[Open-bio-l] Codefest 2010: Final details

Mon Jul 5 19:34:09 UTC 2010

[so straightforward that 3 or 4 introductory slides couldn't possibly hurt?]
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Hilmar Lapp" <hlapp at nescent.org>
Cc: "Heikki Lehvaslaiho" <heikki.lehvaslaiho at gmail.com>; "Brad Chapman" 
<chapmanb at 50mail.com>; "Christopher Bottoms" <maizemu at gmail.com>; 
<open-bio-l at lists.open-bio.org>; "Oliver Hofmann" <ohofmann at hsph.harvard.edu>; 
"Kimberly Begley" <Kimberly at fisciconsulting.com>; "Michael Heuer" 
<heuermh at acm.org>; "Eric Talevich" <eric.talevich at gmail.com>; "James Taylor" 
<james.taylor at emory.edu>; "Enis Afgan" <eafgan at emory.edu>; "Dannon Baker" 
<dannonbaker at me.com>; "Ntino Krampis" <agbiotec at gmail.com>; "Tim Booth" 
<tbooth at ceh.ac.uk>; "Richard Holland" <holland at eaglegenomics.com>; "Mark Jensen" 
<maj at fortinbras.us>; "Kam Dahlquist" <kdahlquist at lmu.edu>; "John David N. 
Dionisio" <dondi at lmu.edu>; "Steffen Möller" <steffen_moeller at gmx.de>; "Bela 
Tiwari" <btiwari at ceh.ac.uk>; "Dominique Belhachemi" <domibel at cs.tu-berlin.de>; 
"Toshiaki Katayama" <ktym at hgc.jp>; "Mitsuteru Nakao" <mn at dbcls.jp>; "Dave 
Messina" <David.Messina at sbc.su.se>; "Christian Zmasek" <czmasek at burnham.org>; 
"Akira KINJO" <akinjo at protein.osaka-u.ac.jp>; "Naohisa Goto" <ng at bioruby.org>; 
"Yasunori Yamamoto" <yy at dbcls.jp>; "Raoul J.P. Bonnal" <bonnalraoul at ingm.it>; 
"Atsuko Yamaguchi" <atsuko at dbcls.jp>
Sent: Monday, July 05, 2010 3:02 PM
Subject: Re: Codefest 2010: Final details

I can probably come up with something (I have a few slides).  The design for 
both Biome and bioperl6 is fairly straightforward (interfaces -> roles), but it 
would be nice to sit down with those interested to see what would be the best 
path to take design-wise regarding future development, mistakes learned, etc.

chris

On Jul 5, 2010, at 1:51 PM, Hilmar Lapp wrote:

> I agree that would be great!
>
> -hilmar
>
> On Jul 5, 2010, at 1:57 PM, Heikki Lehvaslaiho wrote:
>
>> Chris,
>>
>> I'd love to hear an overview of Biome project (bioperl in perl6) and
>> design decisions you have taken there. That would help me understand
>> it better. Do you think you could do that?
>>
>>    -Heikki
>>
>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>> cell: +966 545 595 849  office: +966 2 808 2429
>>
>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>> 4700 King Abdullah University of Science and Technology (KAUST)
>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>
>>
>>
>>
>> On 4 July 2010 21:51, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> Christopher, Chris, Heikki and Hilmar;
>>> Nice discussion. If you have an overview of what you are hoping
>>> to tackle on the BioPerl side, please add it on the wiki page. The
>>> getting started part of the coding sessions is always the hardest
>>> part, so it'll be a huge help if we can stand up at the beginning,
>>> describe the project ideas, and then let people break into groups:
>>>
>>> http://www.open-bio.org/wiki/Codefest_2010#ToDo_List
>>>
>>> Edit away and this'll point us all in the right direction.
>>> Looking forward to next week,
>>> Brad
>>>
>>>> I will be there on the afternoon of the 7th.  There are a couple of 
>>>> projects one can look into for Moose and Perl 6 (Biome and BioPerl6).  I 
>>>> think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not 
>>>> sure where that is (might be surplanted by SQLite work?).  Would be nice to 
>>>> talk with Mark re: the wrapper system for BioPerl as well.
>>>>
>>>> So lots of stuff to think over and plan for.  Maybe we should move this to 
>>>> open-bio-l, or bioperl-l?
>>>>
>>>> chris (fields)
>>>>
>>>> On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote:
>>>>
>>>>> Chris,
>>>>>
>>>>> I do not have too much experience on cloud computing, either. There
>>>>> will be quite a few people from BioPerl . We'll meet and  come up with
>>>>> a plan first thing in the morning. Unless someone has a very good one
>>>>> ready for sharing...
>>>>>
>>>>>    -Heikki
>>>>>
>>>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>>>> cell: +966 545 595 849  office: +966 2 808 2429
>>>>>
>>>>> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
>>>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 3 July 2010 08:36, Christopher Bottoms <maizemu at gmail.com> wrote:
>>>>>> Hi all,
>>>>>>
>>>>>> I was originally planning on working on cloud computing at the Codefest.
>>>>>> However, the 2-day cloud computing tutorial that I was going to attend in
>>>>>> mid June was canceled. Does anyone have any programming that they would 
>>>>>> like
>>>>>> help with? I have experience with Perl 5, including Moose, and I am 
>>>>>> starting
>>>>>> to dabble in Perl 6. I have also programmed in Java in the past. I hear
>>>>>> Python is easy to learn, so I'd be open to working on a Python project as
>>>>>> well.
>>>>>>
>>>>>> Thanks,
>>>>>> Christopher Bottoms
>>>>>>
>>>>>> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>>>>>>
>>>>>>> Hi all;
>>>>>>> Codefest 2010 is finally here: next Wednesday and Thursday at
>>>>>>> Harvard Medical School and Massachusetts General Hospital in
>>>>>>> beautiful Boston. All of the logistics, directions and details
>>>>>>> are on the wiki page:
>>>>>>>
>>>>>>> http://www.open-bio.org/wiki/Codefest_2010
>>>>>>>
>>>>>>> If you want the short version: show up at Harvard Medical School on
>>>>>>> Wednesday at 10am and we'll take care of the rest. Thanks to the
>>>>>>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll
>>>>>>> have coffee, lunches and internet. Thanks to Steffen and Ntino,
>>>>>>> we'll have Amazon credits to utilize. And of course, there will be
>>>>>>> BBQ and drinking on Thursday night when we are finished.
>>>>>>>
>>>>>>> I'm looking forward to a fun and productive time. The general plan
>>>>>>> will be to spend a bit of time on Wednesday morning organizing
>>>>>>> ourselves into like minded groups of folks, and then commence with
>>>>>>> coding and collaborating.
>>>>>>>
>>>>>>> If you aren't able to make it and you're listed on the wiki page under
>>>>>>> participants, please do cross your name off so we have a good idea of
>>>>>>> final numbers. Likewise, if you are coming but haven't put your name up
>>>>>>> there please add it.
>>>>>>>
>>>>>>> If you are interested in helping with making software and data
>>>>>>> available on shared cloud resources, here are the latest Amazon
>>>>>>> AMIs, snapshots, and the code base:
>>>>>>>
>>>>>>> Cloud BioLinux images:
>>>>>>> 64bit: ami-d62cc4bf
>>>>>>> 32bit: ami-5423cb3d
>>>>>>>
>>>>>>> An EBS public snapshot with indexed genomes:
>>>>>>> snap-67446d0f
>>>>>>>
>>>>>>> Infrastructure:
>>>>>>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/
>>>>>>>
>>>>>>> Send an e-mail with any questions, thoughts or concerns. My phone
>>>>>>> number is 617-447-8586 in case you end up hopelessly lost somewhere
>>>>>>> in Boston and are desperate to begin programming.
>>>>>>>
>>>>>>> Looking forward to seeing everyone next Wednesday,
>>>>>>> Brad
>>>>>>
>>>>>>
>>>>
>>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>