Attendees: Emek, Gary, Geeta, Jeremy, Dan, Alan, Ken, Ranjani, Andrea, Joanne, Jonathan
1.Development status update
DXTrackWorkplan status update (Emek/Gary): Emek will post States and Generics today. Gary has posted the Genetic Interactions proposal. Alan wanted to know who the interested groups were . Gary identified Gramene, CSHL Cell Signalling, Gary, Geeta and Ranjani. Alan wanted to know the schedule for the Gene Regulation proposal Gary said that it would be dependent on the States proposal.
Late 2005 Proposal for BioPAX Development/Discuss related tools update: ReleaseToolsProposal Dan has a proposal on the wiki based on upper ontologies and design patterns which he believes would be more productive in the future and save time spent on custom tracking. Alan added a link to the proposal and suggested that we should work on getting the proposals out for the meeting. Gary mentioned that there would be time to discuss it at the F2F.
BioPAX Validator / PAXerve interoperability (Ranjani) Currently have been working to gather requirements talking with Ethan, Emek and Gary. Emek will work on providing an API for the next level once the meeting is done.
[WWW] debugging the bug E.coli data merge project (Jeremy/Alan) ([WWW] code repository) status update DebuggingTheBugMetabolicExample200606
Jeremy talked about merging reactions and compounds from Ecocyc and Palsson's E.coli data. The group used a number of methods including manual techniques, subclass hierarchies, matching references and chemical formulae. Reactions were merged using the compounds and qualified cardinality restrictions (way of representing how many times the range of a property appears). They played around with presence/absence of hydrogen in the reaction, compartment information and subclassing reactions. Alan pointed out the example posted on the wiki. This will be presented at the CSHL meeting.
2. Governance. Gary action item to provide alternative wording for BioPAX Governance (action item from 3 calls ago). Wording is at CommunityDevelopmentProcess, and discussion at CommunityProcessDiscussion/Discussion_page. Gary has provided some alternative wording on the Discuss page.
Access control lists on wiki pages Alan would like an explicit policy defined or not use the feature till the Governance issue is resolved. Dan seconded this and Joanne agrees. Gary noted that he turned the feature on to prevent deletion of the proposal pages he is currently working on. Alan pointed out there has to be group agreement to do this and we should go through the process. Emek pointed out that it was more a technical issue and used to prevent accidental deletion of pages. Alan pointed out that it is a powerful feature and there are other methods in case something happens such as using backups, reverting etc. and insisted there needs to be a process in place. Ranjani wanted to know if an email informing the group would be considered sufficient. Alan said that he would be fine with it. Gary will not add it to any more pages. Alan has offerd to remove the access controls set up so far. Emek pointed out that this needs to be discussed in person. Gary was happy to discuss this at the F2F.
Status of [MAILTO]
![[MAILTO]](/wiki/modern/img/moin-email.png)
pax@cbio.mskcc.org email list. Alan wanted to know if this list should be retired and Gary agreed. Emek will talk with the Sys admin. Discussion: BIND patent - can it affect us or our users? Gary said that there was some discussion on the SBML list and suggested talking with Mike Hucka.
Publication Guidelines Joanne added this to the agenda. She mentioned that Gary, Chris and Mike were writing a paper and requested that it be circulated for comments. Gary said that it was one of the ISMB abstracts being resubmitted as a paper.
3. Future meetings
1.Cold Spring Harbor meeting organization report (Emek) CSHF2Fmeeting/OrganizationMeetingNotes
Budget - who is not going to use the CSHL meal plan. Geeta and Alan were not going to use it. Geeta suggested having the local organizer check to see if costs can be lowered.
Discussion: What does acceptance of a DX proposal imply. Alan has provided some wording. The aim is to gain acceptance from the community, not just the stkeholders. Alan proposed that the DX Proposal be handled as a terminal process to handle the requests of a subset of stakeholders who identified needs and that it should be evaluated based on DX-standards. Gary said that he had added a sentence to call these beta-releases and about making them available for people to test.
ISMB. Biopathways SIG will be held at ISMB but presentation not submitted there. Gary will not be at ISMB. Alan and Ken will be there.
ICSB/SBGN To be held in Japan and Ken is one of the local organizers, so there will be at least one representative for BioPAX. Joanne has a note to contact Kitano's lab. She suggested that a sub-group be formed to avoid duplication of effort.