[Neurobureau-hubs] next large group call

[joshua vogelstein]

here's what i would love to do:

lowering the bar for contributing to neuroscience, in general.
nothing here is brilliant, but all pretty easily doable, given some time:
(based on what i'm doing for the EM data)

create an API for uploading data,
to a server with effectively unlimited space
perhaps automatically "process" the data
to obtain a variety of "data derivatives" (times-series, correlation
matrices, etc)
make all the raw data and derivatives easily available
as well as the scripts we wrote to process the data
and an API for uploading new data derivatives
(so people can compute, for instance, new graph metrics, etc.)

that is just the beginning
is anybody familiar with the polymath projects?
http://michaelnielsen.org/polymath1/index.php?title=Main_Page

the basic idea has been that somebody (a "big name person") announces a
problem
(eg, classifying connectomes)
and then the community is all welcome to contribute to solving the problem
together
there is a blog to discuss things, and a wiki page to keep the good ideas,
the barrier to entry is literally access to the internet
anybody can contribute comments, without even needing to login
eventually, a quorum of knowledge is reached,
the community decides to draft a manuscript
whenever it reaches a stable state
and then they submit it
interestingly, authorship has not been an issue for these projects
there is a nice self-selection bias:
people who invest effort already are supportive of the idea,
so they don't sweat the authorship details

one of my favorite parts of this,
is that one of the co-authors can be "the neuro bureau"

the service that such a project provides to the community is obvious
besides a bunch of data
all the code and analysis is made available to the community
as well as the results

FCP and ADHD-200 are amazing starts to this
now is the opportunity to take it to the next step
make the analysis open and the results open
invite everyone to join with open arms
and do some awesome science together

so anyway, this is what i want to do
at the open connectome project <http://www.openconnectomeproject.org/>, it
is already what we are doing with EM connetomes
we are very interested in doing this for MR connectomes as well
in fact, we are already starting to do that,
i would love for the neuro bureau to be as much a part of this as possible
i would love to hear what you guys think about this
obviously, some of you have already done a bunch of work required for this
to happen
i'm actively working on some of it
it is the most fun and exciting project i can think of being a part of
and doing it together with a bunch of people i love only makes it
better.....

cheers,
joshua



--
If it makes you feel better, please remember to consider humanity before
doing stuff. Otherwise, please just have a nice day.
openconnectomeproject.org




On Sat, Jul 9, 2011 at 11:57 PM, Michael Milham <milham01 at gmail.com> wrote:

> Folks,
>
> Sitting in back of car stuck in traffic...so figured I'd give my standard 2
> cents sideline view commentary. When thinking through what to do with an
> organization to make it meaningful, it is important to identify what are the
> unaddressed needs of the community and what are the services you can
> provide. I think it is important that folks think through how you want to
> position the neurobureau in the community that will make it both unique and
> effective (I.e., capable of taking ideas and making them reality) for the
> community.
>
> With respect to grants, do not underestimate the environment we are heading
> into at the NIH...Tom Insel has been very open about the reality of the
> times for NIMH and the challenges ahead for funding...same true for the
> other institutes. Review will be harder than ever and more competitive.
> Foundations and philanthropy will be very important. And so will tempering
> expectations, and increasing distribution of work...when you see efforts
> like the 1000 functional connectomes project, INDI and ADHD-200...those were
> all done without dedicated funding...they are worth it, but do take a toll
> on those executing them (Maarten will readily testify to this, as I am sure
> Cameron will in his more recent efforts). One hopes their efforts can obtain
> funding over time as they become established enough...but that is over time.
> So, my point is efforts up front will likely be the product of folks working
> overtime or gaining philanthropic support. Would set goals for neurobureau
> to ensure feasibility.
>
> Hope that makes sense.
>
> With respect to openness...my limited view of the situation is that it may
> feel closed in that folks see pins and branding all over the place...but not
> much saying "email us here to become a member"...keeps people who do not
> know the inner circle looking from the outside...don't think that is
> intentional...and my view can be off.
>
> Traffic has lightened...so, I will sign off on that note.
>
> Sent from my iPhone
>
> On Jul 9, 2011, at 11:32 PM, Pierre Bellec <pierre.bellec at criugm.qc.ca>
> wrote:
>
> @Donald
>
> Yes, yes, yes !!! I love the idea of a workshop where people would try to
> create something, rather than listen to talks. We had actually started
> discussing something along those lines. One other idea was to have half
> participants "senior" (should know what they're doing) and the other half
> wanting to learn on a technique/set of techniques. We would pair seniors and
> juniors based on interests. So it would also be an educational workshop.
> Another idea would be to have a number of artists joining to work on one or
> several pieces around the theme of the workshop, in interaction with the
> scientists. In the case of Nathalie for example, there could even be some
> imaging experiments going on as part of the workshop. Finally, I believe
> there should be pre-workshop meetings on the web to discuss the work before
> the event. 3, 4 or even 5 days are too short to achieve something if it's
> not carefuly planned.
>
> Cheers,
>
> Pierre Bellec, PhD
> Chercheur adjoint
> Département d'informatique et de recherche opérationnelle
> Centre de recherche de l'institut de Gériatrie de Montréal
> 4565, Chemin Queen-Mary
> Montréal (Québec)
> H3W 1W5
> Université de Montréal
> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
> (001)(514) 340 3540 #3367
>
>
>
>
> 2011/7/9 MCLAREN, Donald < <mclaren.donald at gmail.com>
> mclaren.donald at gmail.com>
>
>> I'm stealing this idea from the Advanced Psychometrics Workshop (its
>> partially funded by the NIH).
>>
>> Each year, we should pick a place -- somewhere unique -- and hold a
>> small workshop. I'm thinking 30 people maximum where they would apply
>> and we'd choose the people. At the workshop, there would be some talks
>> and then we'd divide into 3-4 workgroups and analyze a dataset. From
>> this one or more papers could be produced from each group.
>>
>> I should also point out, that all the papers could form a special
>> issue (e.g. Brain and Behavior is having a special issue just on the
>> papers from the Advanced Psychometrics Workshop this year).
>>
>> After a year or two, we could probably get some NIH funding. This
>> would be a good starting point for building a research focused
>> organization. I also think that once we get going, then it would be
>> easiest to be driven by corporate money. I think there will be a lot
>> of resistance from institutions in the US from letting faculty apply
>> for grants through the NB. To much lost revenue from the indirect
>> costs.
>>
>> Now, if its truly a research institution, with its own facility,
>> that's another story. However, I think that is probably a number of
>> years away.
>>
>> At least that is how it seems.
>>
>> Best Regards, Donald McLaren
>> =================
>> D.G. McLaren, Ph.D.
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Research Fellow, Department of Neurology, Massachusetts General Hospital
>> and
>> Harvard Medical School
>> Office: (773) 406-2464
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>>
>> On Sat, Jul 9, 2011 at 10:56 PM, Pierre Bellec
>> < <pierre.bellec at criugm.qc.ca>pierre.bellec at criugm.qc.ca> wrote:
>> > This conversation is starting to have an interesting spin. The debate
>> has
>> > started !
>> > Here is a couple of comments, and a summary of what I'd like the
>> neurobureau
>> > to be in the future.
>> >   * The neurobureau really is who we are. What excites me about the
>> > neurobureau is to engage with people such as Daniel, Cameron, Alex,
>> Clare,
>> > Oliver, Catie, Heather, Nathalie, to name a few who I had wonderful
>> > discussions with over the past couple of weeks (sorry for those I
>> forgot).
>> > The roots of it is a mixture of science and social. Great principles
>> don't
>> > matter too much at the end of the day. I totally agree with Cameron when
>> he
>> > says that everyone is a member of the neurobureau. But because of who we
>> > are, people like Joshua are more likely to actively join us than, well,
>> > someone not like Joshua. I think it's fine this way. After joining, it's
>> up
>> > to the people to actually find their place in one or multiple ones of
>> our
>> > projects, or to seed their own.
>> >   * I think we need slightly more formal organization. To elaborate on
>> the
>> > few guidelines I had sent in my first email, we would have :
>> >     * A core set of members pushing a general agenda, like giving a
>> legal
>> > status to the bureau, organizing large group calls, updating the website
>> to
>> > advertise our initiatives, etc ... We need to have at least one large
>> group
>> > call a month to discuss projects advancements and new ideas.
>> >     * As many ad-hoc work-groups as needed, as long as there are people
>> to
>> > actively sustain their growth. Within each work-group, we need at least
>> a
>> > leader. For the art at HBM there were other roles that could easily be
>> defined,
>> > like dealing with OHBM, contacting artists, posting on the blog, etc.
>> It's
>> > up to every member to step up and be part of the actions. But it's up to
>> the
>> > leaders to make sure everyone in the bureau knows about our grand plans,
>> so
>> > that interested members can actually step up.
>> >     * We need money. Some work groups could be organized around the idea
>> of
>> > a grant application. I already started something like that with Alex,
>> Clare,
>> > Daniel and Cameronn targeted at human frontier. I think that the
>> work-group
>> > who gets the grant should be free to manage it. Hopefully, some of the
>> money
>> > we'll get can serve the greater purposes of the bureau. One thing we
>> need to
>> > put into place, funded or not, is a open data & tool sharing network.
>> That's
>> > Mike's idea and I have no doubt this should be one of our future
>> (important)
>> > goals. There are several ways to try to get that funded. We can discuss
>> it
>> > during the call, or maybe we should have a dedicated work-group.
>> >     * We need to have a publication plan per work group, if appropriate.
>> > Authorship should be discussed as early as possible, so people know what
>> > their expectations should be. I have a pretty inclusive view when it
>> comes
>> > to authorship, but in any case that should be discussed on a per-case
>> basis.
>> >     * I believe we need senior members. And also, we would need to ask
>> about
>> > 5 seniors who are morally very much in-line with the bureau (or
>> ahead) to
>> > join an advisory board (I am thinking about at least Mike Milham, Xavier
>> > Castellanos, Alan Evans). We would ask for their opinion by email or
>> > conference call regarding our main strategic initiatives, like grants,
>> > workshops, etc ... What we're trying to achieve is not completely new,
>> and
>> > there is some experience out there we could really use. I actually had
>> this
>> > kind of discussions informally already, along with other members, and
>> they
>> > turned out to be amazingly useful. We should turn this into a formal
>> > mechanism.
>> > Looking forward to see you all next week, please fill in the doodle if
>> you
>> > haven't yet,
>> > Pierre Bellec, PhD
>> > Chercheur adjoint
>> > Département d'informatique et de recherche opérationnelle
>> > Centre de recherche de l'institut de Gériatrie de Montréal
>> > 4565, Chemin Queen-Mary
>> > Montréal (Québec)
>> > H3W 1W5
>> > Université de Montréal
>> > <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
>> > (001)(514) 340 3540 #3367
>> >
>> >
>> >
>> >
>> > 2011/7/9 Oliver Lyttelton < <oliver.c.lyttelton at gmail.com>
>> oliver.c.lyttelton at gmail.com>
>> >>
>> >> Hi Cameron,
>> >>
>> >> Yes... I do remember the distinction between membership and leadership
>> >> being made that evening, thank you for drawing this back into the
>> discussion
>> >> space. I think your email is direct and clear, and hopefully will
>> provide a
>> >> springboard for further thoughts. Some of mine, interspersed through
>> what
>> >> you said.
>> >>
>> >> >Ideally in the future we will have a democratic process in which the
>> >> > >membership chooses the leadership, but at this point that is
>> impractical.
>> >> Okay, so what would it take to make it practical? If this is what you
>> want
>> >> then how do we get there?
>> >>
>> >> >Here are a few things that I would like the Neuro Bureau to be:
>> >> >- an independent research institution
>> >>
>> >> This is news to me. Do you mean a full on institution that receives
>> grant
>> >> money and hires researchers? Interesting.
>> >>
>> >> >- an organization that supports open neuroscience through openly
>> >sharing
>> >> > tools, data, ideas, and effort
>> >>
>> >> Sounds good, I guess this is where were heading. The work you have done
>> >> for the ADHD project is amazing in this direction.
>> >>
>> >> >- a diverse community of people who like brains and open collaboration
>> >>
>> >> Okay... but a community of members, or a community of hubs? At the
>> moment,
>> >> I think it is only the latter, the "leadership" as you call it, which
>> brings
>> >> me back to wondering about how "open" we really are. What is it that we
>> >> offer to non-hub "members" that we don't offer the entire imaging
>> community?
>> >> the parties and wearing the badge?
>> >>
>> >> >- a positive force in the universe
>> >> Nice sentiment, I agree
>> >> >- something to be proud of
>> >> Nice sentiment, I agree
>> >>
>> >
>> >
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>> >
>> >
>>
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