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Home : MGED Board : Board Meetings : Fourth Board Meeting

Tues 9/24/02 MGED board meeting at MGED 5 in Tokyo

Board members attending:
1) Alvis Brazma
<brazma@ebi.ac.uk>
    (president)
2) Jason Goncalves
<jason.goncalves@iobion.com>
3) Helen Parkinson <parkinson@ebi.ac.uk>
4) Gavin Sherlock
<sherlock@genome.stanford.edu>
5) Paul Spellman
<spellman@bdgp.lbl.gov>         
    (treasurer)
6) Yoshio Tateno
<ytateno@genes.nig.ac.jp>
    (MGED 5 host & organizer)
7) Ronald Taylor
<Ronald.Taylor@UCHSC.edu>
    (secretary)

Board members absent:
1) Cathy Ball
<ball@genome.stanford.edu>
2) Helen Causton
<helen.causton@csc.mrc.ac.uk>
3) Terry Gaasterland
<gaasterl@cleo.rockefeller.edu>
                     - also:
tgbb@rockefeller.edu
4) Pascal Hingamp
<hingamp@ciml.univ-mrs.fr>
5) Barbara Jasny
<bjasny@aaas.org>
6) John Quackenbush
<johnq@tigr.org>
7) Martin Ringwald
<ringwald@informatics.jax.org>
8) Jason Stewart
<jason@openinformatics.com>
9) Chris Stoeckert
<stoeckrt@SNOWBALL.pcbi.upenn.edu>
10) Charles Troup
<charles_troup@agilent.com>

Guests:
1) Kenichi Matsubara
   chair of the local MGED 5 organizing committee
   Nara Institute of Science and Technology
  
matsubara@ns.dna-chip.co.jp
   (Dr. Matsubara and his colleagues initiated the so-called Body Mapping at almost the same time as Dr. Venter's ESTs.)
2) Kazuho Ikeo
   DDBJ-NIG          
kikeo@genes.nig.ac.jp
2) Yasushi Okazaki  
   RIKEN             
okazaki@gsc.riken.go.jp
   (Dr. Ikeo is leading a project constructing full-length cDNAs for mouse chromosomes 1 and 2)
3) Takashi Ito      
   Kanazawa U        
titolab@kenroku.kanazawa-u.ac.jp
   (Dr. Ito is conducting 2-hybrid system studies)
4) Takashi Gojobori  
   DDBJ-NIG, JBIRC   
tgojobor@genes.nig.ac.jp
5) Rob Andrews
   Sanger Institute  
rma@sangerac.uk
6) Kate Rice     
   Sanger Institute  
cmr@sanger.ac.uk
7) Jaak Vilo     
   EGeen, Inc        
jaak.vilo@egeeninc.com
8) Luis Cornide
   ALMA Bioinformatica 
lcornide@almabioinfo.com
9) Juan Carlos Oliveros
   ALMA Bioinformatica 
oliveros@almabioinfo.com
10) Tina Hernanadez-Boussard
    Stanford          
boussard@genome.stanford.edu
11) Samuel Granjeaud
    (representing MGED 6 and Pascal Hingamp)
    U of Aix-Marseille  
granjeau@erm206.univ-mrs.fr

Note: DDBJ-NIG is the DNA Data Bank of Japan at the National Institute of Genetics. The DDBJ will be a portal site for many Japanese major producers of gene expression data, thanks to the efforts of Dr. Matsubara.

Note: JBIC is the Japan Biological Informatics Consortium.

-----------------------------------------------------

Summary

12:38 PM

round-robin introduction of people attending

Alvis welcomed the guests and led a round of applause for our local MGED 5 organizers. He then formally opened the board meeting. We proceeded through the agenda sent out earlier by Alvis, item by item. These discussions are summarized below.


Meeting items:

--------
1) questions related to MGED 5

Yoshio briefly described the MGED 5 program. Board members who are giving talks or tutorials then gave very short summaries of what they hoped to say or get done. Dr. Gojobori introduced Dr. Kenichi Matsubara, the chair of the MGED 5 organizing committee, to the board. Dr. Matsubara gave the board an update on the status of the DDBJ as a public gene expression data repository: there are 40 - 50 major producer groups in Japan who have agreed to give the DDBJ gene expression data in the future.

--------
2) the MGED task list

Alvis: believes the content is good, but the writeup still needs work.

Alvis: we need the web site at EBI for short term goal (1). Fortunately, he can commit some staff time for next 2 years on that, funded from one of his grants.

There was a discussion of the MGED conference numbering system, and what is the purpose of the two types of meetings. To summarize: the annual AAAS/MGED meeting serves as a general functional genomics meeting and we are using it to advertise our goals. And it's big, which is what we want for that purpose. The annual (numbered) MGED meetings are smaller and the focus is on the sharing of gene expression data. There is only one numbered MGED meeting per year now, so actually the arrangement is simple. We are an integral part of the AAAS annual meeting once a year (non numbered; the next such meeting being held in Feb 2003 in Denver) and we have a smaller MGED meeting once a year (which is numbered; MGED 6 now being set for Sept 2003 in France). We will have a yearly cycle for true MGED meetings, aiming for a fall time frame each year. There will be MGED tutorials at both yearly meetings.


Paul: we need to contact the organizers of the important functional genomics meetings to arrange for MGED tutorials at their meetings. We need to come up with a list of who to contact for this. We need to find out which MGED board members can and will go to what meetings to give such tutorials. Some of the possible meetings are ISMB, TIGR, PSB, GSAC, Cold Spring Harbor Genome Sequencing meeting, Am Society for Human Genetics meeting, the HUGO meeting.

Alvis: asked Paul to put together a list of conferences we should contact in regard to giving tutorials.  He also asked Kate Rice to specifically help with the Cold Spring Harbor Genome Sequencing meeting, using her contacts there.

Board: agreed.

Alvis: we need to agree on a deadline as to when to send tutorial proposals to ISMB-03. We have three possibilities for tutorials: MAGE, normalization, and ontologies.  However, ontologies may not have enough material for a full tutorial.

Alvis: shall we agree to reach some conclusion by the end of October? That is, we will discuss and settle this at the next board meeting in October. Then those board members we agree will give the tutorials will quickly write the tutorial proposals to send to the ISMB-03 organizers.

Board: agreed.

Gavin asked if MGED will support travel for those board members giving tutorials at ISMB-03 in Brisbane? Alvis said yes, if we have the money.

Paul asked if MGED 7 in fall 2004 will be in Hinxton, England.  Alvis said that is not clear. We should revisit this at the board meeting at the Feb 03 AAAS/MGED conference.


Board: agreed.

There was a general discussion on how to handle feedback on the MIAME checklist, now that people will be using it for their journal submissions. Tina said that we need a web site location where people can submit commments on our checklist. Jason G asked what is the process to resolve issues if we get feedback on the MIAME checklist. Paul said that we may need an arrangement with each journal as to how to resolve disputes and complaints on the checklist. Jason G thought we need to review the checklist at a board meeting after we start getting feedback. Alvis said we can arrange a session specifically on that subject at MGED 6 in September 2003.

Gavin said that in regard to the work of the normalization and transformations working group, he has talked to John Q and Cathy and they have decided to modify the goals of the group. They want to develop quality metrics. Also, it is clear to him that people will not use what we do unless there is easily available documentation. So the working group needs to put out review articles and publications. The first thing to be done for quality metrics will be to find out what are the operating procedures people use.

Alvis: we need to finalize this set of short and long term task goals. He will put together the next draft, but we need a working group to finish this off. He proposed these members for the working group: Gavin, Paul, Helen, Jason G, and Alvis. Next draft to be ready by our board meeting in October.

Board: agreed.

Jason G said that the new working group can meet here at MGED 5, to get started. Agreed.

--------
3) the concept of an advisory board

Alvis started the discussion by saying that we need to discuss why we need such a board and what can we expect from it. He believes that an advisory board makes our organization more inclusive. Such an advisory board can be published on our MGED web site, and such a board allows feedback from people in the field, and allows us to more easily spread our ideas.

Paul asked whether we need a formal, specified advisory board. Perhaps we could instead have a flexible, changing set of advisors, who we ask for advice. The question of using memberships, giving memberships to people rather than putting them on an advisory board, was raised. But Alvis and Paul agreed that would be complicated due to voting issues. Jason G asked if the aim of an advisory board is to show legitimacy and support, or to get advice.

Alvis's answer: both.

Paul noted that the working groups are open. If you join and are hard-working, we can elect you to the board of directors at the next annual election. We can pick the people to add who are actually doing something to help.

Alvis: we already have 17 board members. However, we can add more members. Kate Rice could be added, and he can already think of several others. Yoshio said that he would like to nominate Prof Kousaku Okubo of Kyushu University as an MGED board member. Paul reminded us that we cannot vote on anything today. The annual election is in May 2003 (though we can change the bylaws to alter that, if needed).

Alvis: we can expand the MGED board at the next election. Can we decide on using working groups and board recommendations on making the board more inclusive? Let's agree that we will revisit the question before the next board election in May. If the number of people we want to add to the board is far larger than 25, then we will revisit the question of adding an advisory board. We will try to come up a list of prospective members for an expanded board by the board meeting at the Feb 2003 AAAS/MGED meeting.

Board: agreed.

Jaak asked what is the definition of being part of a working group. Is there a formal list?

Paul and Gavin: there are no formal lists.

Alvis: we can send an email to each of the working group lists, asking if each recipient wants to be listed as a formal member of that working group on our web site.

Board: agreed.

4) finances

Alvis: noting that we were running low on time, he asked that Paul, as our treasurer, give a  5 minute report on our finances.

Paul: Ron and I had a conference call. That was the first official finance working group meeting. We came up with a budget that assumes raising 120K a year. We believe that should be enough money to cover our budget. The finance committee members present (Ron, Helen, and I) and anyone else who wants to come will meet at lunch tomorrow (Wednesday Sept 25th), here, to further discuss financial issues, such as approaching sponsors.

In response to questions from an observer, Alvis said that we should have a focused session/track on public repository databases in Denver in Feb 2003. We can have a half-day session on how to exchange data and what is going on the public repository databases. Attendees can be one or several people from the three public repositories (DDJB, GEO, ArrayExpress) and Stanford. Also, Paul or Jason S. can attend as MAGE reps.

5) Sept 2003 MGED 6 meeting

Samuel (for Pascal Hingamp): re MGED 6 in France, how many people should Pascal plan for? Paul: 300-400 people. Yoshio: on Friday Sept 27th we can discuss that and other MGED 6 questions at the closing MGED 5 post-session.


Meeting closed by Alvis at 2:49PM.
 

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