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Difference between revisions of "Talk:BOSC 2010"

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(→‎Important Dates: changed call for abstracts date to Jan 18 instead of Jan 15)
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This page is being used for planning purposes.  For official information, please see the [[BOSC 2010 | BOSC 2010 Main Page]].
 
This page is being used for planning purposes.  For official information, please see the [[BOSC 2010 | BOSC 2010 Main Page]].
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[http://www.phdcomics.com/comics/archive.php?comicid=1335 Suggestion for next year's Call for Abstracts]
  
 
== Important Dates ==
 
== Important Dates ==
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* '''December 1, 2009''': [[Media:Dahlquist_BOSC_2010.pdf | BOSC Special Interest Group Letter of Intent]] submitted to the ISMB SIG committee.
 
* '''December 1, 2009''': [[Media:Dahlquist_BOSC_2010.pdf | BOSC Special Interest Group Letter of Intent]] submitted to the ISMB SIG committee.
−
* '''December 18, 2009''': SIG Acceptance Notification
+
* '''December 18, 2009''': SIG Acceptance Notification.  '''''SIG has been accepted by ISMB as of 12/19/09'''''
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* ''January 18, 2010'': Instance of OCS set up and tested; Call for Abstracts opens
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* ''January 18, 2010'': Instance of OCS set up and tested
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* '''February 26, 2010''': [[Media:Dahlquist_BOSC_2010_InformationRequested.pdf | Information supplied to ISMB for posting on ISMB web site]]
 
* '''March 9, 2010''': ISMB and BOSC registration opens
 
* '''March 9, 2010''': ISMB and BOSC registration opens
 
* '''March 12, 2010''': SIG Preliminary Program Due
 
* '''March 12, 2010''': SIG Preliminary Program Due
−
* ''April 15, 2010'': Abstract deadline
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* April 15, 2010: Abstract deadline
 
* ''April 15-30, 2010'': Review period
 
* ''April 15-30, 2010'': Review period
 
* '''April 23, 2010''': SIG Program (preliminary) Available on Web
 
* '''April 23, 2010''': SIG Program (preliminary) Available on Web
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* '''May 21, 2010''': SIG Complete Program on Web
 
* '''May 21, 2010''': SIG Complete Program on Web
 
* '''May 28, 2010''': Early Registration Discount Cut-off Date
 
* '''May 28, 2010''': Early Registration Discount Cut-off Date
−
* '''June 25, 2010''': Handout Materials Due
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* '''June 9, 2010''': Handout Materials Due
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<!--June 30, 2010: list of complimentary registrations due to Steven Leard-->
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* July 7-8, 2010:  [[Codefest 2010]]
 
* '''July 9-10, 2010''':  BOSC 2010!
 
* '''July 9-10, 2010''':  BOSC 2010!
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* August 15, 2010:  Manscript deadline for BOSC Proceedings in BMC Bioinformatics
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== Suggestions for Dinner Locations for the Friday, July 9 Board Meeting ==
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These suggestions came from Brad Chapman:
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* Legal Sea Foods
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** Standard Boston seafood
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** Ste 103, 800 Boylston Street, Boston, MA 02199-8046
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* [http://www.charleys-restaurant.com/ Charley's]
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** American food; a nice Boston only place
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* [http://www.solasboston.com/solasboston/ Solas]
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**Irish Pub Food
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* [http://www.pizzapieer.com/live/index.php Pizza Pie-er]
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* Food court in Prudential center
 +
 +
 
  
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== Sessions ==
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 +
<!--== Brainstorming Ideas ==
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Thanks for everyone's suggestions.  These have been incorporated into the main [[BOSC 2010]] page.
 +
 
 +
From the e-mail sent to the O|B|F Membership on 12/18/09:
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 +
The BOSC organizing committee is soliciting your input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community.  You may respond with your suggestions by editing this page or by sending an e-mail to [mailto:bosc@open-bio.org bosc@open-bio.org].  Please respond to any or all of the questions below:
 +
 
 +
=== Types of Sessions ===
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 +
For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions.  Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:
 +
 
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==== Tutorials ====
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Would you like to have tutorials where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier.  '''Would you be willing to organize/lead such a session for your project?'''
 +
 
 +
==== Discussions ====
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Would you like to have discussions following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The "speaker" would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them.  '''Would you be willing to organize/lead such a session for your project?'''
 +
 
 +
==== Mini-hackathon ====
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 +
Would you like to have a mini-hackathon either before, during, or after the 2-day BOSC.  The subject of the hackathon would need to be organized by the individual project leaders/teams.  Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal.  '''Would you be willing to organize/lead this type of session?'''
 +
 
 +
==== LiveCD ====
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Would you like to organize/create a LiveCD or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community.  '''Would you be willing to organize/lead this type of session?'''
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 +
==== Session Topics====
  
 
* '''Bio* Updates''': updates from O|B|F-sponsored projects
 
* '''Bio* Updates''': updates from O|B|F-sponsored projects
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Please make suggestions for special topic sessions for BOSC 2010 here:
 
Please make suggestions for special topic sessions for BOSC 2010 here:
  
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== Keynote Speakers ==
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==== Keynote Speakers ====
  
 
Please make suggestions for keynote speakers for BOSC 2010 here, or e-mail the organizing committee at [mailto:bosc@open-bio.org bosc@open-bio.org]
 
Please make suggestions for keynote speakers for BOSC 2010 here, or e-mail the organizing committee at [mailto:bosc@open-bio.org bosc@open-bio.org]
  
−
== Brainstorming Ideas ==
 
  
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=== From Brad Chapman ===
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=== Proceedings ===
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 +
The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC.  If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000?  We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.
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=== Call for Volunteers ===
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It's not too late to volunteer for BOSC.  Please let us know if you would be willing to serve in any capacity.  We need volunteers to review abstracts.  The abstract review period will take place between April 15 and May 5.-->
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 +
<!--=== Timeline for Input ===
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 +
We are planning on putting out the Call for Abstracts in mid-January.  To be on track, we would like to receive your input by Friday, January 8.  If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.-->
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 +
<!-- == Call for Abstracts ==
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This is the announcement that went out originally on 3/1/10.
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Call for Abstracts for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010)
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 +
An ISMB 2010 Special Interest Group (SIG)
 +
Date: July 9-10, 2010
 +
Location: Boston, Massachusetts, USA
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BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010
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Abstract submission via Open Conference System site:
 +
http://events.open-bio.org/BOSC2010/openconf.php
 +
E-mail: bosc@open-bio.org
 +
Bosc-announce list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce
 +
 
 +
Important Dates
 +
April 15: Abstract deadline
 +
May 5:  Notification of accepted abstracts
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May 28: Early Registration Discount Cut-off date
 +
July 8-9:  Codefest 2010
 +
July 9-10: BOSC 2010
 +
August 15:  Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics
 +
 
 +
The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.
 +
 
 +
We have some exciting things planned this year, including:
 +
 
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-- Codefest 2010 programming session for the two days preceeding BOSC:  See http://www.open-bio.org/wiki/Codefest_2010 for details.
 +
 
 +
-- OpenBio Solution Challenge:  See session description below and http://www.open-bio.org/wiki/SolutionChallenge for details.
 +
 
 +
-- Student Travel Fellowships:  Through generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2010. Each winner will be awarded $250 to defray the costs of travel to BOSC 2010.  See http://www.open-bio.org/wiki/BOSC_2010#Student_Travel_Awards for details.
 +
 
 +
-- First-ever BOSC Proceedings will be published in the Open Access journal, BMC Bioinformatics.  Manuscripts will be due after BOSC on August 15.  See http://www.open-bio.org/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings for details.
 +
 
 +
-- Sessions on approaches to analyzing high-throughput 'omics data, cloud-based approaches to improving software and data accessibility, the semantic web in open source bioinformatics, see below:
 +
 
 +
We invite abstracts for talks at the following sessions:
 +
 
 +
OpenBio SolutionChallenge -- Bioinformatics library providers: please join us in a friendly competition to solve a shared biological problem, demonstrating the utility of your toolkit alongside other developers. Instead of the traditional Bio* updates that we've had at previous conferences, this year, we're planning to organize these talks around a central theme: the OpenBio Solution Challenge. We start with a biological question of general interest, and the project talks will focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). Specific challenges are being discussed on the SolutionChallenge page and through the various Bio* mailing lists. Alternately, each project could highlight a challenge that they particularly do well, focusing tutorial-style on how to solve a particular problem.  (Of course, we would still welcome traditional Bio* Update abstracts, too!)
 +
 
 +
Approaches to analyzing high-throughput 'omics data -- Presentation of projects that use the MapReduce framework either for parallelized analysis of possibly terabyte size data sets from next-gen sequencing and mass spec proteomics or parallelization of bioinformatics algorithms in general (e.g., the Apache Mahout project). Projects may involve Hadoop (MapReduce API + HDFS) as well as associated open source toolkits (Hbase, Hive, Pig, Cascading, etc.) or other NoSQL non-relational data stores.
 +
 
 +
Cloud-based approaches to improving software and data accessibility -- The emergence of cloud computing has made highly scalable cluster computing available to computational biologists. Services such as Amazon Elastic Compute Cloud combined with publicly available datasets promise to lower the overhead to participate in large scale data analyses. We are interested in talks focused around how the community can build up resources and datasets for cloud infrastructure, as well as the sharing of insights, and the contribution of implemented workflows. Current implementations and initiatives are encouraged to submit abstracts for talks and join in the pre-conference Codefest session.
 +
 
 +
The Semantic Web in open source bioinformatics -- Emerging Semantic Web technologies promise to improve data interoperability and accessibility. Seeing these developments as promising for life science researchers who struggle daily with new file formats and incompatible datasets, BioHackathon 2010 focused around current semantic resources and tools for bioinformatics. We solicit session talks from researchers using RDF and related technologies in their research and data analyses, with a special focus on documenting how these tools can contribute to open data access.
 +
 
 +
Open Source Software -- Open source software that does not fit neatly into the above categories.
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 +
Lightning Talks -- short, 5 minute talks intended to introduce very recent developments, initiate discussion, or highlight resources of interest to BOSC attendees. Abstracts for Lightning Talks will be accepted up to the first day of BOSC and will be accepted based on space availability and conformance to the Open Source License Requirement.
  
−
* In terms of the focus of the conference, I was also doing a little brainstorming about options for the layout of the two days. What would you all think about moving away from the presentation and question/answer format towards something a bit more interactive? My rough idea would be to divide the days up into:
+
BOSC 2010 Organizing Committee:
−
** Tutorial day -- In depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier.
+
Kam D. Dahlquist (Chair), Brad Chapman, Nomi Harris, Michael Heuer, Darin London, Steffen Möller, Anton Nekrutenko, Jim Procter, Ron Taylor, Chris Dagdigian, Hilmar Lapp, Jason Stajich
−
** Discussion day -- Following the hands on tutorial ideas, these would be interactive sessions focused around dealing with unsolved issues. The "speaker" would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them.
 
−
* One of the unique and awesome things about open source is that there are so many solutions out there that you have never heard about or don't know how to use. This sort of teaching and discussion forum could help lower the learning curve for people who have trouble getting started, and expand the set of toolkits for those who are already rolling with open source science work.
 
  
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=== From O|B|F Board Meeting Conference Call on 12/14/09 ===
+
=== Mailing lists that announcement went to ===
  
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* Hold a mini-hackathon in conjunction with BOSC.  Kam has the action item of polling the project leaders/teams to see if people will come forward to organize.  Some ideas for the hackathon:
+
==== 3/1/10 ====
−
** Next-gen sequencing
 
−
** Organizing bugs/tasks so that new beginners can start contributing to the project easily; working on some of those bugs/tasks.
 
−
** Something like the [http://www.fruitfly.org/GASP1/ Genome Annotation Assessment Project (GASP)] contest.
 
−
* Reach out to the [http://teachingopensource.org/index.php/Main_Page Teaching Open Source] organization to invite them to participate in some fashion.
 
  
−
=== From Steffen Moeller ===
+
* bosc@open-bio.org
 +
* members@open-bio.org
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* bosc-announce@open-bio.org
 +
* e-mail to ISCB student council through their web site
  
−
* Organization of a LiveCD; Debian download
+
-->

Latest revision as of 19:17, 9 July 2010

This page is being used for planning purposes. For official information, please see the BOSC 2010 Main Page.

Suggestion for next year's Call for Abstracts

Important Dates

NOTE: Dates in BOLD are determined by ISMB. Dates in italics are "penciled" in for planning purposes.

  • December 1, 2009: BOSC Special Interest Group Letter of Intent submitted to the ISMB SIG committee.
  • December 18, 2009: SIG Acceptance Notification. SIG has been accepted by ISMB as of 12/19/09
  • January 18, 2010: Instance of OCS set up and tested
  • February 26, 2010: Information supplied to ISMB for posting on ISMB web site
  • March 9, 2010: ISMB and BOSC registration opens
  • March 12, 2010: SIG Preliminary Program Due
  • April 15, 2010: Abstract deadline
  • April 15-30, 2010: Review period
  • April 23, 2010: SIG Program (preliminary) Available on Web
  • April 30-May 4: Resolution of conflicting reviews, decisions made
  • May 5, 2010: Notification of accepted abstracts
  • May 21, 2010: SIG Complete Program on Web
  • May 28, 2010: Early Registration Discount Cut-off Date
  • June 9, 2010: Handout Materials Due
  • July 7-8, 2010: Codefest 2010
  • July 9-10, 2010: BOSC 2010!
  • August 15, 2010: Manscript deadline for BOSC Proceedings in BMC Bioinformatics

Suggestions for Dinner Locations for the Friday, July 9 Board Meeting

These suggestions came from Brad Chapman:

  • Legal Sea Foods
    • Standard Boston seafood
    • Ste 103, 800 Boylston Street, Boston, MA 02199-8046
  • Charley's
    • American food; a nice Boston only place
  • Solas
    • Irish Pub Food
  • Pizza Pie-er
  • Food court in Prudential center




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