[Neurobureau-hubs] next large group call

Pierre Bellec pierre.bellec at criugm.qc.ca
Tue Jul 12 08:40:32 PDT 2011


Dear all,

I booked an EVO meeting for tomorrow's large group call at 2:00 p.m.
(Montreal time) on Evo. Sorry Oliver, you were the only one unavailable at
this time. We'll try to keep the meeting an hour long, 1:30 at the most.
I'll put together an agenda with all the points raised in the discussion
latter today.

The details of the meeting follow :

Title:          The Neurobureau
Description:
Community:      Universe
Password:       TNB

Meeting Access Information:
- Meeting URL

http://evo.caltech.edu/evoNext/koala.jnlp?meeting=MMMeMn2v2tD9Du9I9BD29M

- Password: TNB
- Phone Bridge
       ID: 370 3573
       Password: 3055

Eastern Daylight Time (-0400)
       Start   2011-07-13  14:00
       End     2011-07-13  16:00

Japan Standard Time (+0900)
       Start   2011-07-14  03:00
       End     2011-07-14  05:00

Central European Summer Time (+0200)
       Start   2011-07-13  20:00
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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




2011/7/11 Oliver Lyttelton <oliver.c.lyttelton at gmail.com>

>
> Like!
>
>
> On 11 July 2011 14:32, joshua vogelstein <joshuav at jhu.edu> wrote:
>
>> 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
>>>> =====================
>>>> 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 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.
>>>> >>>> _______________________________________________
>>>> >>>> Neurobureau-hubs mailing list
>>>> >>>> Neurobureau-hubs at www.nitrc.org
>>>> >>>> http://www.nitrc.org/mailman/listinfo/neurobureau-hubs
>>>> >>>
>>>> >>
>>>> >>
>>>> >> _______________________________________________
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>>>> >> Neurobureau-hubs at www.nitrc.org
>>>> >> http://www.nitrc.org/mailman/listinfo/neurobureau-hubs
>>>> >>
>>>> >
>>>> >
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>>>> > http://www.nitrc.org/mailman/listinfo/neurobureau-hubs
>>>> >
>>>> >
>>>>
>>>
>>>
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>>
>
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