[Neurobureau-hubs] next large group call

[MCLAREN, Donald]

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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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
>>>> 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.
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>>>
>>
>>
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