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cannin edited this page Jun 10, 2016 · 1 revision

SBGN editors conference call, 6 August, 2015.

Participants: Stuart, Augustin, Huaiyu


  • Specification publication in JIB
  • Specification release update
  • SBGN website
  • COMBINE meeting
  • SBGN competition


Specification publication in JIB

  • HM: The AF spec is done.
  • AL: ER is almost done. There are a couple of minor items that need to check with Anatoly. Also, there is a technical problem related to generating the PDF file. It requires the latest version LaTex. Should be done soon.
  • AL: According to Falk, the deadline for submission is this coming Sunday (Aug. 9th)
  • SM: About PD, the question is weather we should release version 2 or just the existing release. The content of version 2 has been discussed in the past 2 years at SBGN workshops, COMBINE and HARMONY. However, the latest version has not been circulated. One option is to release V.2 as a release candidate. SBML is going to do that.
  • HM: We probably should not publish V.2 without circulating it in the community. We probably should publish the current release.
  • AL: It is probably not ideal to put a release candidate in a publication. It should be a more final version.
  • SM: Then we can just publish the V.1.3, which is about 4 years old.
  • HM: That is fine. If we can V2. circulated and blessed by the community, we may be able to replace it in the publication.
  • AL: According the Falk, this will probably be an annual publication, so we can alwasys update.
  • Action: By Sunday, both ER and PD will be finalized and submitted.

Specification release update

Most of the discussions in the previous item is relevant to this.

  • We should target to release PD V.2 before or around COMBINE 2015, which means we should start to circulate it in early September.
  • There is one more spelling issue that needs to be fixed (precide).
  • There is also a submap issue identified by Tobias. It needs to be fixed before it can be released.

SBGN website

This is related to the email trail about SBGN website down at the end of July 2015.

  • SM: The ideal thing is the move the website to another host that uses standardized wiki system and copy the content over. The current website is hosted on a non-production (research) machine at EBI, which runs an old version of mediaWiki that was highly customized by Mike. The website was originally set up at CalTech, and was moved to EBI by Nico Rodriguous. There was no documentation about the moving and configurations. Alice once wanted to clone it and move it to a different machine, but gave up because it was too complicated.
  • HM: There are two issues we need to address. The first is the host. We probably need a host that can be accessed easily. (EBI machine are not accessible by people outside of EBI). The second is the resource to do the migration.
  • SM: Sourceforge had a lot ofproblem recently. Don't know if that is an option.
  • AL: BioPAX is currently being moved to gitHub. There is a wiki function. Maybe we should host the website there.
  • HM: Is an CS undergraduate capable of doing this?
  • AL: Yes.
  • SM: May ask Falk to see if there are students at his school who can do it. Also, i may have some small fund to pay student for the repetitive work of copying the content.
  • Action: Currently, we will tell Nicolas that the website will continue to be hosted at EBI. We will continue to explore options to move the website to a new host.

COMBINE meeting

  • HM: The COMBINE 2015 is from Oct 12-16. The NSF grant for the COMBINE 2014 got extended for one more year, so there is some leftover fund that can support us to the conference.
  • SM: There is a clash with another meeting, so won't be able to make it.
  • AL: Can go.
  • HM: There should be enough fund to support TC, AL and HM to the meeting.

SBGN competition

Since Robin is not at the call, this is not discussed. HM will contact him to discuss further.

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