Minutes recorded here: 2005-11-08 Conference Call Minutes
Carl, Mike, Ken, Ranjani, Gary, Emek, Alan, Jonathan, Elgar, Mustafa, Joanne, Jeremy
Draft Agenda (please comment)
Development status update
BioPAX Level 2 Release candidate status (KEQ, DELTA-G status, adoption/nonadoption)
No strong opinion voiced on the call. But Mike made a good point that we should finish it for Level 2 because if Level 3 breaks backwards compatibility, then people can still use Level 2 for work covered by those use cases. It would be useful to know how much data is out there? Consult Peter Karp - he should be able to make this decision, since he likely has the strongest opinion about this. Gary will e-mail Peter and cc Alan. Alan also raised the question about whether keq is only a 5-tuple or any number of tuples.
Adoption/non-adoption of Level 2. Level 3 may not be backwards compatible with Level 2 (e.g. the way we might find a better way of dealing with open controlled vocabularies and also states will be added). We would like to get past Level 2 and release it, but how should we deal with this. Level 2 is fine for a number of use cases and we should write a note to users (included in the documentation) what these are and which use cases are not covered. Gary and Alan + others interested will draft this in Japan.
Report on BioPAX Level 1 validator
Ranjani R from OHSU (and Vincent Y in Shannon McWeeney's group) has developed a Level 1 validator in Java that checks best practices from BioPAX Level 1 that are not captured by OWL tools and will not be deteceted by an OWL validator. It is at a release stage. They will be happy to release it. They are starting on Level 2. This will be moved forward more when Level 2 is released. Alan asked about the Cyc databases - there was about a 1% error rate and Ranjani will post some more information on this after discussions with Shannon.
Future meetings
Report on organization of technical workshop for JapanF2Fmeeting: Nov 2005
Ken - workshop starts on Wed. hackathon earlier. 2 day workshop starting from Nov.16th. Symposium will happen on Friday with interpreters. Ken received a report on Monday - about 111 Japan registrants + 30 workshop participants - will probably have about 150 participants for the symposium. Hackathon meals - pizza + beverage. Lunch boxes on Nov.16-17. Dinner on Nov.17. Symposium lunch for workshop participants. + Coffee service for all days from Nov.15-18. We will have 2 projectors + whiteboards + DV cam + recorder
Alan - technical workshop schedule is now available. Will be fairly quickly paced - lots of 10 minute talks (required for funding + desired so that we know what people are working on). Kitano and Hucka sessions on second afternoon.
Unfortunately, Mustafa can't make it due to visa issues, but suggests that we have teleconference ability (e.g. AccessGrid). Ken will check on this.
Hackathon - It would be useful for everyone to know what people are working on. People's expertise should also be known. We can have a discussion session up front to cover this. Ask people about what tools they have knowledge on, etc.
We need to set up a wiki page for the hackathon with requirements. What people need to bring. Is there a common file server? Wired connections are required (no wireless) - every desk has ethernet.
TODO: send mail to inform speakers at workshop. Gary will draft and send to Ken, Alan and Joanne.
2nd workshop day - workshop ends at 5:30 - speaker of the first session should check their equipment in the conference room after the workshop ends.
On Day 18 - we need session chairs for the Symposium - we will finalize on Monday next week in Japan.
Grant/budget reporting action items
Decided to discuss this with Chris in Japan. Gary will inform Chris about this