or a program, > that knows what the matrix is for. I understand that there's no direct way to get those triples out, that's OK. But using an appropriate ontology (CDAO?), I would want to be able to use a reasoner that infers from a phenotype being associated with a state that the taxon that has the state is then also, by some relationship, related with the phenotype. I understand that that's not what the XSLT is doing - rather it hard- codes that logic I suppose. But if we can use a reasoner and an ontology that declares the semantics of matrix, state, TU, and character, we would supposedly not need to hard-code that but simply run the reasoner to infer the taxon-phenotype relationship from the state-phenotype relationship. Am I off-track here? > > We need a way to embed what the actual link between the taxon and > the state/phenotype is (because now we have multiple options). I see. So the relationship between state and phenotype does now no longer unambiguously determine the inferable relationship between taxon and phenotype. Is that what you are saying? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Jim B. <ba...@ne...> - 2009-12-09 22:33:04
|
On Dec 9, 2009, at 4:31 AM, Rutger Vos wrote: >> In the meantime, can we stick the phenotype in NeXML as its own >> "think" that gets an ID, and then relate it to the state *and* the >> taxon using the ID and the applicable relationships? (I'm also copying >> the NeXML list here in case they can help with answering that.) > > States are defined per column (character) and are linked per cell to > the applicable taxon, so this should be possible if the phenotype > definition is an annotation of a state. I guess Hilmar is asking for pure RDFa way to end up with a triple linking an OTU to a state. I don't think this is possible - it requires some NeXML-aware application code, be it XSLT or a program, that knows what the matrix is for. We need a way to embed what the actual link between the taxon and the state/phenotype is (because now we have multiple options). I think we can do this by putting annotations in cells, and read them in our applications. However this still won't automatically provide the triples that Hilmar is looking for. - Jim |
From: Arlin S. <sto...@um...> - 2009-12-09 17:26:16
|
Dear all-- I've been threatening for a long time to tackle the issue of what sorts of things are trees, clades, OTUs and so on, and how do they relate to each other. The CDAO team has not yet worked out these issues. This is not an abstract exercise without implications. Its relevant for basic issues like, when a user asks for a "clade" in PhyloWS, do we return a subtree (on the grounds that a clade is a part of a tree), or a collection of nodes (on the grounds that a clade is a collection of TU things)? The VoCamp last month made these issues more poignant, and so on the train ride back from Montpellier to Paris, I scribbled many pages of notes, which I recently put on the wiki here: http://www.evoio.org/wiki/UpperOntology Feel free to edit this page. If you don't have edit permissions, sign up for an account at NESCent. This is a rough sketch. It does not get to the point of making specific recommendations in CDAO yet. However, its a start. As a next step, I'm inviting comments and discussion on this. If there is enough interest, we could have a teleconference about it. 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 |
From: Peter M. <pet...@gm...> - 2009-12-09 14:18:59
|
Resent to cdao-discuss from the registered email. peter Brandon and Rutger developed an XSLT script to convert Nexml to CDAO aware rdf, which we used at the Vocamp. The resulting rdf includes each cell in the matrix, specified by TU, Character, and State, so this should be possible, once we solve the previous problem with the XML literals in Phenex Nexml files. Peter On Dec 8, 2009, at 14:51, Hilmar Lapp wrote: > > On Dec 8, 2009, at 2:26 PM, Jim Balhoff wrote: > >> On Dec 8, 2009, at 2:14 PM, Hilmar Lapp wrote: >> >>> On Dec 8, 2009, at 2:00 PM, Jim Balhoff wrote: >>> >>>> The relationship is asserted via the matrix, so we have not >>>> specified the link anywhere so far. I suppose we could add >>>> metadata to each cell stating what relationship to use between the >>>> taxon and the state. >>> >>> So there must be a relationship according to spec, and in order to >>> meet RDFa compliance. To what is the phenotype related right now >>> (the state? character?), and using which relationship? Or is that >>> not how it works right now? >> >> The phenotype is related to the state via >> "phenoscape:describesPhenotype". In this way it is RDFa compliant, >> but there is no RDF triple which can be extracted relating the >> phenotype to any taxon. This must be created by a NeXML-aware >> application, as this is what the matrix is there for. > > Could a CDAO-aware application reason though that if taxonA hasState > state1 and state1 describes:Phenotype phenotypeA then taxonA exhibits > phenotypeA? > > If not, we should work on getting there. I'm copying the CDAO list > here as I know that they are very excited about the Phenoscape use- > cases for applying CDAO. > > In the meantime, can we stick the phenotype in NeXML as its own > "think" that gets an ID, and then relate it to the state *and* the > taxon using the ID and the applicable relationships? (I'm also copying > the NeXML list here in case they can help with answering that.) > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > _______________________________________________ > Nexml-discuss mailing list > Nex...@li... > https://lists.sourceforge.net/lists/listinfo/nexml-discuss |
From: Rutger V. <rut...@gm...> - 2009-12-09 09:32:01
|
> In the meantime, can we stick the phenotype in NeXML as its own > "think" that gets an ID, and then relate it to the state *and* the > taxon using the ID and the applicable relationships? (I'm also copying > the NeXML list here in case they can help with answering that.) States are defined per column (character) and are linked per cell to the applicable taxon, so this should be possible if the phenotype definition is an annotation of a state. -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
From: Arlin S. <sto...@um...> - 2009-12-08 23:47:48
|
I just wanted to remind everyone that its been a week since our teleconference where we agreed on some action items below. Does anyone have updates to share? I plan to finish my year-end report and distribute somem info on RSS feeds later this week. When our wiki is ready I will put it on the wiki. Arlin On Dec 1, 2009, at 4:29 PM, Arlin Stoltzfus wrote: > ---------- > Notes from CDAO telecon, 1 December, 2009 > > ==Overview and action items== > > The teleconference included Francisco, Enrico, and Arlin, and lasted > just over an hour. After going over the schedule for the next few > telecons, Arlin gave a review of results of the project in 2009. > Then we discussed possible goals for 2010. We ended by committing > to the following action items, to be completed before the next > telecon on Jan 11: > > * Enrico - can't commit to anything other than CREST proposal > (possible ToLWeb connection to discuss with Arlin) > * Francisco - investigate options to convert web site to wiki > (either on sourceforge or the NESCent-managed site at > evolutionaryontology.org) > * Francisco - get some more concrete information on the data- > annotation use-case for phylogenetics > * Arlin - finish a brief year-end report and distribute this > * Arlin - set up experimental RSS feed > * Arlin - find a volunteer (from among those not present) to collect > resources for a tutorial |
From: Peter E. M. <pet...@ya...> - 2009-12-08 20:24:06
|
Brandon and Rutger developed an XSLT script to convert Nexml to CDAO aware rdf, which we used at the Vocamp. The resulting rdf includes each cell in the matrix, specified by TU, Character, and State, so this should be possible, once we solve the previous problem with the XML literals in Phenex Nexml files. Peter On Dec 8, 2009, at 14:51, Hilmar Lapp wrote: > > On Dec 8, 2009, at 2:26 PM, Jim Balhoff wrote: > >> On Dec 8, 2009, at 2:14 PM, Hilmar Lapp wrote: >> >>> On Dec 8, 2009, at 2:00 PM, Jim Balhoff wrote: >>> >>>> The relationship is asserted via the matrix, so we have not >>>> specified the link anywhere so far. I suppose we could add >>>> metadata to each cell stating what relationship to use between the >>>> taxon and the state. >>> >>> So there must be a relationship according to spec, and in order to >>> meet RDFa compliance. To what is the phenotype related right now >>> (the state? character?), and using which relationship? Or is that >>> not how it works right now? >> >> The phenotype is related to the state via >> "phenoscape:describesPhenotype". In this way it is RDFa compliant, >> but there is no RDF triple which can be extracted relating the >> phenotype to any taxon. This must be created by a NeXML-aware >> application, as this is what the matrix is there for. > > Could a CDAO-aware application reason though that if taxonA hasState > state1 and state1 describes:Phenotype phenotypeA then taxonA exhibits > phenotypeA? > > If not, we should work on getting there. I'm copying the CDAO list > here as I know that they are very excited about the Phenoscape use- > cases for applying CDAO. > > In the meantime, can we stick the phenotype in NeXML as its own > "think" that gets an ID, and then relate it to the state *and* the > taxon using the ID and the applicable relationships? (I'm also copying > the NeXML list here in case they can help with answering that.) > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > _______________________________________________ > Nexml-discuss mailing list > Nex...@li... > https://lists.sourceforge.net/lists/listinfo/nexml-discuss |
From: Hilmar L. <hl...@ne...> - 2009-12-08 19:55:39
|
On Dec 8, 2009, at 2:26 PM, Jim Balhoff wrote: > On Dec 8, 2009, at 2:14 PM, Hilmar Lapp wrote: > >> On Dec 8, 2009, at 2:00 PM, Jim Balhoff wrote: >> >>> The relationship is asserted via the matrix, so we have not >>> specified the link anywhere so far. I suppose we could add >>> metadata to each cell stating what relationship to use between the >>> taxon and the state. >> >> So there must be a relationship according to spec, and in order to >> meet RDFa compliance. To what is the phenotype related right now >> (the state? character?), and using which relationship? Or is that >> not how it works right now? > > The phenotype is related to the state via > "phenoscape:describesPhenotype". In this way it is RDFa compliant, > but there is no RDF triple which can be extracted relating the > phenotype to any taxon. This must be created by a NeXML-aware > application, as this is what the matrix is there for. Could a CDAO-aware application reason though that if taxonA hasState state1 and state1 describes:Phenotype phenotypeA then taxonA exhibits phenotypeA? If not, we should work on getting there. I'm copying the CDAO list here as I know that they are very excited about the Phenoscape use- cases for applying CDAO. In the meantime, can we stick the phenotype in NeXML as its own "think" that gets an ID, and then relate it to the state *and* the taxon using the ID and the applicable relationships? (I'm also copying the NeXML list here in case they can help with answering that.) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Arlin S. <sto...@um...> - 2009-12-02 13:06:19
|
I'm sorry for not sending it out a day in advance as promised. I didn't realize that some people might be getting the emails in "daily digest" mode. Arlin On Dec 2, 2009, at 7:27 AM, Julie Thompson wrote: > I apologise for not being on the teleconference, but I didnt get the > connection info until today. > > Julie > ----- Original Message ----- > From: cda...@li... > Date: Wednesday, December 2, 2009 13:03 > Subject: CDAO-discuss Digest, Vol 4, 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. teleconference this afternoon (2:00 pm > > Eastern, GMT-5): > > connection info (Arlin Stoltzfus) > > 2. Re: teleconference this afternoon (2:00 pm > > Eastern, GMT-5): > > connection info (Arlin Stoltzfus) > > > > > > ----------------------------------------------------------------- > > ----- > > > > Message: 1 > > Date: Tue, 1 Dec 2009 10:50:51 -0500 > > From: Arlin Stoltzfus <sto...@um...> > > Subject: [CDAO-discuss] teleconference this afternoon (2:00 pm > > Eastern, GMT-5): connection info > > To: cda...@li... > > Message-ID: <474...@um...> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed; > delsp=yes > > > > Below are the details on the teleconference later today (sorry > > for not > > sending out this message yesterday as promised). > > Everyone involved > > in developing or using CDAO is invited to participate. > > Note that this > > is a long-distance call that will be charged to your phone. > > > > date: Tuesday, December 1, 2009 > > time: 2:00 pm Eastern (GMT -5) > > dial-in number (long-distance charges apply): 1-213-289-0500 > > participant access code: 375259 > > > > Agenda: > > > > 1. teleconferences (schedule for next few months; > > technology; > > accessibility) > > 2. what happened at the Phyloinformatics VoCamp > > 3. project goals for 2010 > > 4. (if time allows) consolidating and updating web sites > > > > Arlin > > > > On Dec 1, 2009, at 6:29 AM, Francisco Prosdocimi wrote: > > > > > De: Arlin Stoltzfus [mailto:sto...@um...] > > >> The results of the poll indicate high availability for > > Tuesday, Dec 1 > > >> at 2:00 pm Eastern US time. Please mark your > > calendars. Connection > > >> information will be sent out on Monday, the day before. > > > > > > Hello Arlin-- > > > > > > I didn't receive anything yesterday about the connection > > information > > > on our teleconference. > > > Might you please confirm that it is gonna happen today and > > inform > > > how to proceed with the connection. > > > > > > Thank 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: Arlin Stoltzfus [mailto:sto...@um...] > > > Enviada: qua 25/11/2009 05:24 > > > Para: cda...@li... > > > Assunto: Re: [CDAO-discuss] scheduling for next > > meeting;regular > > > monthly meetings > > > > > > On Nov 20, 2009, at 10:07 AM, Arlin Stoltzfus wrote: > > > > > >> 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 > > > > > > The results of the poll indicate high availability for > > Tuesday, Dec 1 > > > at 2:00 pm Eastern US time. Please mark your > > calendars. Connection > > > information will be sent out on Monday, the day before. > > > > > >> 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 > > > > > > Based on limited responses, I am going to suggest the 2nd > > Monday of > > > the month at 10:00 Eastern. Monday is a hard compromise > > between> Julie's & Enrico's schedule. Starting any earlier > > than 10:00 am > > > Eastern would be prohibitive for our friends on the left coast > > of the > > > US, and starting later is prohibitive for our friends in > > Europe. The > > > next monthly teleconferences then would be: > > > > > > Monday, Dec 14, 10:00 am (Eastern US) -- probably will cancel > > this one > > > Monday, Jan 11, 10:00 am (Eastern US) > > > Monday, Feb 8, 10:00 am (Eastern US) > > > Monday, Mar 8, 10:00 am (Eastern US) > > > > > > Please mark your calendars. > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 1 Dec 2009 16:29:05 -0500 > > From: Arlin Stoltzfus <sto...@um...> > > Subject: Re: [CDAO-discuss] teleconference this afternoon (2:00 pm > > Eastern, GMT-5): connection info > > To: cda...@li... > > Message-ID: <25D...@um...> > > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > > Dear all-- > > > > Below are the notes from the CDAO telecon that happened > > this > > afternoon. I'm writing these notes in MediaWiki syntax > > because we > > intend to use it in the future. > > > > I'm looking for someone who can start assembling resources for > > a > > tutorial. The tutorial might explain what it means to do > > "reasoning" > > or "inference" using ontologies, illustrated with concepts from > > CDAO. > > Any takers? > > > > Arlin > > > > ---------- > > Notes from CDAO telecon, 1 December, 2009 > > > > ==Overview and action items== > > > > The teleconference included Francisco, Enrico, and Arlin, and > > lasted > > just over an hour. After going over the schedule for the > > next few > > telecons, Arlin gave a review of results of the project in > > 2009. Then > > we discussed possible goals for 2010. We ended by > > committing to the > > following action items, to be completed before the next telecon > > on Jan > > 11: > > > > * Enrico - can't commit to anything other than CREST > > proposal > > (possible ToLWeb connection to discuss with Arlin) > > * Francisco - investigate options to convert web site to wiki > > (either > > on sourceforge or the NESCent-managed site at > > evolutionaryontology.org)* Francisco - get some more concrete > > information on the data- > > annotation use-case for phylogenetics > > * Arlin - finish a brief year-end report and distribute this > > * Arlin - set up experimental RSS feed > > * Arlin - find a volunteer (from among those not present) to > > collect > > resources for a tutorial > > > > ==Present== > > > > Francisco, Enrico and Arlin participated. Arlin > > facilitated the > > meeting and took notes. Enrico had to leave just before > > 3:00 pm. > > Arlin and Francisco stayed on until 3:15. > > > > > > ==Agenda items== > > > > === teleconferences === > > > > Regular telecons will be on the '''Second Monday''' of each > > month at > > '''10:00 am Eastern (GMT -5)'''. The next ones (given that > > we are > > canceling the one on Dec 14) are: > > * Monday, Jan 11, 10:00 am (Eastern US) > > * Monday, Feb 8, 10:00 am (Eastern US) > > * Monday, Mar 8, 10:00 am (Eastern US) > > > > === Project update === > > > > Overview of 2009 (Arlin) > > * changes to CDAO > > * community development > > * projects > > ** data interop hackathon > > ** Nexplorer3 > > ** VoCamp > > ** Triple store and portal (Enrico) > > > > Comment (Francisco). Colleagues have a use-case for > > annotation. > > Input data. Annotate clade & lineage, other things. > > > > === Discussion of goals for 2010 === > > > > We did not have enough people and time to complete this, but we > > got > > started. > > > > # Development and evaluation of CDAO content > > #* Higher-level relations of concepts, e.g., how does an OTU > > relate to > > a "tree" (Arlin) > > #* support for various annotations > > # Growing a community of active developers and users > > # Disseminating results and updates to broader community > > #* more consistent, up-to-date web site > > #* experiment with having an RSS feed > > # Projects and use-cases > > #* User interface for querying and annotation (Enrico) > > #* MIAPA (Francisco) > > # Funding prospects > > #* NIH proposal (Enrico, Arlin, Gopal) > > #* CREST proposal (Enrico) > > > > On Dec 1, 2009, at 10:50 AM, Arlin Stoltzfus wrote: > > > > > Below are the details on the teleconference later today (sorry > > for not > > > sending out this message yesterday as promised). > > Everyone involved > > > in developing or using CDAO is invited to participate. > > Note that this > > > is a long-distance call that will be charged to your phone. > > > > > > date: Tuesday, December 1, 2009 > > > time: 2:00 pm Eastern (GMT -5) > > > dial-in number (long-distance charges apply): 1-213-289-0500 > > > participant access code: 375259 > > > > > > Agenda: > > > > > > 1. teleconferences (schedule for next few months; technology; > > > accessibility) > > > 2. what happened at the Phyloinformatics VoCamp > > > 3. project goals for 2010 > > > 4. (if time allows) consolidating and updating web sites > > > > > > Arlin > > > > > > --------------------------------------------------------------- > > --------------- > > > Join us December 9, 2009 for the Red Hat Virtual Experience, > > > a free event focused on virtualization and cloud computing. > > > Attend in-depth sessions from your desk. Your couch. Anywhere. > > > http://p.sf.net/sfu/redhat-sfdev2dev > > > _______________________________________________ > > > CDAO-discuss mailing list > > > CDA...@li... > > > https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > > > > > > > > > ------------------------------ > > > > ----------------------------------------------------------------- > > ------------- > > Join us December 9, 2009 for the Red Hat Virtual Experience, > > a free event focused on virtualization and cloud computing. > > Attend in-depth sessions from your desk. Your couch. Anywhere. > > http://p.sf.net/sfu/redhat-sfdev2dev > > > > ------------------------------ > > > > _______________________________________________ > > CDAO-discuss mailing list > > CDA...@li... > > https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > > > > > End of CDAO-discuss Digest, Vol 4, 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 > ------------------------------------------------------------------------------ > Join us December 9, 2009 for the Red Hat Virtual Experience, > a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere. > http://p.sf.net/sfu/redhat-sfdev2dev_______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Julie T. <ju...@ig...> - 2009-12-02 12:33:37
|
I apologise for not being on the teleconference, but I didnt get the connection info until today.Julie----- Original Message -----From: cda...@li...Date: Wednesday, December 2, 2009 13:03Subject: CDAO-discuss Digest, Vol 4, 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. teleconference this afternoon (2:00 pm > Eastern, GMT-5):> connection info (Arlin Stoltzfus)> 2. Re: teleconference this afternoon (2:00 pm > Eastern, GMT-5):> connection info (Arlin Stoltzfus)> > > -----------------------------------------------------------------> -----> > Message: 1> Date: Tue, 1 Dec 2009 10:50:51 -0500> From: Arlin Stoltzfus <sto...@um...>> Subject: [CDAO-discuss] teleconference this afternoon (2:00 pm> Eastern, GMT-5): connection info> To: cda...@li...> Message-ID: <474...@um...>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes> > Below are the details on the teleconference later today (sorry > for not > sending out this message yesterday as promised). > Everyone involved > in developing or using CDAO is invited to participate. > Note that this > is a long-distance call that will be charged to your phone.> > date: Tuesday, December 1, 2009> time: 2:00 pm Eastern (GMT -5)> dial-in number (long-distance charges apply): 1-213-289-0500> participant access code: 375259> > Agenda:> > 1. teleconferences (schedule for next few months; > technology; > accessibility)> 2. what happened at the Phyloinformatics VoCamp> 3. project goals for 2010> 4. (if time allows) consolidating and updating web sites> > Arlin> > On Dec 1, 2009, at 6:29 AM, Francisco Prosdocimi wrote:> > > De: Arlin Stoltzfus [mailto:sto...@um...]> >> The results of the poll indicate high availability for > Tuesday, Dec 1> >> at 2:00 pm Eastern US time. Please mark your > calendars. Connection> >> information will be sent out on Monday, the day before.> >> > Hello Arlin--> >> > I didn't receive anything yesterday about the connection > information > > on our teleconference.> > Might you please confirm that it is gonna happen today and > inform > > how to proceed with the connection.> >> > Thank 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: Arlin Stoltzfus [mailto:sto...@um...]> > Enviada: qua 25/11/2009 05:24> > Para: cda...@li...> > Assunto: Re: [CDAO-discuss] scheduling for next > meeting;regular > > monthly meetings> >> > On Nov 20, 2009, at 10:07 AM, Arlin Stoltzfus wrote:> >> >> 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> >> > The results of the poll indicate high availability for > Tuesday, Dec 1> > at 2:00 pm Eastern US time. Please mark your > calendars. Connection> > information will be sent out on Monday, the day before.> >> >> 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> >> > Based on limited responses, I am going to suggest the 2nd > Monday of> > the month at 10:00 Eastern. Monday is a hard compromise > between> Julie's & Enrico's schedule. Starting any earlier > than 10:00 am> > Eastern would be prohibitive for our friends on the left coast > of the> > US, and starting later is prohibitive for our friends in > Europe. The> > next monthly teleconferences then would be:> >> > Monday, Dec 14, 10:00 am (Eastern US) -- probably will cancel > this one> > Monday, Jan 11, 10:00 am (Eastern US)> > Monday, Feb 8, 10:00 am (Eastern US)> > Monday, Mar 8, 10:00 am (Eastern US)> >> > Please mark your calendars.> >> > 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> >> >> >> >> >> >> > > > > ------------------------------> > Message: 2> Date: Tue, 1 Dec 2009 16:29:05 -0500> From: Arlin Stoltzfus <sto...@um...>> Subject: Re: [CDAO-discuss] teleconference this afternoon (2:00 pm> Eastern, GMT-5): connection info> To: cda...@li...> Message-ID: <25D...@um...>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes> > Dear all--> > Below are the notes from the CDAO telecon that happened > this > afternoon. I'm writing these notes in MediaWiki syntax > because we > intend to use it in the future.> > I'm looking for someone who can start assembling resources for > a > tutorial. The tutorial might explain what it means to do > "reasoning" > or "inference" using ontologies, illustrated with concepts from > CDAO. > Any takers?> > Arlin> > ----------> Notes from CDAO telecon, 1 December, 2009> > ==Overview and action items==> > The teleconference included Francisco, Enrico, and Arlin, and > lasted > just over an hour. After going over the schedule for the > next few > telecons, Arlin gave a review of results of the project in > 2009. Then > we discussed possible goals for 2010. We ended by > committing to the > following action items, to be completed before the next telecon > on Jan > 11:> > * Enrico - can't commit to anything other than CREST > proposal > (possible ToLWeb connection to discuss with Arlin)> * Francisco - investigate options to convert web site to wiki > (either > on sourceforge or the NESCent-managed site at > evolutionaryontology.org)* Francisco - get some more concrete > information on the data- > annotation use-case for phylogenetics> * Arlin - finish a brief year-end report and distribute this> * Arlin - set up experimental RSS feed> * Arlin - find a volunteer (from among those not present) to > collect > resources for a tutorial> > ==Present==> > Francisco, Enrico and Arlin participated. Arlin > facilitated the > meeting and took notes. Enrico had to leave just before > 3:00 pm. > Arlin and Francisco stayed on until 3:15.> > > ==Agenda items==> > === teleconferences ===> > Regular telecons will be on the '''Second Monday''' of each > month at > '''10:00 am Eastern (GMT -5)'''. The next ones (given that > we are > canceling the one on Dec 14) are:> * Monday, Jan 11, 10:00 am (Eastern US)> * Monday, Feb 8, 10:00 am (Eastern US)> * Monday, Mar 8, 10:00 am (Eastern US)> > === Project update ===> > Overview of 2009 (Arlin)> * changes to CDAO> * community development> * projects> ** data interop hackathon> ** Nexplorer3> ** VoCamp> ** Triple store and portal (Enrico)> > Comment (Francisco). Colleagues have a use-case for > annotation. > Input data. Annotate clade & lineage, other things.> > === Discussion of goals for 2010 ===> > We did not have enough people and time to complete this, but we > got > started.> > # Development and evaluation of CDAO content> #* Higher-level relations of concepts, e.g., how does an OTU > relate to > a "tree" (Arlin)> #* support for various annotations> # Growing a community of active developers and users> # Disseminating results and updates to broader community> #* more consistent, up-to-date web site> #* experiment with having an RSS feed> # Projects and use-cases> #* User interface for querying and annotation (Enrico)> #* MIAPA (Francisco)> # Funding prospects> #* NIH proposal (Enrico, Arlin, Gopal)> #* CREST proposal (Enrico)> > On Dec 1, 2009, at 10:50 AM, Arlin Stoltzfus wrote:> > > Below are the details on the teleconference later today (sorry > for not> > sending out this message yesterday as promised). > Everyone involved> > in developing or using CDAO is invited to participate. > Note that this> > is a long-distance call that will be charged to your phone.> >> > date: Tuesday, December 1, 2009> > time: 2:00 pm Eastern (GMT -5)> > dial-in number (long-distance charges apply): 1-213-289-0500> > participant access code: 375259> >> > Agenda:> >> > 1. teleconferences (schedule for next few months; technology;> > accessibility)> > 2. what happened at the Phyloinformatics VoCamp> > 3. project goals for 2010> > 4. (if time allows) consolidating and updating web sites> >> > Arlin> >> > ---------------------------------------------------------------> ---------------> > Join us December 9, 2009 for the Red Hat Virtual Experience,> > a free event focused on virtualization and cloud computing.> > Attend in-depth sessions from your desk. Your couch. Anywhere.> > http://p.sf.net/sfu/redhat-sfdev2dev> > _______________________________________________> > CDAO-discuss mailing list> > CDA...@li...> > https://lists.sourceforge.net/lists/listinfo/cdao-discuss> > > > > ------------------------------> > -----------------------------------------------------------------> -------------> Join us December 9, 2009 for the Red Hat Virtual Experience,> a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere.> http://p.sf.net/sfu/redhat-sfdev2dev> > ------------------------------> > _______________________________________________> CDAO-discuss mailing list> CDA...@li...> https://lists.sourceforge.net/lists/listinfo/cdao-discuss> > > End of CDAO-discuss Digest, Vol 4, 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 |
From: Arlin S. <sto...@um...> - 2009-12-01 21:29:25
|
Dear all-- Below are the notes from the CDAO telecon that happened this afternoon. I'm writing these notes in MediaWiki syntax because we intend to use it in the future. I'm looking for someone who can start assembling resources for a tutorial. The tutorial might explain what it means to do "reasoning" or "inference" using ontologies, illustrated with concepts from CDAO. Any takers? Arlin ---------- Notes from CDAO telecon, 1 December, 2009 ==Overview and action items== The teleconference included Francisco, Enrico, and Arlin, and lasted just over an hour. After going over the schedule for the next few telecons, Arlin gave a review of results of the project in 2009. Then we discussed possible goals for 2010. We ended by committing to the following action items, to be completed before the next telecon on Jan 11: * Enrico - can't commit to anything other than CREST proposal (possible ToLWeb connection to discuss with Arlin) * Francisco - investigate options to convert web site to wiki (either on sourceforge or the NESCent-managed site at evolutionaryontology.org) * Francisco - get some more concrete information on the data- annotation use-case for phylogenetics * Arlin - finish a brief year-end report and distribute this * Arlin - set up experimental RSS feed * Arlin - find a volunteer (from among those not present) to collect resources for a tutorial ==Present== Francisco, Enrico and Arlin participated. Arlin facilitated the meeting and took notes. Enrico had to leave just before 3:00 pm. Arlin and Francisco stayed on until 3:15. ==Agenda items== === teleconferences === Regular telecons will be on the '''Second Monday''' of each month at '''10:00 am Eastern (GMT -5)'''. The next ones (given that we are canceling the one on Dec 14) are: * Monday, Jan 11, 10:00 am (Eastern US) * Monday, Feb 8, 10:00 am (Eastern US) * Monday, Mar 8, 10:00 am (Eastern US) === Project update === Overview of 2009 (Arlin) * changes to CDAO * community development * projects ** data interop hackathon ** Nexplorer3 ** VoCamp ** Triple store and portal (Enrico) Comment (Francisco). Colleagues have a use-case for annotation. Input data. Annotate clade & lineage, other things. === Discussion of goals for 2010 === We did not have enough people and time to complete this, but we got started. # Development and evaluation of CDAO content #* Higher-level relations of concepts, e.g., how does an OTU relate to a "tree" (Arlin) #* support for various annotations # Growing a community of active developers and users # Disseminating results and updates to broader community #* more consistent, up-to-date web site #* experiment with having an RSS feed # Projects and use-cases #* User interface for querying and annotation (Enrico) #* MIAPA (Francisco) # Funding prospects #* NIH proposal (Enrico, Arlin, Gopal) #* CREST proposal (Enrico) On Dec 1, 2009, at 10:50 AM, Arlin Stoltzfus wrote: > Below are the details on the teleconference later today (sorry for not > sending out this message yesterday as promised). Everyone involved > in developing or using CDAO is invited to participate. Note that this > is a long-distance call that will be charged to your phone. > > date: Tuesday, December 1, 2009 > time: 2:00 pm Eastern (GMT -5) > dial-in number (long-distance charges apply): 1-213-289-0500 > participant access code: 375259 > > Agenda: > > 1. teleconferences (schedule for next few months; technology; > accessibility) > 2. what happened at the Phyloinformatics VoCamp > 3. project goals for 2010 > 4. (if time allows) consolidating and updating web sites > > Arlin > > ------------------------------------------------------------------------------ > Join us December 9, 2009 for the Red Hat Virtual Experience, > a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere. > http://p.sf.net/sfu/redhat-sfdev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Arlin S. <sto...@um...> - 2009-12-01 15:51:05
|
Below are the details on the teleconference later today (sorry for not sending out this message yesterday as promised). Everyone involved in developing or using CDAO is invited to participate. Note that this is a long-distance call that will be charged to your phone. date: Tuesday, December 1, 2009 time: 2:00 pm Eastern (GMT -5) dial-in number (long-distance charges apply): 1-213-289-0500 participant access code: 375259 Agenda: 1. teleconferences (schedule for next few months; technology; accessibility) 2. what happened at the Phyloinformatics VoCamp 3. project goals for 2010 4. (if time allows) consolidating and updating web sites Arlin On Dec 1, 2009, at 6:29 AM, Francisco Prosdocimi wrote: > De: Arlin Stoltzfus [mailto:sto...@um...] >> The results of the poll indicate high availability for Tuesday, Dec 1 >> at 2:00 pm Eastern US time. Please mark your calendars. Connection >> information will be sent out on Monday, the day before. > > Hello Arlin-- > > I didn't receive anything yesterday about the connection information > on our teleconference. > Might you please confirm that it is gonna happen today and inform > how to proceed with the connection. > > Thank 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: Arlin Stoltzfus [mailto:sto...@um...] > Enviada: qua 25/11/2009 05:24 > Para: cda...@li... > Assunto: Re: [CDAO-discuss] scheduling for next meeting;regular > monthly meetings > > On Nov 20, 2009, at 10:07 AM, Arlin Stoltzfus wrote: > >> 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 > > The results of the poll indicate high availability for Tuesday, Dec 1 > at 2:00 pm Eastern US time. Please mark your calendars. Connection > information will be sent out on Monday, the day before. > >> 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 > > Based on limited responses, I am going to suggest the 2nd Monday of > the month at 10:00 Eastern. Monday is a hard compromise between > Julie's & Enrico's schedule. Starting any earlier than 10:00 am > Eastern would be prohibitive for our friends on the left coast of the > US, and starting later is prohibitive for our friends in Europe. The > next monthly teleconferences then would be: > > Monday, Dec 14, 10:00 am (Eastern US) -- probably will cancel this one > Monday, Jan 11, 10:00 am (Eastern US) > Monday, Feb 8, 10:00 am (Eastern US) > Monday, Mar 8, 10:00 am (Eastern US) > > Please mark your calendars. > > 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 > > > > > > |
From: Julie D. T. <ju...@ig...> - 2009-12-01 06:53:43
|
Message from Julie Dawn Thompson: This article from BMC Bioinformatics (http://www.biomedcentral.com/home) might be interesting for us... The ontology of biological sequences Robert Hoehndorf, Janet Kelso, Heinrich Herre BMC Bioinformatics 2009 10:377 This article is published under open access, meaning that you can read the full text without a subscription: Abstract = http://www.biomedcentral.com/1471-2105/10/377/abstract Full Text = http://www.biomedcentral.com/1471-2105/10/377 PDF = http://www.biomedcentral.com/1471-2105/10/377/pdf BMC Bioinformatics is an open-access journal, publishing original, peer-reviewed research. Why not submit your next paper to BMC Bioinformatics - see http://www.biomedcentral.com/info/authors/ for more information. About BioMed Central BioMed Central is an independent online publishing house committed to providing immediate free access to the peer-reviewed biological and medical research it publishes. This commitment is based on the view that open access to research is essential to the rapid and efficient communication of science. In addition to open-access original research, BioMed Central also publishes reviews and other subscription-based content. Register with BioMed Central and receive regular email updates http://www.biomedcentral.com/registration/ Submit your own article to a BioMed Central journal http://www.biomedcentral.com/info/authors |
From: Arlin S. <sto...@um...> - 2009-11-25 17:24:37
|
On Nov 20, 2009, at 10:07 AM, Arlin Stoltzfus wrote: > 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 The results of the poll indicate high availability for Tuesday, Dec 1 at 2:00 pm Eastern US time. Please mark your calendars. Connection information will be sent out on Monday, the day before. > 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 Based on limited responses, I am going to suggest the 2nd Monday of the month at 10:00 Eastern. Monday is a hard compromise between Julie's & Enrico's schedule. Starting any earlier than 10:00 am Eastern would be prohibitive for our friends on the left coast of the US, and starting later is prohibitive for our friends in Europe. The next monthly teleconferences then would be: Monday, Dec 14, 10:00 am (Eastern US) -- probably will cancel this one Monday, Jan 11, 10:00 am (Eastern US) Monday, Feb 8, 10:00 am (Eastern US) Monday, Mar 8, 10:00 am (Eastern US) Please mark your calendars. 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 |
From: Enrico P. <epo...@cs...> - 2009-11-22 18:02:37
|
* best of the week : M = F > W > Th= Tu * best week 1=2=3 (i'll be out of touch after the 17th * best time Eastern US: 9:00 > 10:00 > 12:00 (some of these times are impossible for certain days) Enrico On Nov 22, 2009, at 8:19 AM, Julie Thompson wrote: > For the monthly meetings, my preferences are: > > * best day of the week: W=Th>M>F>T > > * best week of the month: 1=2=3=4 > > * best time of the day (Eastern US): 8:00>10:00>14.00>12:00 > > Julie > > ----- Original Message ----- > From: cda...@li... > Date: Saturday, November 21, 2009 13:04 > Subject: CDAO-discuss Digest, Vol 3, Issue 3 > 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. scheduling for next meeting; regular monthly meetings > > (Arlin Stoltzfus) > > 2. RES: scheduling for next meeting; regular > > monthly meetings > > (Francisco Prosdocimi) > > > > > > ----------------------------------------------------------------- > > ----- > > > > Message: 1 > > Date: Fri, 20 Nov 2009 10:07:21 -0500 > > From: Arlin Stoltzfus <sto...@um...> > > Subject: [CDAO-discuss] scheduling for next meeting; regular monthly > > meetings > > To: cda...@li... > > Message-ID: <A35...@um...> > > Content-Type: text/plain; charset="us-ascii" > > > > 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 > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 20 Nov 2009 14:35:10 -0300 > > From: "Francisco Prosdocimi" <fra...@uc...> > > Subject: [CDAO-discuss] RES: scheduling for next > > meeting; regular monthly meetings > > To: "Arlin Stoltzfus" <sto...@um...>, > > <cda...@li...> > > Message-ID: <0C9...@su...> > > Content-Type: text/plain; charset="iso-8859-1" > > > > 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 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 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 > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > ----------------------------------------------------------------- > > ------------- > > Let Crystal Reports handle the reporting - Free Crystal Reports > > 2008 30-Day > > trial. Simplify your report design, integration and deployment - > > and focus on > > what you do best, core application coding. Discover what's new with > > Crystal Reports now. http://p.sf.net/sfu/bobj-july > > > > ------------------------------ > > > > _______________________________________________ > > CDAO-discuss mailing list > > CDA...@li... > > https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > > > > > End of CDAO-discuss Digest, Vol 3, Issue 3 > > ****************************************** > > 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 > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july_______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Julie T. <ju...@ig...> - 2009-11-22 15:19:34
|
For the monthly meetings, my preferences are:* best day of the week: W=Th>M>F>T* best week of the month: 1=2=3=4* best time of the day (Eastern US): 8:00>10:00>14.00>12:00Julie----- Original Message -----From: cda...@li...Date: Saturday, November 21, 2009 13:04Subject: CDAO-discuss Digest, Vol 3, Issue 3To: 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. scheduling for next meeting; regular monthly meetings> (Arlin Stoltzfus)> 2. RES: scheduling for next meeting; regular > monthly meetings> (Francisco Prosdocimi)> > > -----------------------------------------------------------------> -----> > Message: 1> Date: Fri, 20 Nov 2009 10:07:21 -0500> From: Arlin Stoltzfus <sto...@um...>> Subject: [CDAO-discuss] scheduling for next meeting; regular monthly> meetings> To: cda...@li...> Message-ID: <A35...@um...>> Content-Type: text/plain; charset="us-ascii"> > 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> > > > > > -------------- next part --------------> An HTML attachment was scrubbed...> > ------------------------------> > Message: 2> Date: Fri, 20 Nov 2009 14:35:10 -0300> From: "Francisco Prosdocimi" <fra...@uc...>> Subject: [CDAO-discuss] RES: scheduling for next > meeting; regular monthly meetings> To: "Arlin Stoltzfus" <sto...@um...>,> <cda...@li...>> Message-ID: <0C9...@su...>> Content-Type: text/plain; charset="iso-8859-1"> > 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 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 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> > > > > > > > > > ------------------------------> > -----------------------------------------------------------------> -------------> Let Crystal Reports handle the reporting - Free Crystal Reports > 2008 30-Day > trial. Simplify your report design, integration and deployment - > and focus on > what you do best, core application coding. Discover what's new with> Crystal Reports now. http://p.sf.net/sfu/bobj-july> > ------------------------------> > _______________________________________________> CDAO-discuss mailing list> CDA...@li...> https://lists.sourceforge.net/lists/listinfo/cdao-discuss> > > End of CDAO-discuss Digest, Vol 3, Issue 3> ******************************************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 |
From: Vision, T. (Biology) <tj...@bi...> - 2009-11-21 14:17:01
|
Folks, You might want to give EVO a try for your teleconferences. It is free to use, is extremely tunable and powerful (can be used for video, data, etc), and seems to be working quite robustly for the phyloseminar group: http://phyloseminar.org/connect.html Plus, can't beat the name. Cheers, Todd On 11/21/09 7:04 AM, "cda...@li..." <cda...@li...> wrote: > 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. scheduling for next meeting; regular monthly meetings > (Arlin Stoltzfus) > 2. RES: scheduling for next meeting; regular monthly meetings > (Francisco Prosdocimi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Nov 2009 10:07:21 -0500 > From: Arlin Stoltzfus <sto...@um...> > Subject: [CDAO-discuss] scheduling for next meeting; regular monthly > meetings > To: cda...@li... > Message-ID: <A35...@um...> > Content-Type: text/plain; charset="us-ascii" > > 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 > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Fri, 20 Nov 2009 14:35:10 -0300 > From: "Francisco Prosdocimi" <fra...@uc...> > Subject: [CDAO-discuss] RES: scheduling for next meeting; regular > monthly meetings > To: "Arlin Stoltzfus" <sto...@um...>, > <cda...@li...> > Message-ID: <0C9...@su...> > Content-Type: text/plain; charset="iso-8859-1" > > 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! |