[Neurobureau-hubs] next large group call

[joshua vogelstein]

my vote:

every being is already part of the NB

signing up makes one a vertex of the neuro bureau network

vertices collectively appoint hubs and advisory boards and such

this potentially includes non-academics. we strive to be open....

in peace,
j

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




On Mon, Jul 11, 2011 at 1:59 PM, Oliver Lyttelton <
oliver.c.lyttelton at gmail.com> wrote:

>
> I hear your point, and it may be better that way.
>
> Just to be clear, I wasn't suggesting membership of the bureau should be
> just for students, but that the hubs should be drawn from the student body.
>
> I totally agree that having junior faculty on board both as members and
> also in a leadership role is vital.
>
> sort of:
> students elect hubs
>
> hubs mature into leadership roles...
>
>
>
> On 11 July 2011 13:18, MCLAREN, Donald <mclaren.donald at gmail.com> wrote:
>
>> I think it should extend to junior faculty in addition to post-docs.
>> There are a number of junior faculty who could also benefit from the
>> resources and contribute to the education and mentoring of students.
>>
>> 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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>> agent
>> responsible for delivering it to the intended recipient, you are hereby
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>> 406-2464 or email.
>>
>>
>>
>>
>> On Mon, Jul 11, 2011 at 1:05 PM, Oliver Lyttelton
>> <oliver.c.lyttelton at gmail.com> wrote:
>> >
>> >
>> > Hi everyone,
>> >
>> > I kind of like the guerilla/commune aspect of the bureau. As we all get
>> on
>> > in our careers, aspirations mature, and certainly encouraging "open
>> > neuroscience" extends a lot further than a subversive PhD/Post-doc
>> society
>> > aimed at getting the big power-players to bring down their walls and
>> allow
>> > us to work together easily.
>> >
>> > But as we move beyond those ideas towards creating an "open
>> neuroscience"
>> > infrastructure we hit straight into other big projects aimed in the same
>> > arena, and I think, risk losing our identity.
>> >
>> > Since I can't make wednesday, ( I have a 3 hour meeting with my
>> > supervisor...) and it looks like that will probably be the day for the
>> > meeting, based on everyone else's availability, here is my wish list:
>> >
>> > ------------------------------------
>> >
>> > 1) Whatever else the neurobureau becomes, I'd like to see it maintain
>> its
>> > role as an international student/(masters/phd/postdoc) support
>> > group/watchdog championing the cause of people who are often severely
>> > disenfranchised by the scientific establishment.
>> >
>> > 2) Open membership. I'd like to see that at every event the bureau
>> hosts,
>> > everyone is encouraged to become a member, as Mike pointed out, with
>> simple
>> > instructions as to how to join. Somewhere there should be a list of
>> members,
>> > and an infrastructure in place to help people reach their local hubs and
>> set
>> > up their own local, student initiatives. Why not use Facebook?
>> >
>> > 3) I would like to see hubs elected by the members. I'd like to see a
>> date
>> > set for the first elections (perhaps next year) and a roadmap as to how
>> to
>> > get there.
>> >
>> > 4) Anyone who is no longer a student (and in my mind not eligible to run
>> for
>> > election as hub) could become part of the of leadership structure,
>> beyond
>> > the hubs, which interact and interface between the hubs and the existing
>> > power structures within the field, championing the cause of
>> > open-neuroscience, and looking after the rights of the student body.
>> >
>> > Thanks for reading,
>> >
>> > with my best wishes to everyone,
>> >
>> > Oliver
>> >
>> >
>> >
>> > On 10 July 2011 12:40, Pierre Bellec <pierre.bellec at criugm.qc.ca>
>> wrote:
>> >>
>> >> Dear Joshua et al,
>> >> What you describe makes me think of one of the idea initiated by Mike
>> >> Milham. Basically we would have a number of research centers which
>> would
>> >> provide some free space for datasets and some free resources for
>> >> computation, with as many tools as possible. I think it's important to
>> have
>> >> multiple data repository centers to have "mirrors" and cut down access
>> time
>> >> in various part of the world. These mirrors can be linked to multiple
>> >> places, such as NITRC. The key idea is that you can use the data and
>> the
>> >> resources, or even upload your own data to process it there, but then
>> you
>> >> have to commit to make it public, at least at some defined point.
>> That's a
>> >> viral model for open data (and tool) sharing. Of course, the sites
>> would
>> >> have common protocols, and share their databases to a large extent so
>> they
>> >> would be driving forces in that network. What's cool about that model
>> is
>> >> that there is no need to install a virtual machine to share tools or
>> data,
>> >> and no limit to the computational power you can access (if the centers
>> are
>> >> plugged into high-performance computing facilities).
>> >> I am definitely working towards that at my level. As I mentioned to
>> you, I
>> >> am a "pipeliner" and I have developed software specifically targeted at
>> >> pipeline development and deployment (PSOM and NIAK, which are the
>> >> octave/matlab equivalent of NIPYPE and NIPY). There is also the project
>> of
>> >> Alan Evans, CBRAIN, which aims at providing a generic interface to
>> >> download/upload databases, and send processing on a grid of
>> supercomputers.
>> >> Currently CBRAIN interfaces about 50000 cores, but this has not been
>> >> negotiated for open access. I am pretty sure it could though, if rules
>> were
>> >> defined. Instead of writing this ridiculously long email, I should
>> actually
>> >> be writing a paper about a generic system to deploy any pipeline coded
>> using
>> >> PSOM into CBRAIN. That's how we (me, Sébastien Lavoie-Courchesne and
>> >> François Chouinard-Decorte) have preprocessed the ADHD200 dataset. Alan
>> also
>> >> applied for a 5 Pb data storage (I am on that application) so, if that
>> goes
>> >> through, Montreal could be one of the mirroring site. We could try to
>> >> implement this computational infrastructure at various sites of the
>> >> neurobureau and make it happen. It's all possible in a short time. It
>> could
>> >> maybe even get funded, but as Mike pointed out that's not a necessity.
>> >> BTW, because this project fits a number of large efforts in the field,
>> I
>> >> think it's important for us to be connected with the key senior players
>> >> somehow. That's partly what motivated me to propose this "senior
>> advisory
>> >> board" (it could be beneficial beyond that particular point though). If
>> we
>> >> can be some sort of proof of concept for a larger effort, good.
>> Conversely,
>> >> if someone gets funded to do that, hopefully we'll be part of it.
>> >> Finally, re the polymath project, one of the Alex of the neurobureau
>> wrote
>> >> something about that on the neurobureau blog. We don't actually need a
>> big
>> >> infrastucture for that. All we need is a "grand challenge" as well as a
>> >> dataset where this grand challenge can be resolved. Actually, the grand
>> >> challenge could be the target of the workshop Donald suggested. I have
>> an
>> >> idea for a grand challenge, will do a separate email about that.
>> >> Please let me know what you think,
>> >> 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
>> >> (001)(514) 340 3540 #3367
>> >>
>> >>
>> >>
>> >>
>> >> 2011/7/10 joshua vogelstein <joshuav at jhu.edu>
>> >>>
>> >>> ah, thank you for bringing up this point! i agree that this is a very
>> >>> important discussion, and that there are gradations of openness.
>> consider
>> >>> wikipedia: it is not the case that anybody can just write anything
>> they
>> >>> want.  wikimedia established guidelines, users are expected to follow.
>>   the
>> >>> same is true of arxiv.  i expect that we will want to establish
>> similar
>> >>> guidelines establishing what we are open to, and what we are not.  and
>> i
>> >>> imagine that those guidelines will be organic and grow with us as we
>> learn
>> >>> more and get more capabilities.
>> >>> cheers, j
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> If it makes you feel better, please remember to consider humanity
>> before
>> >>> doing stuff. Otherwise, please just have a nice day.
>> >>> openconnectomeproject.org
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> On Sun, Jul 10, 2011 at 10:03 AM, MCLAREN, Donald
>> >>> <mclaren.donald at gmail.com> wrote:
>> >>>>
>> >>>> Along the discussion of openess. I think one of the early decisions
>> if
>> >>>> if there will be a new central data repository (a number already
>> >>>> exist) or if we will use an existing one or if we will use multiple
>> >>>> systems that are distributed. The other decision related to this is
>> >>>> whether it should be fully open -- anyone can add to it -- or OPEN
>> >>>> access -- where an 'elected' committe would review and vote on the
>> >>>> submission or processing request -- or OPEN access -- where the
>> >>>> storage owners would decide what is valuable enough to put on the
>> >>>> system.
>> >>>>
>> >>>> These two questions will go hand in hand.
>> >>>>
>> >>>> On Saturday, July 9, 2011, 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 adjointDépartement d'informatique et de recherche
>> >>>> > opérationnelle
>> >>>> > Centre de recherche de l'institut de Gériatrie de Montréal
>> >>>> > 4565, Chemin Queen-Mary
>> >>>> > Montréal (Québec)
>> >>>> > H3W 1W5Université de Montréal
>> >>>> > http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
>> >>>> > (001)(514) 340 3540 #3367
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > 2011/7/9 MCLAREN, Donald <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
>> >>>> > =====================
>> >>>> > This e-mail contains CONFIDENTIAL INFORMATION which may contain
>> >>>> > PROTECTED
>> >>>> > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which
>> is
>> >>>> > intended only for the use of the individual or entity named above.
>> If
>> >>>> > the
>> >>>> > reader of the e-mail is not the intended recipient or the employee
>> or
>> >>>> > agent
>> >>>> > responsible for delivering it to the intended recipient, you are
>> >>>> > hereby
>> >>>> > notified that you are in possession of confidential and privileged
>> >>>> > information. Any unauthorized use, disclosure, copying or the
>> taking
>> >>>> > of any
>> >>>> > action in reliance on the contents of this information is strictly
>> >>>> > prohibited and may be unlawful. If you have received this e-mail
>> >>>> > unintentionally, please immediately notify the sender via telephone
>> at
>> >>>> > (773)
>> >>>> > 406-2464 or email.
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > On Sat, Jul 9, 2011 at 10:56 PM, Pierre Bellec
>> >>>> > <
>> >>>>
>> >>>> --
>> >>>> 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
>> >>>> =====================
>> >>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain
>> >>>> PROTECTED
>> >>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which
>> is
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>> >>>> reader of the e-mail is not the intended recipient or the employee or
>> >>>> agent
>> >>>> responsible for delivering it to the intended recipient, you are
>> hereby
>> >>>> notified that you are in possession of confidential and privileged
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>> of
>> >>>> any
>> >>>> action in reliance on the contents of this information is strictly
>> >>>> prohibited and may be unlawful. If you have received this e-mail
>> >>>> unintentionally, please immediately notify the sender via telephone
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>> >>>> (773)
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>> >>>> 406-2464 or email.
>> >>>> _______________________________________________
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>> >>>
>> >>
>> >>
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