Catering at BOSC CodeFest 2014

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc.

Thanks to this sponsorship, this year the organisers will able to include catering for the participants – I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

If you are wondering what happens exactly at a CodeFest, I suggest Brad’s blog post from the BOSC Codefest 2013, or Möller et al (2013). Basically these meeting are a chance for developers of open source bioinformatics (not just the OBF’s Bio* projects) to get together and work on common interests. Things work best with some pre-meeting planning on the usual project development mailing lists or IRC, but are also a great way to meet other scientists and developers in person with more time to chat than during a conference coffee break.

Please note that while there is no registration fee for the BOSC Codefest 2014, please do fill in the registration form to help with the planning/catering.

We’re hoping all the Codefest participants will stay for the BOSC meeting itself, which requires formal paid registration as one of the big ISCB 2014 conference’s SIG satellite meetings. Note that we’re offering a BOSC fee waiver for student speakers, this year. If you are going to BOSC, please remember to submit your BOSC abstracts this week!

Peter

Posted in Blogroll, BOSC/ISMB, Code, Community, Development, General, OBF, OBF Projects | Tagged , , , , , , , , , | 4 Comments

Free registration to student presenters at BOSC 2014

To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we’re waiving the registration fee for accepted student presenters. When you submit your abstract (BOSC abstract call open until 4th April), you must tick the student box:

Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.

Please note that because BOSC registration is via the ISCB as one of the ISCM SIG meetings, eligible students must contact us before filling in their ISCB registration to ensure the BOSC SIG fee is waived.

Furthermore, as in previous years, BOSC Student Travel Awards sponsored by Eagle Genomics will be awarded to the top student presentations to help with your travel and accommodation costs.

 

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , | 15 Comments

OBF GSoC 2014: Call for student applications

Google Summer of Code 2014Are you a university student and interested in spending the summer developing open-source bioinformatics software?

(Good! Keep reading.)

On Monday, March 10, Google Summer of Code 2014 (GSoC) will begin accepting student applications to work with mentoring organizations like OBF.

Here are the steps for you to prepare an application and apply for GSOC 2014 with OBF:

  1. Check the OBF ideas page for potential projects you’d like to work on, and identify one or a few that you’re most interested in doing.
  2. Read our guide for prospective GSoC students on the OBF wiki. Also see Google’s GSoC FAQ and GSoC student guide, if you’re with us so far.
  3. Introduce yourself on the OBF GSoC mailing list. Tell us which project(s) you like, any modifications to them you’d like to make, or propose your own idea.
  4. Once you’ve settled on a project or two and contacted your potential mentors, begin preparing a detailed project timeline for the summer. This timeline should cover each week of the summer, as far as you can plan it, describing the week’s specific goals, coding tasks, anticipated problems and open questions. (Example 1, Example 2)
  5. Submit your application to Google early. You can keep revising it on the Melange website until the deadline on March 21, but once you’ve submitted your basic information we can begin giving you feedback and suggestions to improve your application. In addition to your weekly timeline, you can link to examples of code you’ve written (e.g. on GitHub); a small contribution of code (e.g. a bug fix) to the project you’re applying to work with would really impress us.

Feel free to contact us on the mailing list or Google Plus if you have any questions.

Posted in OBF | 5 Comments

BOSC 2014 call for abstracts

Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.

[BOSC Logo]

Important Dates:

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.

BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

We invite you to submit one-page abstracts for talks and posters. This year’s session topics are:

[Eagle Genomics Logo]
  • Open Science and Reproducible Research
  • Software Interoperability
  • Genome-scale Data and Beyond
  • Visualization
  • Translational Bioinformatics
  • Bioinformatics Open Source Libraries and Projects
GigaScience Journal Logo

Once again we thank Eagle Genomics for sponsoring the BOSC Student Travel Awards, and welcome the open access journal GigaScience as a new sponsor for BOSC 2014.

BOSC 2014 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , | 24 Comments

OBF accepted as a mentoring organization for Google Summer of Code 2014

Open Bio is officially a mentoring organization for Google Summer of Code 2014!
See Google’s official announcement for more details on what this means in general.

What’s next? Google’s GSoC timeline lays out what we need to do as a mentoring organization during the coming weeks. Students can apply March 10–21 through the official GSoC 2014 website to work with OBF. Up to that point, we’ll be reaching out to potential students and mentors, and contining to develop potential project ideas. If you’d like to get involved, introduce yourself on our Google Plus community or on the mailing lists.

Posted in Code, Community, Development, Google Summer of Code, OBF | 4 Comments

OBF applies for Google Summer of Code 2014

On Friday, OBF applied to be a mentoring organization for Google Summer of Code 2014. The core of our application to Google is our list of project ideas and our team of mentors supporting them. (We also have a separate page for general information about GSoC and OBF’s involvement.) As another way to interact with potential GSoC students, we’ve created a Google Plus page for OBF and a G+ community for OBF’s GSoC activities.

Highlights of this year’s Ideas list:

  • All of the Bio* projects (except BioSQL and EMBOSS) are represented. BioPerl contributed the greatest number of ideas.
  • The BioJava team focused on a Java implementation of the Structural Biology Markup Language called JSBML. The JSBML developers created a SBML-specific list of GSoC ideas, which we’ve included under the OBF umbrella. There is also a great opportunity here to support SBML in other languages and Bio* projects through the JVM.
  • We also have a category for cross-language project ideas, i.e. those involving two or more programming languages or Bio* project communities.

But for now we have a lull, until Feb. 24 when Google announces the accepted mentoring organizations. (Fingers crossed!)

Thanks to everyone who helped us pull together this application. We’re eager to hear your thoughts on how this process went and how we can keep adapting for future GSoCs.

Posted in Code, Community, Development, Google Summer of Code, OBF | 8 Comments

Call for Ideas for OBF’s 2014 Google Summer of Code

Google Summer of Code is on again for 2014, and OBF is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors.

Since OBF is an umbrella organization covering several member projects, most of these GSoC ideas will likely be associated with a specific Bio* community. For our GSoC application, and for the convenience of students, we aggregate each Bio* project’s ideas on the GSoC page of the OBF wiki, but the details of each idea are posted on the specific Bio* project’s own wiki. So, if you have an idea for a Summer of Code project, please post your idea on your Bio* project mailing list for discussion and start an outline on the corresponding wiki page. Feel free to reuse or adapt ideas from 2013 or previous years that were not taken on by a student already, if you feel the idea is still viable.

We also welcome ideas that fit with OBF’s mission but are not part of a single Bio* project, or span multiple projects — these ideas can be posted on the OBF wiki page and discussed on the OBF mailing list.

Potential students, we’re interested in your ideas, too! This is a good occasion to introduce yourself to the OBF community.  If you have an idea for something you’d particularly like to work on during GSoC 2014, please ask us on the mailing list and we’ll try to find a suitable mentor.

Here’s to another fun and productive Summer of Code!

Posted in Code, Community, Development, Google Summer of Code, OBF | 7 Comments

Call for Organization Admins for OBF’s 2014 Google Summer of Code participation

Update: The deadline for responding has been extended to January 25.

GoogleSummer_2014logo The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects in 2010, 2011, and 2012. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve.

An org admin’s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to “keep it together.” Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org’s mentors. The org admin’s responsibilities include:

  • Representing our online face to GSoC, in particular to GSoC students
  • Shepherding our mentoring organization application, and submitting it.
  • Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises.
  • Knowing GSoC rules and processes, and making sure ours are consistent with them.
  • Reminding participants of rules, and enforcing them in the event it is necessary.
  • Mediating, and sometimes arbitrating between students and mentors when needed.
  • Ensuring that GSoC timelines are met by everyone.

The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener.

If you are interested in helping us out in this role, please email us (by Jan 25, 2014) a statement at board@open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project’s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects.

We are looking forward to hearing from you!

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | 7 Comments

BOSC 2014 Keynote Speakers

Thanks to those who participated in the BOSC 2014 Keynote Competition! Our winner is Manuel Corpas, who correctly surmised Philip Bourne:

(In fact, we had already confirmed Philip Bourne as our second keynote speaker before his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to BOSC 2014!

Dr. Bourne’s keynote talk will be entitled “Biomedical Research as an Open Digital Enterprise”:

The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.

Our other keynote speaker at BOSC 2014, as already announced, will be Titus Brown, whose topic is “A History of Bioinformatics (in the Year 2039)”.

Posted in Blogroll, BOSC/ISMB, Community, General, OBF | Tagged , , , , , , | Leave a comment

BioPerl release 1.6.923

The latest BioPerl release (v1.6.923) is now available on CPAN. This is a point release to address a few bugs, as well as push out the recent code updates that Francisco Ossandón has made to improve Windows support and improve Bio::Location (among other bits and pieces).

Contributing to the release:

  • Francisco Ossandón
  • Brian Osborne
  • Dave Messina
  • Carnë Draug
  • Chris Fields
  • Benjamin Warren

Enjoy!

chris

Posted in BioPerl, Code, Community | 5 Comments