BOSC/Prepare for Vienna

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This page has been set up to provide a forum for discussion regarding the planning of BOSC 2007.

BOSC Mandate:

  1. provide developers with a forum for displaying the results of their development efforts to the wider research community;
  2. provide a focused environment for developers and users to interact and share ideas about software development, and practical techniques in bioinformatics;
  3. Inform the Research Community of important developments occuring within the Open Source Bioinformatics Developer community.

To this end, the BOSC conference must endeavor to meet these goals using the 16 hours of time that we are alloted during the two day ISMB SIG.

Comments/questions to consider:

  1. How do we facilitate the integration of disperate communities, or at least avoid excessive fragmentation. Suppose we create separate sessions for, say, Project Updates, and Emerging Informatics. What is going to prevent the developers from choosing to skip the Emerging Informatics session because they dont get anything out of it? Isn't one goal of BOSC to provide a forum for the discussion of new areas where Bioinformatics Infrastructure, especially Open Source Infrastructure, is needed? Remember that it is perfectly acceptable for people to wander from SIG to SIG with the price of their admission. They are not a captive audience.
  2. In relation to the above, how do we prevent one community from completely taking over the conference for their own purposes?
  3. How do we ensure that BOSC stays relevant to the wider ISMB-SIG audience? Is this important?

requirements and deadlines

  • Friday Dec. 15th. Submit Proposal for BOSC to ISCB Organizing Committee
  • Proposal Requirements
  •  ??? Some time in Dec. call for community feedback if we want input for categories/speakers to create/invite
  •  ??? Early January. Announce and Call for Papers??? BOSC 2007
  •  ??? Secondary Call???
  •  ??? Submission due date
  •  ??? A few days before June 1(early reg deadline) Announce Accepted Speakers
  • July 19,20 BOSC 2007


  1. Create separate sessions for different categories of talks. These should include, but not be limited to, a section for project updates by the developers of various projects. Define better requirements for acceptance of submission to each of the talk sessions, and communicate these requirements in the call for speakers.
  2. Shorten the talk times, to allow more time for discussion and questions.
  3. Expand on the idea of the keynote speaker. Create a special session for invited speakers. Call for greater involvement from the Open Source Developer community to decide which areas to concentrate on, and which experts to invite.
  4. Organize a forum for informal, relaxed discussion and socializing among BOSC attendees, such as a dinner or visit to a local pub after the days activities.
  5. Organize a forum for inter-SIG collaboration. Possibly create a slot to allow someone from the other SIGs to present needs, ideas to the Open Source Community, while also supporting the export of our own ideas to their SIGs.
  6. Create A Developer Challenge Forum. The year before BOSC (possibly at the end of each BOSC), teams of developers would be called on to submit a proposal for the development of a significant software product. Each team would be given a wiki on the upcoming BOSC 2XXX wiki site where they would communicate significant problems, resolutions, and achievements. At BOSC, there could be a session where these teams present the results of their work. If we had outside funding, we might be able to award travel fellowships to the team voted to have done the best work by the BOSC community, but we might need other criteria to be met before they could be entered into the competition?
  7. Do more targeted invitations to people who would give interesting talks. Hilmar pointed out the zebrafish project does usability testing including videotaping people using their system. I would be interested in knowing more about that.

Thoughts from Andrew

This is something I wrote up for the board list on a thread related to this topic. I've extracted the part where I talk about what I want to see in a conference.

I want something very hands on.

"hacker sessions" in old-skool parlance. The current phrase is "bar camp". See http://en.wikipedia.org/wiki/BarCamp and http://barcamp.org/ .

People don't just show up and give talks or demos. They also come to code. For examples mostly based on this year's abstracts, people might write new services for BioMOBY and Taverna, try out ZMap and provide feedback, use some of the BioPostgres extensions, or learn a bit of Ruby through bioruby. BOSC is open source so we have the advantage that anyone can install the software on their laptops.

This means some preparation beforehand, like the "Ridiculously Easy MOBY Service Creation" document at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/deployingServices.html

I don't like training seminars though.

A popular event I've seen elsewhere is a "bake off" as a way to compare/contrast two technologies. To me the most famous of these was "the Great CHI'97 Browse-Off" was reproduced in part at BayCHI in http://www.baychi.org/calendar/19970812/

One topic: "using your web framework of choice, make a blah" where blah can be "biosql browser" or "BLAST job manager" or ...

Another: load the same data set into different tools (eg, annotation data in Apollo, GBrowse, etc) and evaluate some common use cases, a la the browse off.

I want discussion about newer technology

Some of the hot topics over the last couple of years: P2P, tagging and folksonomies, AJAX, Ruby on Rails, Web 2.0. How might these affect bioinformatics? Collaborative tagging of GenBank records? What about using off-the-shelf P2P libraries for collaborative curation? Dojo-style widget sets for highly-interactive browser-based sequence display? Setting up RSS/Atom feeds for job process notification?

The current BOSC schedule is derived from a scientific program where people show results. By its nature it won't include wild ideas which may be the seeds of the next generation of software.

I want more emphasis on software development

I mean this as something stronger than "programming" but not to the point of "software engineering" (I don't think the field is mature enough yet for there to be "engineering.")

I think bioinformatics - and chemical informatics and structural biology and molecular modeling - are years behind the times in how to write software. Here are some things to think about:

  • how many bioinformatics GUIs support undo/redo? How does one implement such a system?
  • how many applications had any usability/human-centered design/user testing as an explicit part of the development process?
  • do any of the projects have a buildbot system continuously checking that the code in version control works, along with enough tests to make that check meaningful?
  • what do the web-based projects used for automated testing of their servers?
  • does anyone do fuzz testing? Security analysis? What about a "break my web app" session where us black-hat wannabes find flaws and exploits in others' servers?

That's not saying commercial non-bioinformatics software do these. I'm saying that bioinformatics software, and the culture of writing bioinformatics software, should stretch and include good modern development practices and techniques.

But this has nothing to do with science and nearly every software developer in this field has a science background so regards these topics as having less importance or uninteresting, assuming any knowledge at all. So says my experience.

That lack of interest, btw, is part of a general frustration I have with scientific software development. Good software is often seen as second to good science, when it should be an essential part of doing good science. I've found many of the talks at BOSC pretty boring because they only cover programming. I'm very good at programming and don't need a 20 minute lecture for each topic.

Tangentially, what about a round-table discussion somewhere for people to hear different viewpoints on a set of topics?


If a future BOSC was arranged along the above lines then I would be very excited to go. I know of almost nothing like it in the bio/chem software fields. The closest would be sprints and hackathons, but this isn't either. It's more like an informally structured educational environment in which to learn about about the state-of-the-art for software in and outside of bioinformatics.

Doing this would almost totally alter the current BOSC format. Such a change may be too much for next year, but perhaps chaning one day would work. The first day is my preference.

Would people go for it? I don't know. I would like to think so.

Darin Comments

Initial Thoughts

I think that Andrew's thoughts point out the divergence in 'needs' between the typical BOSC attendee (currently a subset of the typical ISMB attendee), and the typical OBF programmer. I, too, would like to see many more of his ideas in BOSC. However, finding the right balance between the Traditional (presentation-of-results/project updates) and the Unconference which will maitain a base of ISMB subset attendees, while drawing back in the OBF developers will be tricky. It is pretty clear that BOSC doesnt survive serving only one of these two populations.

Unconferences require more infrastructure than what ISMB currently provides (A/V + screens). We havent even been granted free WIFI yet in the conference rooms (I have asked for this repeatedly). This year it was there in principal, but the signal was too weak to use. We would need to set up our own wifi on the wire that they provide us. Not a huge obstacle, but something to think about.

Bar Camps

I really like the idea of the Bar Camp. We could devote all, or part of the second day to this, and keep the first day a little more traditional ( I know Andrew wanted the first day to be changed). We could then allow presenters to generate enthusiasm during their presentations for a barcamp sessions the next day. We have seen this in its infancy in many occasions where people did the main talk, and a demo during the lightning talk sessions.

Bake Offs

This might be easier to generate by inviting key developers of competing projects (EnsEMBL vs USCD, bioPerl vs bioPython, etc) to demonstrate a sophisticated problem that their system solves that the other system does not, or some other way of playing key stakeholders off against each other for our mutual enjoyment/education. We could call for nominations from the OBF developer community to decide who to invite.

New Technologies

Currently, any conference is going to be generated by the miliue of its community. The OBF developer community currently doesnt have any examples of these technologies (although I, myself, have thought about how to use a del.icio.us framework for annotation). You could create a session where people are invited to talk about potential uses of one or more of these technologies. However, these often lead to the same criticism that is generated by those trying to get the OBF developer community to set its sights on new areas where informatics infrastructure is weak or nonexistant. Basically, you get the 'what did that talk do for me' mentality from both communities.

Software Engineering Best Practices

This could be a separate session. It would probably be best to invite the OBF developer community to nominate, and vote on one or two projects to be invited to talk about their software development practices. The 'Break My XXX' would probably be best as a BarCamp session.

Links of Interest

Example Schedule

ISMB 2007 Deadlines

Schedule Ideas

1st Day:
8:35 Call To Order, Announcements while people mill in
9:00 Keynote: Carole Goble On Significant Challenges to Developing Bioinformtics Software
10:00 Currently Intractable Problems In Bioiformatics: Five to ten minute talks presenting a hard area of computer science or bioinformatics relevant to the community and as yet not thoroughly solved. Talks would be of the form of a use case which currently cannot be satisfied with readily available toolkits and a summary of the problem.
10:30 coffee
10:50 More Currently Intractable Problems
11:50 Break For Lunch
1:15 Talks on developments or ideas for using New Informatics Technologies to support Biological Research (10 minute talks on folksonomies, web 2.0, Rest, SOAP, etc.)
2:45 Project Update Section: Lead Bio* Developers or their Designates are invited to present updates of major developments on their projects
3:30 coffee
3:50 OBF CD Session: Session laying the groundwork for the creation and management of an single CD of OBF applications, libraries for easy installation. The goal is to create a CD to distribute for the next BOSC. Something like software for starving students, www.softwarefor.org.
4:10 Wifi Workshops: We make the wifi available (if it isnt already, e.g. one of us needs to bring a wifi router, I'll bring mine if I have to), and open it up to people to present interactive demos, network with users, etc in small, BOF-like subgroups within the hall. This would be a wifi enhanced BOF for people to use to demo their system, or interact with users.
5:30 Dismiss for Dinner (to be announced)

2nd Day:
8:35 Call To Order, Announcements while people mill in
8:45 Keynote: Insert important Bioinformatics Person Here...????
9:30 Typical BOSC Talks, e.g. abstract submission, review, and acceptance before the conference
10:30 coffee
10:50 More Typical Talks
12:00 Lunch
1:15 Intro Software Design session: Get someone to talk about Software Design (Maybe Andrew could give the talk he always wanted to hear :) )
1:40 Invite people to present on Design Practices in their Open Source Project, or an Open Source Project they have used and were happy with (we dont want gripe sessions, do we)?
3:30 coffee
4:00 Ideas for Solving Currently Intractable Problems in Bioinformatics: Here is the chance for developers to present ideas for using current technologies, or developing new technologies, to solve issues presented in the Keynote Session on Day 1. Those presenting problems in the first day are required to summarize ideas revolving around their submitted problem
5:30 Dismiss

BOSC 2007

The Bosc Pair

The 8th annual Bioinformatics Open Source Conference (BOSC 2007) will take place in Vienna, Austria, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 15th International Conference on Intelligent Systems for Molecular Biology.

This year is shaping up to be very exciting. We have changed our format to add room for more development oriented talks and discussions, in an effort to fully utilize the conference to stimulate new development efforts in all areas of Open Source Bioinformatics Software development. The primary focus of the conference revolves around the delineation of areas of IT or Bioinformatics which are not well serviced by existing toolkits. The Keynote session will be headed up by Carol Goble, of Manchester University. Speakers in this session will be invited to present detailed descriptions of an 'Intractible Problem In Bioinformatics'. The last session of the conference has been setup for speakers to present ideas for solving any of the problems presented in the keynote session. Other sessions will be set up to allow presentations on new Software Design Patterns, Software Engineering ideas, and more traditional BOSC talks (see below for details and deadlines). There will be a session of talks by developers in the major Bio* projects giving overviews of recent developments in their projects. Finally, the Birds of a Feather sessions will be enhanced with wifi to create 'Wifi Workshops'. All in all, this should be a great conference.

Important Dates

June 1 Early Registration Discount Cutoff Date
July 19,20 BOSC 2007

BOSC Eventful Group : This site provides an ICAL feed which will include all deadlines associated with BOSC 2007
BOSC Announcement Blog : This Blog will contain all Important BOSC announcements. You can include it in any RSS Reader.

Keynote Speakers

Carol Goble


SIG Rate (registering for ISMB as well):

Corporate : TBA
Academic : TBA
Student : TBA


Sig-only Rate (not registering for ISMB):

Corporate : TBA
Academic : TBA
Student : TBA


Notes on Submissions

The Open Bioinformatics Foundation is dedicated to promoting the practice and philosophy of Open Source Software development within the 
Biological Research Community. To promote this mission, the organizing committee will favor submissions for projects that apply a recognized 
Open Source License, or adhere to the general Open Source Philosophy.

See the following websites for further details:

All submissions should be emailed to the BOSC mailing list at bosc@open-bio.org.

Call for Speakers and Abstracts

This year BOSC is requesting submissions for a variety of different venues. All submissions should be recieved by Monday, May 14th to be considered for inclusion:

  1. Currently Intractable Problems In Bioinformatics: This session will follow the Keynote, and will be devoted to the delineation of areas of Bioinformatics or Information Technology which are currently not solved or serviced by the current suite of Bioinformatics Software in existence. Speakers are invited to submit a detailed use case which currently cannot be satisfied with readily available toolkits and a summary of the problem sufficient to engage developers into discussions on how to solve the problem. The last venue of day two will be devoted to allow attendees to present ideas for solving these problems. Talks for both venues will be 5 minutes long, with a few minutes for questions from the audience. All problems, and ideas for solution will be published on the BOSC web site.
  2. New Informatics Technologies in Bioinformatics: This venue is devoted to the development of systems which make use of newer Information Technology practices, such as WebServices (SOAP or REST), Folksonomies/Tagging, RSS, Social Networking, and other design patterns collectively described as web 2.0 . Talks will be 10 minutes long, with a few minutes for questions from the audience. All abstracts will be published on the BOSC website.
  3. Open Source Software Presentations: This venue will allow speakers to present talks on their use, development, or philosophy of open source software in bioinformatics to the BOSC attendees. The committee will select several submitted abstracts for 10-minute talks, with a few minutes for questions afterward. Accepted abstracts will be published on the BOSC web site.
  4. Discussions of Software Design and Engineering: This venue will allow speakers to to present Design Practices in their Open Source Project, or an Open Source Project they have used and were happy with, or present ideas on the practice of Software Design which would benifit the Open Source Developer Community. Talks will be 5 minutes long, with a few minutes for questions afterward. Accepted abstracts will be published on the BOSC web site.

Call For Wifi Workshops

This year, the BOSC committee will enhance the infrastructure for what were currently labeled Birds of a Feather sessions with a wireless router. This will allow groups to interact with software or websites much more while they are discussing their favorite projects. The BOSC committee will accept ideas for these up to the last day of the conference, on a first come-first-served basis until no more space is left in the conference room.

Lets Create an OBF Software CD!

This year we will be devoting a small BOSC session to the task of laying the groundwork for the creation and management of a single CD of OBF applications, libraries for easy installation. The goal is to start the process create a CD to distribute for the next BOSC.

Call for Volunteers

The BOSC Organizing Committee would like to invite attendees to take a more active role in making BOSC a successful conference by volunteering your services. The following opportunities for assistance exist:

  • Set up, Clean up: Volunteers are needed to help set up and clean up any aspects of the conference room that are not done by the conference organizers.
  • Historian/Photographers: Volunteers are needed to help record aspects about BOSC 2007 for future reference. Possibilities include blogging the conference, writing up a review article for the ISCB, etc.. The Photographer will take digital photographs of all speakers, recording each speakers name with their image name for easy inclusion on the BOSC summary website after the conference.