Minutes:2011 ConfCall


  1. Old business
  2. Action items from the 2010 meeting
  3. New business
    1. BOSC
      • BOSC 2011 (Nomi) – held with ISMB2011 in Vienna, Austria
        • Money spent/made, attendee number, any other feedback
      • BOSC 2012 – with ISMB 2012 in Long Beach, CA
        • 2012 Organizing Committee chair
        • Plans for the conference
    2. Google Summer of Code
      • Org admin’s summary report (Rob Buels)
    3. Treasurer’s 2011 report: File:2011-OBF-Treasurers-Report v1.pdf (Chris Dagdigian)
    4. BoD membership and succession.
      • Nominations: Peter Cock
      • Plan to elect new BoD members and rotate officers.
    5. Additional topics proposed by community
      • How to become an affiliate project? (Alan R Williams)
      • BioSmalltalk as an OBF member project? (Hernán Morales)
      • CloudBiolinux as an OBF member project? (Pjotr Prins, Brad Chapman)
      • OBF Europe and Asia (Steffen Möller), branch organisations for tax free donations from the public or industry. Possibly in conjunction with Debian’s Software in the Public Interest setup.
      • OBF holding copyright as a community organization using the Apache model for licensing (Jean Peccoud)

Minutes from the meeting

Venue: held by conference call, scheduled for Nov 8, 2011, 11am EST (16:00 UTC).


  • Directors: Jason Stajich, Chris Dagdigian (until 12pm), Hilmar Lapp, Nomi Harris
  • Guests: Neil Bahroos, Pjotr Prins, Brad Chapman, Alan Williams, Peter Rice, Neil Bahroos, Steffen Möller, Peter Cock (call report shows about 12 people who called in for significant amounts of time).


Hilmar calls meeting to order at 11.08am EST.

Approval of old business:

  • Approval of 2010 BoD meeting minutes. Hilmar moves to approve, Nomi, Jason, and Chris second. 2010 BoD minutes approved by unanimous consent.
  • 2010 Financial Report still not ready for approval, because the missing 2010 BOSC travel award still has not been added. Postponed for a second 2011, or the 2012 BoD meeting.

2010 action items

  • Status of 2010 BOSC keynote speaker reimbursements unclear. Hilmar to follow up with Kam.
  • BOSC proceedings: Didn’t do a survey but talked to several people. Resolution was that the effort wasn’t worth making, and consequently proceedings weren’t planned for 2011. Can be revisited for 2012, though.
  • Codefest: Did a brief verbal announcement about what happened at the 2011 BOSC. Should expand this a bit in 2012.
  • Documentation for and status of 2010 BOSC travel fellowships: ChrisD will investigate and follow up with Kam to make sure all 3 awards have been paid and are accounted for in the financial report.
  • Board membership recruitment hasn’t been but should be pursued among member projects.
  • Biopython.org domain ownership transfer: in the process of being completed, control being transfered to ChrisD, which is the same as for the other Bio* domain names. Complete for admin and technical contacts, not yet for billing contacts.
  • Hosting services plan: happened in a mostly organic manner on root-l. But our server hardware is very old and can fail any time. We imminently need a plan forward so we can determine whether we migrate to all-cloud or continue to host some services on our own hardware. This is particularly urgent as our web presence is at risk.
  • BOSC 2010 mailing list: turned out not to be necessary.
  • GMOD getting more involved with BOSC: there has been contact with Scott Cain and encouragement to submit an abstract. There needs to be more reaching out to member and affiliated projects to participate in the conference.

BOSC 2011

  • Very well attended: 115 attendees, which marks the best attended BOSC since 2004; also received a record number of abstracts (78), most of which were of pretty high quality. We were able to award talk slots only to 35 submissions.
  • Had a poster session, to which abstracts were admitted that did not get a talk slot. Oral presenters were also given the option to present a poster in addition to their talk, and more than half of them accepted.
  • Preliminary balance from the conference is a surplus is about $6,000. Final balance sheet still due from Stephen Leard. The surplus will be added to our ISMB escrow account, which currently (before the BOSC 2011 balance) stands at about $15,000.
  • The 2011 keynote speakers had a significant fractions of their expenses paid by other sources, which helped with the surplus.
  • Feedback overall very positive, except for some things that we have little control over (such as catering running out of coffee). These were relayed back to ISMB. Feedback on the poster session was quite positive, and we plan to repeat it in 2012. The poster session does not incur any additional expenses, as it is already included in ISMB’s SIG package.
  • Program received very good feedback. Some questions arose about people presenting almost the same talk at BOSC and subsequently at ISMB. However, the topics were highly relevant and appropriate for BOSC, so excluding them if they also present at ISMB does not seem a good option. In the future encourage them to choose different emphases for both talks so that they are complementary rather than redundant. Some of the Bio* projects felt ignored. This will be addressed for 2012 by having a track devoted to member project updates, and we will personally approach project representatives and encourage them to present updates at BOSC 2012.
  • Can OBF subsidize representatives from OBF member projects to attend BOSC if they couldn’t otherwise afford to come?
    • This could provide an opportunity to leverage the funds sitting in the otherwise locked up ISCB escrow account for the good of the community.
    • Nonetheless, would need to make sure that the process is well-defined, fair, and makes the best use of the escrow account. Things to consider include:
      • For subsidizing people, it would be simpler to absorb their registration fee rather than reimburse them for travel expenses.
      • There are other categories of people deserving of or benefitting from support than OBF member project affiliates, including students (we already offer a few student travel fellowships, but there are other students who would like to attend BOSC), BOSC organizing committee members, and “invited speakers” (in addition to keynote speakers).
  • Hilmar moves for the Board to express a vote of gratitude and appreciation for Nomi’s service. Jason and ChrisD second, approved by unanimous consent.

BOSC 2012

  • Nomi volunteered to serve again and is the sole chair. (Peter Rice will be changing jobs, but will maintain a supporting role.)
  • Organizing committee will have two new members, Jan Aerts and Chris Fields. Also, 2 (Darin London and Ron Taylor) of the 2011 committee are rotating off due to other obligations, but remain committed to help out with reviewing abstracts.
  • ISMB SIGs have to re-apply every 3 years, which for us was this year. Our application (put together by Nomi) has just been accepted.
    • One of the recommendations was to interface (or even merge) with the (also accepted) new Software Interoperability SIG (led by Galaxy and GenePattern PIs). If we do this, it needs to happen in a way that doesn’t take much talk time away, so we don’t further constrain the already very limited time available for awarding slots to submissions.
    • Another point raised in the review comments is that unlike 12 years ago when BOSC started, the value of open source projects is widely recognized today, and this should be considered when thinking about where BOSC should concentrate in the future.
  • Ongoing questions for the program include whether or not to schedule a 3rd keynote, in an effort to stem attendee attrition in the afternoon of the second day. One keynote speaker (Suzi Lewis) is already confirmed, conversation with a second one to nail down a suitable talk topic are ongoing.
  • We are keeping some of the popular session topics from last year (e.g., Cloud Computing), retiring some, and introducing some new ones, such as Translational Bioinformatics. We will make an effort to solicit talks for these new sessions by contacting researchers in those areas and encouraging them to submit abstracts.
  • Other plans for BOSC 2012 include a session dedicated to affiliated project updates (Bio*, etc.); a panel discussion, tentatively on “Interfacing with Industry”; an “audience favorite” talk award; and an explicit time slot for the CodeFest organizers to present a summary.
  • Nomi is asking everyone who has ideas and suggestions to come forward and contact either her or the committee through the BOSC mailing list.
  • Hilmar moves for the Board to give a vote of confidence and appreciation for her service to Nomi. Jason and ChrisD second. Motion approved by unanimous consent.

Google Summer of Code

  • Rob Buels, our organization admin for 2011, was not on the call to report.
  • Hilmar (who served as backup admin) reports as a heads-up that we had 6 students, all of whom seem to have been successful in their projects and passed. We also sent two mentors (Andreas Prlic – Biojava, Rob Buels – BioPerl, GMOD) to the Google Summer of Code Mentor Summit, which took place at Google’s headquarters in Mountain View, CA, in October.
  • Participation in the program, aside from the main benefits for the students, the participating affiliate projects, and the mentors, yielded a $3,000 payment ($500 per student mentored) from Google to the mentoring organization, i.e., O|B|F. This has been invoiced, and receiving the funds is expected before year end.
  • The mentoring organization payment for our 2010 participation (also $3,000) has been forfeited because we failed to invoice in a timely manner. This is true also for reimbursement for the flight costs of our 2010 Mentor Summit delegates (who were also Andreas and Rob), and hence OBF had to absorb those costs (see financial report).
  • See attached written report from Rob Buels for further details.

Additional community-proposed topics:

  • How to become an affiliate project? What is the process one has to go through, and what are the criteria applied? (Alan R Williams)
    • There hasn’t been an official process. Will also depend on what resources are being needed.
    • Historically, (most of) our member projects came first, and then the need for the OBF umbrella organization arose to better run and fund the IT infrastructure for collaborative software development. However, meanwhile most or all of the IT infrastructure can be found at 3rd party service providers, often for free, and at sophisticated and robust levels of quality and service.
    • Our aim isn’t to compete with organizations such as Bioinformatics.org where open-source projects can enlist for infrastructure. So what are the specific advantages that being an OBF member or affiliate project would provide that can’t be easily had from these other organizations?
    • Most notable advantage would be being part of a community of bioinformatics projects. It’s not the listing, but a community in which projects work together, for example in activities such as the Codefest.
    • OBF affiliation could supply the community and a stamp of expectation that the project will stick around. In this sense, some projects don’t have critical mass yet to join the OBF.
    • Does it need to be the Board that decides this? Couldn’t it be the community instead? Perhaps have a committee established that makes the process reasonably efficient, and among other things votes on applications of projects to join.
      • Should still have some form of oversight, monitoring, or perhaps final approval by the BoD, though, so that decisions made and their consequences don’t overwhelm the means of the OBF.
      • Brad, Peter, Pjotr, and Neil will draft, with community and membership input, a proposal on what this process could look like. Hilmar will for now serve as the Board liaison in this group, and weigh in accordingly.
  • CloudBioLinux as an OBF member project? (Pjotr)
    • Deployment is a difficult part of software lifecycle. Idea is that CloudBioLinux simplifies and standardizes this for all Bio* (or OBF) member projects, and thus works with all of them. OBF can help with preventing duplication and maintaining the community and project ties.
    • Future status as an OBF member project will be subject to the to-be-drafted process (see above).
  • OBF Europe and Asia (Steffen Möller)
    • Idea is to create separate, local branches for the OBF organization.
    • One immediate opportunity that this could provide is better ability to raise funds in local currency. Also, acquiring and maintaining tax-exempt status is much cheaper in Germany, and therefore depending on local laws there may be very little reason for why donations can’t be tax-deductible.
    • Could also serve as a vehicle to organize local meetings when ISMB (and therefore BOSC) are in the US.
    • Acquiring and maintaining tax-exempt 501(c)3 status in the US is expensive, though. However, as has been discussed at a previous Board meeting, we can accomplish tax-deductible donations to fund most of our expenses through a fiscal sponsorship organization, such as the Software Freedom Conservancy, or Software in the Public Interest.
      • Such organizations exist, for example, in Europe (Germany, Italy, UK), too, and we could affiliate with different ones to cover different currencies and jurisdictions. Doing so need not require creating local branches.
      • Steffen will gather further information about relevant organizations and contacts in European jurisdictions.

Adjourned at 1.03pm. Board elections could not be held as planned due to loss of quorum with ChrisD leaving the call at shortly after 12pm.

Google Summer of Code 2011 Report for OBF

Prepared by Rob Buels, who served as organization administrator for the OBF.

We had 6 students this year, the same number as last year. I had hoped we might grow the program somewhat over last year’s numbers, but the number and quality of applications turned out approximately the same. However, the solicitations for student applications went out quite a bit later this year than last year. I think us having a similar applicant pool despite the late solicitations may point to there being a latent potential to grow the program next year, if I make sure to be more on top of the schedule, which I intend to do.
As for this year’s 6 students, they were quite a good group. Pasted from the OBF GSoC page, the 6 student projects were:

Justinas Vygintas Daugmaudis, Michele dos Santos da Silva (2 students), mentored by Thomas Hamelryck and Eric Talevich
Mocapy++Biopython: from data to probabilistic models of biomolecules BioPython Integration and Mocapy++ Plugin System

Chuan Hock Koh, mentored by Peter Troshin, Andreas Prlic, and Jay Vyas: Amino Acid Physico-Chemical Properties Calculation

Michał Koziarski, mentored by Raoul J.P. Bonnal and Francesco Strozzi: Represent bio-objects and related information with images

Sheena Scroggins, mentored by Robert Buels and Chris Fields: Major BioPerl reorganization

Mikael Eric Trellet, mentored by João Rodrigues and Eric Talevich: Interface analysis module for BioPython

Happily, all of the students accomplished their project objectives and were eligible for full stipend payments from Google. This is a bit better than last year, when we had one student who failed to complete the program.

I myself only have direct experience with the BioPerl project, which I also mentored, but all of the projects turned their evaluations in on time, and all of them also satisfactorily maintained frequently-updated progress report pages (which are linked from the OBF wiki).

Based on conversations I had with other organization administrators at the Google Summer of Code Mentor Summit (a GSoC unconference held a couple of weeks ago at the Google headquarters in California), the OBF is very fortunate in having a very GSoC-ready pool of project members on which to draw. That is, since most participants in OBF projects come from academia, they are already quite familiar with the process of mentoring students to complete projects, and generally need relatively little prompting to keep their students on track.This contrasts with the stories I heard from other organization administrators at the mentor summit: apparently, many other organizations have considerably more difficulties with mentors and students failing to complete projects, turning evaluations in late or failing to turn them in at all, and so forth. This makes me feel quite optimistic for the continued success of the GSoC students mentored by OBF organizations.