Planning the Asilomar meeting.
Jason Stajich
I started a file to suggest potential tools and topics that could be
discussed in the google docs shared folder - the link you got via the
mailing list *should* work even if you don't have a google account but
you may not be able to edit it without a google account - email me if
you cannot access.
I emailed Linda and Steve about options for a lunchtime or pre-meeting
workshop for the fungal genome tools session at Fungal Genetics 2011.
One option is doing a session during a lunchtime.
Advantages: No extra scheduling of travel, most people should be able to
attend, no extra cost;
Disadvantages: 1 - 1.5 hrs is short time to discuss the topic at hand.
Another option is to have a pre-conference workshop the day before.
Advantages: Will have plenty of time to cover the topics;
Disadvantages: incurs a cost and requires some additional scheduling and
for attendees to come early, less people will likely be able to attend;
may conflict with other pre-meetings.
I know Igor had discussed some ideas about scheduling a session on
current/in-progress genomes so I could see an advantage of tying these
two together if we have a large enough group of people willing to
attend, present, and discuss to make this worthwhile.
The pre-meetings have the advantage that we aren't exhausted yet too.
[From Linda & Steve]
*Regarding a lunch-time meeting on Fungal Genome Tools - We don't see
any problem other than scheduling to avoid conflict for most attendees
with other lunch sessions. Alternatively, if you did want a pre-meeting
session, you will have to pay for it. If that is what you want please
contact Kathy Borkovich and Marc Orbach (Marc especially). For the
lunch session alternative, we have time before we need numbers. You
would need the right sized venue and the box lunches.
*Please let me know if you have strong feelings either way so I can
explore options.*
*-jason*
*
--
Jason E. Stajich, PhD
Assistant Professor
Department of Plant Pathology & Microbiology
University of California
Riverside, CA 92521
jason....@ucr.edu
office: 951.827.2363
http://lab.stajich.org http://twitter.com/stajichlab
http://fungalgenomes.org/blog
http://plantpathology.ucr.edu http://genomics.ucr.edu http://cepceb.ucr.edu
lijun ma
Thank you for including me in this interesting section. Obviously you have put quite bit thoughts into this workshop already, and I would be more than happy to contribute anything in my capacity. Yes, I can access the files, however it doesn't allow me to edit as I tried. It could be an issue with my computer, I will poke around a bit more.
One quick question: will this workshop target special audience group, or mainly for our own interest?
Regarding the time of the section, I may prefer it to be a lunchtime section. Simply because we have scheduled a pre-meeting workshop for Fusarium. But if most people prefer have it as a pre-meeting event, I will try to work out the schedule to attend part of both.
Best regards,
Li-Jun
Lijun Ma
73 Asbury Street
Lexington MA 02421
Phone: 781 274 7491
Gavin Sherlock
Either of these options works for me, as obviously I'm local. However, I think it unlikely that you'll get that many people traveling a day early to come to this. Much as they want to attend, I'm not sure they'll give up a whole day for it, while I'm certain they'd give up a lunchtime. Is it possible to have the morning session end a little early, and the afternoon start a little late, so this could be somewhat extended? To be honest, I don't think we want it too long either. While I'm sure we've all got something interesting to say, you start to zone out when the umpteenth tool/database shows up. I would suggest 10, or possibly even 5 minutes per presenter (and unfortunately, Asilomar has no reliable internet for demos), so people are forced to be to the point, rather than droning on.
Cheers,
Gavin
Jason Stajich
I tried changing the setting for the document so it is viewable and
editable to the world at this point since I can't reliably expect
everyone to have a google account.
In terms of the target of the audience, I was imaging this to be mainly
focused on developers of tools to get together and discuss our projects,
think about ways that data can be shared more effectively, and linked
together, and establish something of a community around data
developers. I am fully happy for lots of things to happen by email list
but I think that it is helpful for the project managers and developers
to get together and discuss directions the tools and data are going.
My hope is this avoid a reinvention of new file formats, data standards,
etc from each community and also can encourage some interconnection
between projects.
I think the lunchtime is going to be the plan unless someone makes a
strong case for the other option.
-jason
lijun ma wrote, On 10/25/10 1:30 PM:
> jason....@ucr.edu <mailto:jason....@ucr.edu>
Jason Stajich
I agree with you -- I think a whole day can be overkill nor do I expect
we will have folks to traveling a day early for this. Not to mention
Li-Jun's reminder of the overlap with the Fusarium and likely other
working groups.
My plan is for there to be a mix of short presentations but also
discussion on how to share ideas, tools, data (and formats) and
eventually work towards some best practices for presenting and sharing
raw data as a community. It feels a bit like everyone is doing their own
thing, which is great, but I wanted to try and build some community
around the data and tools as part of this session.
I'm hoping what can come out of this is also a better understanding of
what groups are working on and also to build up a resource of web links
and eventually ways to interconnect databases and tools to take
advantages of the strengths of different community projects. I also
think there are some common problems we are all solving:
- ortholog calling
- synteny
- SNP identification
- queries across multiple gene expression experiments
- queries that integrate across ChIP,RNA-Seq, experiments
I know that currently this email list is more at the PI/project manager
level not the main developers of the databases and tools, but I think it
would be great if we can start some conversations and see if it brings
the community together more.
There is very little flexibility in the FGC schedule to start or end the
regular conference slots at different times since this is a jam-packed
mtg so I dare not ask for that from the organizers.
As lunch will be provided in the meeting room, I expect we will just
do our best to gather very soon after the morning session ends.
We could try Pecha-Kucha as another way to keep things fast:
http://www.npr.org/templates/story/story.php?storyId=130698873
I also don't need to be the only force for what topics are discussed so
I welcome other directions or thoughts on audience, topics, format.
-jason
Gavin Sherlock wrote, On 10/26/10 5:30 PM:
> Hi Jason,
>
> Either of these options works for me, as obviously I'm local. However, I think it unlikely that you'll get that many people traveling a day early to come to this. Much as they want to attend, I'm not sure they'll give up a whole day for it, while I'm certain they'd give up a lunchtime. Is it possible to have the morning session end a little early, and the afternoon start a little late, so this could be somewhat extended? To be honest, I don't think we want it too long either. While I'm sure we've all got something interesting to say, you start to zone out when the umpteenth tool/database shows up. I would suggest 10, or possibly even 5 minutes per presenter (and unfortunately, Asilomar has no reliable internet for demos), so people are forced to be to the point, rather than droning on.
>
> Cheers,
> Gavin
>
> On Oct 25, 2010, at 11:28 AM, Jason Stajich wrote:
>
>> Dear fungal genome tools enthusiasts -
>>
>> I started a file to suggest potential tools and topics that could be discussed in the google docs shared folder - the link you got via the mailing list *should* work even if you don't have a google account but you may not be able to edit it without a google account - email me if you cannot access.
>>
>> I emailed Linda and Steve about options for a lunchtime or pre-meeting workshop for the fungal genome tools session at Fungal Genetics 2011.
>>
>> One option is doing a session during a lunchtime.
>> Advantages: No extra scheduling of travel, most people should be able to attend, no extra cost;
>> Disadvantages: 1 - 1.5 hrs is short time to discuss the topic at hand.
>>
>> Another option is to have a pre-conference workshop the day before.
>> Advantages: Will have plenty of time to cover the topics;
>> Disadvantages: incurs a cost and requires some additional scheduling and for attendees to come early, less people will likely be able to attend; may conflict with other pre-meetings.
>>
>> I know Igor had discussed some ideas about scheduling a session on current/in-progress genomes so I could see an advantage of tying these two together if we have a large enough group of people willing to attend, present, and discuss to make this worthwhile.
>>
>> The pre-meetings have the advantage that we aren't exhausted yet too.
>>
>> [From Linda& Steve]
>> *Regarding a lunch-time meeting on Fungal Genome Tools - We don't see any problem other than scheduling to avoid conflict for most attendees with other lunch sessions. Alternatively, if you did want a pre-meeting session, you will have to pay for it. If that is what you want please contact Kathy Borkovich and Marc Orbach (Marc especially). For the lunch session alternative, we have time before we need numbers. You would need the right sized venue and the box lunches.
>>
>> *Please let me know if you have strong feelings either way so I can explore options.*
>>
>> *-jason*
>> *
>> --
>> Jason E. Stajich, PhD
>> Assistant Professor
>> Department of Plant Pathology& Microbiology
fred.d...@duke.edu
I suspect a lunch meeting will be better attended than a pre-meeting.
I think that very short presentation (such as 5 minutes) is probably
best so that people can say "here is the main point, for details there
will be a live demonstration and discussion at the poster session"
Best wishes
Fred
Dawn Anne Thompson
I agree that we are all facing the common problems you listed ( I'm
sure there are others like technical advances for the experimental
work ) and have people working to solve them. I also agree that we
would all benefit greatly from sharing of tools and resources instead
of all reinventing the wheel.
I like the idea of the Pecha-Kucha very much.
Best,
Dawn
Dawn Thompson
Research Scientist -Regev Group
Broad Institute of MIT and Harvard
7 Cambridge Center (NE30-6035)
Cambridge, MA 02142
Ph: 617-714-7763
email: da...@broadinstitute.org
Joey Spatafora
I am fine with either format. I will go through the material on the site and get back to you soon.
Cheers,
Joey
On Oct 27, 2010, at 9:27 AM, Dawn Anne Thompson wrote:
> Hi Jason,
>
> I agree that we are all facing the common problems you listed ( I'm sure there are others like technical advances for the experimental work ) and have people working to solve them. I also agree that we would all benefit greatly from sharing of tools and resources instead of all reinventing the wheel.
>
>
> I like the idea of the Pecha-Kucha very much.
>
>
>
> Best,
>
> Dawn
>
>
>
>
> On Oct 26, 2010, at 8:54 PM, Jason Stajich wrote:
>
>> Hi Gavin -
>>
>> I agree with you -- I think a whole day can be overkill nor do I expect we will have folks to traveling a day early for this. Not to mention Li-Jun's reminder of the overlap with the Fusarium and likely other working groups.
>>
>> My plan is for there to be a mix of short presentations but also discussion on how to share ideas, tools, data (and formats) and eventually work towards some best practices for presenting and sharing raw data as a community. It feels a bit like everyone is doing their own thing, which is great, but I wanted to try and build some community around the data and tools as part of this session.
>>
>> I'm hoping what can come out of this is also a better understanding of what groups are working on and also to build up a resource of web links and eventually ways to interconnect databases and tools to take advantages of the strengths of different community projects. I also think there are some common problems we are all solving:
>> - ortholog calling
>> - synteny
>> - SNP identification
>> - queries across multiple gene expression experiments
>> - queries that integrate across ChIP,RNA-Seq, experiments
>>
>> I know that currently this email list is more at the PI/project manager level not the main developers of the databases and tools, but I think it would be great if we can start some conversations and see if it brings the community together more.
>>
>> There is very little flexibility in the FGC schedule to start or end the regular conference slots at different times since this is a jam-packed mtg so I dare not ask for that from the organizers.
>> As lunch will be provided in the meeting room, I expect we will just do our best to gather very soon after the morning session ends.
>>
>> We could try Pecha-Kucha as another way to keep things fast: http://www.npr.org/templates/story/story.php?storyId=130698873
>>
>>
>> I also don't need to be the only force for what topics are discussed so I welcome other directions or thoughts on audience, topics, format.
>>
>>
>> -jason
>>
>> Gavin Sherlock wrote, On 10/26/10 5:30 PM:
>>> Hi Jason,
>>>
>>> Either of these options works for me, as obviously I'm local. However, I think it unlikely that you'll get that many people traveling a day early to come to this. Much as they want to attend, I'm not sure they'll give up a whole day for it, while I'm certain they'd give up a lunchtime. Is it possible to have the morning session end a little early, and the afternoon start a little late, so this could be somewhat extended? To be honest, I don't think we want it too long either. While I'm sure we've all got something interesting to say, you start to zone out when the umpteenth tool/database shows up. I would suggest 10, or possibly even 5 minutes per presenter (and unfortunately, Asilomar has no reliable internet for demos), so people are forced to be to the point, rather than droning on.
>>>
>>> Cheers,
>>> Gavin
>>>
>>> On Oct 25, 2010, at 11:28 AM, Jason Stajich wrote:
>>>
>>>> Dear fungal genome tools enthusiasts -
>>>>
>>>> I started a file to suggest potential tools and topics that could be discussed in the google docs shared folder - the link you got via the mailing list *should* work even if you don't have a google account but you may not be able to edit it without a google account - email me if you cannot access.
>>>>
>>>> I emailed Linda and Steve about options for a lunchtime or pre-meeting workshop for the fungal genome tools session at Fungal Genetics 2011.
Joey Spatafora
Professor & Faculty Athletic Representative
2082 Cordley Hall
Dept. Botany and Plant Pathology
Oregon State University
Corvallis, OR 97331
Email: spat...@science.oregonstate.edu
Tel: 541-737-5304
Fax: 541-737-3573
lijun ma
The overall objective makes perfect sense. It will be an interesting section.
If we will have a lunch meeting instead of a pre-meeting event, maybe we could divide the discussions/presentations into two sections arranged around the start and the end of the conference respectively. For the earlier one, we can lay out what is out there and what is needed as a community. Then a follow up meeting will be called to collect the thoughts and reach some solutions.This way, we can get community inputs and have more time to think things through.
Just a thought,
Li-Jun
Joey Spatafora
Did you decide on a day for the lunch meeting. WE are working on an AFTOL lunch meeting and I do not want them to conflict.
Cheers,
Joey
Joey Spatafora
Jason Stajich
Based on the feedback and the logistics, yes - we plan to go with Lunch
meeting. I will have to get head counts closer to the meeting.
Igor is also tentatively planning a workshop on fungal genome sequencing
opportunities particularly on resources available from the JGI & the
CSP. Maybe other centers will also talk about how one proposes an
organism to get into their pipelines.
Be great if this can avoid conflicting, but I know how hard it will be
for all of these things to be worked in.
-jason
Joey Spatafora wrote, On 11/3/10 10:59 AM:
> Joey Spatafora
> Professor& Faculty Athletic Representative
> 2082 Cordley Hall
> Dept. Botany and Plant Pathology
> Oregon State University
> Corvallis, OR 97331
> Email: spat...@science.oregonstate.edu
> Tel: 541-737-5304
> Fax: 541-737-3573
>
>
>
--