[Neurobureau-hubs] brainhacker school

Pierre Bellec pierre.bellec at criugm.qc.ca
Wed Jan 21 17:12:24 PST 2015 

Dear Joshua,

I think there was some general consensus around the idea of a 2 weeks
summer school, mixing about 50% of talks/hands on on basic programming
skills and neuroimaging analysis software (as well, perhaps, as
neuroimaging techniques such as EEG or MRI), with 50% of projects. The
details of the structure of the projects needs to be further discussed. Of
course the idea would be to bring data scientists with neuroscientists or,
even better, turn neuroscientists into decently skilled data scientists
themselves. Re a multiscale (micro&macro) focus, I would personally be
delighted. Are you still at Johns Hopkins? It would be a great location for
the brain hackademia.

Let us know how the discussion goes. Best,



Pierre Bellec
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
Telephone              (1) 514 713 5596
SIMEXP lab            http://simexp-lab.org

On Wed, Jan 21, 2015 at 6:06 PM, joshua vogelstein <jovo at jhu.edu> wrote:

> hi all - i have a working relationship with the kavli foundation,
> and they have told me that if i have a good hack-a-thon related event to
> plan, they could sponsor it.
> note that their interests is in getting 'data scientists' working with
> neuroscientists.
> for example, the previous link i posted on codeneuro, where industry, data
> scientists, and neuroscientists all came together for a couple days.
> they like stuff like that, especially if we bridge across scales, eg,
> including electron microscopy and light microscopy, in addition to MR style
> stuff.
>
> i could imagine they'd be super supportive of a "hack-a-shop" which
> included some lectures introducing tools from different sub-disciplines
> within neuroimaging, and the hacking goals would include
> cross-fertilization of ideas, and possibly interoperability.
>
> for reference, i am spending the day with them TOMORROW.
> so, if you have ideas you'd like me to pitch on our behalf, speak now :)
>
> cheers, j
>
>
> On Wed Jan 21 2015 at 11:32:10 AM Pierre Bellec <
> pierre.bellec at criugm.qc.ca> wrote:
>
>>  Dear Donald,
>>
>>  I would encourage you to have a look at the link I originally posted
>> https://www.hackerschool.com/
>> The idea of the the hacker school is grounded on project-based learning
>> <http://en.wikipedia.org/wiki/Project-based_learning>, with two key
>> features: self-directed and project-based. I am passionate about teaching
>> and project-based learning. So I am committed to carve out time to develop
>> initiatives along those lines. To make it explicit: I am not personally
>> interested in organizing a traditional lectures (many) + directed hands-on
>> (few) style of workshop, such as:
>>  https://www.nmr.mgh.harvard.edu/training/multimodality
>>
>>  Regarding logistics/funding, just have a look at
>> https://www.nmr.mgh.harvard.edu/training/multimodality
>>  For the record, Brainhack in Paris was almost free, and included food
>> and lodging. Some places will fund longer workshops, I mentioned Banff. A
>> lot of summer schools ask for participants to cover for accommodation, and
>> don't have a problem attracting participants as long as cheap options are
>> available and the program is attractive.
>>
>>  Also, note that this two-week workshop does not generate outcomes such
>> as papers. It generates knowledge and skills for attendants, which is by
>> far the most common outcomes for summer school and definitely not an
>> obstacle to get funded.
>>
>>  Best,
>>
>>  Pierre
>>
>>  Pierre Bellec           http://simexp-lab.org/brainwiki/doku.php?id=
>> pierrebellec
>> Telephone              (1) 514 713 5596
>> SIMEXP lab            http://simexp-lab.org
>>
>> On Wed, Jan 21, 2015 at 11:08 AM, MCLAREN, Donald <
>> mclaren.donald at gmail.com> wrote:
>>
>>> While the idea of 1-week projects sound great in this discussion;
>>> however, I am not sure how one convinces funding agencies to support the
>>> concept and will make it harder to get funding for a longer course; not to
>>> mention the cost to attendees for food and lodging.
>>>
>>>  My original comment was not that we require papers, but rather that
>>> there are several more long-term projects that would use new techniques
>>> that could lead to publications.
>>>
>>>  The key is that we need some metric to measure the success of the
>>> course. If one can develop a metric for measuring the impact of custom
>>> visualization, curating data, or running pre-processing, then I think this
>>> would make the 1 week projects more favorable.
>>>
>>>  One could also make more of the lectures in the first week, and make
>>> more of the second week a work period.
>>>
>>>  There are already several 1-2 week courses teaching advanced brain
>>> imaging techniques:
>>> http://neurometrika.org/Courses
>>>  https://www.nmr.mgh.harvard.edu/training/courses
>>>
>>>  Past brainhack's have gotten minimal funding and have only last 1-3
>>> days. For longer courses, we'll need more support.
>>>
>>>  The big questions -- how do we turn this into something that happens
>>> every year or every other year and how do you make it affordable?
>>>
>>>  The brain connectivity conference was only a few days and was quite
>>> expensive.
>>>
>>>
>>>  Best Regards, Donald McLaren
>>> =================
>>> D.G. McLaren, Ph.D.
>>> Research Fellow, Department of Neurology, Massachusetts General Hospital
>>> and
>>> Harvard Medical School
>>> Postdoctoral Research Fellow, GRECC, Bedford VA
>>> Website: http://www.martinos.org/~mclaren
>>> Office: (773) 406-2464
>>> =====================
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>>>
>>>   On Wed, Jan 21, 2015 at 9:56 AM, Pierre Bellec <
>>> pierre.bellec at criugm.qc.ca> wrote:
>>>
>>>>  Dear all,
>>>>
>>>>  I agree with Cameron. 50/50 may be a good balance for this type of
>>>> event. With the evenings adding another 25 or so, if needed. If we're able
>>>> to attract good instructors there should be no problem attracting good
>>>> participants. I don't think we'll have many instructors willing to commit
>>>> for a full 2 weeks. For those who do, the brainhack school (brain imaging
>>>> hackademy?) shouldn't be full-time teaching, again more like half-time, the
>>>> other half being more of a collaborative retreat. Maybe some instructors
>>>> could come for only one week, or even 1 or 2 days? Again, agree with
>>>> Cameron regarding the publication part, focus should be on learning,
>>>> I think it would be better to have several small projects that you can
>>>> actually finish and feel good about, rather than setting an extremely
>>>> ambitious goal by default. I'd be afraid that in this case people would
>>>> tend to jump on material they already know rather than immerse themselves
>>>> in totally new techniques.
>>>>
>>>>  Maybe students could get an overview of topics by the instructor at
>>>> the beginning of the week, and then come up on their own with an idea for a
>>>> one-week project, in interaction with other attendees & the instructors to
>>>> ensure feasibility ? They would have to define a list of necessary tools,
>>>> milestones and schedule. Having two one-week projects would also help
>>>> manage instructors coming for a short time (we would have a reset with a
>>>> new set of projects in the middle of the school). Examples of projects
>>>> could be setting up a web-browser interface for custom visualization of
>>>> one's dataset/analysis, curating paper's data and implementing a
>>>> meta-analysis on a particular subject using brainspell, running
>>>> preprocessing + ReHo analysis using CAPAC, designing an experiment and
>>>> implementing a pilot (EEG, MRI, psychophysics, BCI). What do you guys think
>>>> about the format?
>>>>
>>>>  Best,
>>>>
>>>>  Pierre Bellec           http://simexp-lab.org/brainwiki/doku.php?id=
>>>> pierrebellec
>>>> Telephone              (1) 514 713 5596
>>>> SIMEXP lab            http://simexp-lab.org
>>>>
>>>>  On Tue, Jan 20, 2015 at 1:16 PM, Alexandre R Franco <
>>>> eng.franco at gmail.com> wrote:
>>>>
>>>>> This is what Cameron is talking about:
>>>>> http://www.ipam.ucla.edu/programs/summer-schools/
>>>>> summer-school-mathematics-in-brain-imaging/?tab=schedule
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>   On Jan 20, 2015, at 3:50 PM, Cameron Craddock <
>>>>> cameron.craddock at gmail.com> wrote:
>>>>>
>>>>> I would like to being back the old mathmatics in brain imaging format.
>>>>> That was two weeks and well attended.
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On Jan 20, 2015, at 12:43 PM, rbrto <robertotoro at gmail.com> wrote:
>>>>>
>>>>> work to publish a paper? like the 1 month things at Santa Fe institut
>>>>> for complex systems... People were very happy to come, because they
>>>>> would have a paper by the end of the month
>>>>>
>>>>> On Tue, Jan 20, 2015 at 6:29 PM, Chris Filo Gorgolewski
>>>>> <krzysztof.gorgolewski at gmail.com> wrote:
>>>>>
>>>>> This is a pretty cool idea, but Mike is right - we need to figure out
>>>>> how to
>>>>> make it easy for participants to convince their supervisors to get
>>>>> funding
>>>>> for this.
>>>>>
>>>>> Best,
>>>>> Chris
>>>>>
>>>>> On Mon Jan 19 2015 at 7:37:37 AM rbrto <robertotoro at gmail.com> wrote:
>>>>>
>>>>> I want 12 months a year of that...
>>>>>
>>>>> On Mon, Jan 19, 2015 at 4:09 PM, Pierre Bellec
>>>>> <pierre.bellec at criugm.qc.ca> wrote:
>>>>>
>>>>> @Cameron agreed, 2 weeks is more realistic.
>>>>>
>>>>> @Daniel, re Banff, there have an on-going program to host workshops in
>>>>> mathematics. They may have a long workshop format, I'll look into it.
>>>>> For
>>>>> locations, the problem is not much different than hosting a traditional
>>>>> brainhack, with maybe more emphasis on local attendants.
>>>>>
>>>>> @Roberto
>>>>> Re Nifti, that's recoding nii2mnc, or even re-inventing the minc
>>>>> format.
>>>>> Looks like some folks are taking this task seriously:
>>>>>
>>>>> http://www.frontiersin.org/10.3389/conf.fninf.2013.09.00069/
>>>>> event_abstract
>>>>>
>>>>> Re FSL, you never know what we'll discover.
>>>>> http://youtu.be/HdWRTleizFU?t=10m54s
>>>>>
>>>>> Re HCP, trying to test the level of actual security of their database
>>>>> may
>>>>> indeed be interesting & useful.
>>>>>
>>>>> Now, regarding what this brainhack school would look like, I guess it
>>>>> would
>>>>> be like a longer version of brainhack, with most of the time devoted
>>>>> for
>>>>> attendants to work on their own projects, self-initiated and managed.
>>>>> We
>>>>> would still have well identified education talks & experts of various
>>>>> tools
>>>>> available onsite, some general (version control, programming) and some
>>>>> more
>>>>> specialized (e.g. AFNI), again very much like brainhack. We could also
>>>>> have
>>>>> some more maker-oriented resources, such as 3D printing, EEG set, or
>>>>> even an
>>>>> MRI depending on the location (I am pretty sure this could be arranged
>>>>> in
>>>>> Montreal or Leipzig for example). Maybe even a vibrating shirt, who
>>>>> knows.
>>>>> In two weeks, participants may be able to take advantage of the
>>>>> availability
>>>>> of large datasets and computational resources, which has not been the
>>>>> case
>>>>> in the short version of brainhack. Also, unlike the short brainhack,
>>>>> participants may be able to actually deliver a concrete output.
>>>>> Finally,
>>>>> the
>>>>> event should be family friendly for obvious reasons :) I'm sure my kids
>>>>> could totally work their way through a two weeks lego projects,
>>>>> especially
>>>>> if we throw in some quadropters as well.
>>>>>
>>>>>
>>>>> Pierre Bellec
>>>>> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
>>>>> Telephone              (1) 514 713 5596
>>>>> SIMEXP lab            http://simexp-lab.org
>>>>>
>>>>> On Mon, Jan 19, 2015 at 8:13 AM, rbrto <robertotoro at gmail.com> wrote:
>>>>>
>>>>> Yes!! Brainhacker school!! We teach people to read the nifti data
>>>>> directly from the file with an hex editor, p0wn the unused fields and
>>>>> write the results in new fancy formats!!! Make FSL do new types of
>>>>> analyses by using buffer overflows, etc :)
>>>>> I'm already loving it!!
>>>>> (anyone tried sql injection in HCP??)
>>>>>
>>>>> On Mon, Jan 19, 2015 at 1:28 PM, Daniel Margulies
>>>>> <daniel.margulies at gmail.com> wrote:
>>>>>
>>>>> I love the idea, Pierre,
>>>>>
>>>>> Any leads on the possibility of doing this as a retreat at the Banff
>>>>> Center?
>>>>> Perhaps there are other locations that might be possible as well?
>>>>>
>>>>> Daniel
>>>>>
>>>>> On Mon, Jan 19, 2015 at 4:21 AM, Pierre Bellec
>>>>> <pierre.bellec at criugm.qc.ca>
>>>>> wrote:
>>>>>
>>>>>
>>>>> Hi guys,
>>>>>
>>>>> Just ran into this:
>>>>> https://www.hackerschool.com/
>>>>>
>>>>> We should probably try to organize a summer brainhacker school
>>>>> modeled
>>>>> after this. 3 months is a tad long, but one month could be doable,
>>>>> especially if we get, say, the banff center to host the event.
>>>>>
>>>>> Best,
>>>>>
>>>>> Pierre Bellec
>>>>> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
>>>>> Telephone              (1) 514 713 5596
>>>>> SIMEXP lab            http://simexp-lab.org
>>>>>
>>>>>
>>>>>
>>>>>
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