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cannin edited this page Jun 10, 2016 · 1 revision


  • Stuart Moodie (SM)
  • Huaiyu Mi (HM)
  • Tobias Czauderna (TC)
  • Robin Haw (RH)
  • Augustin Luna (AL)

Topic: SBOL

Discuss Support

HM: made example diagrams; the diagrams appear as hybrid constructions

TC: asked if stereotypes will be used SM: AF activity nodes could be used with an image of the stereotypes overlaid HM: Current examples are not AF not PD, but Kevin Clancy provided additional examples

AL/SM: believed that each that each node is separate in SBOL diagrams TC: Is it the nested entity from ER? SM: connect activity nodes requires spatial ordering HM: the entire construct is connected.

SM/HM: We need to apply for funding for working on hybrid maps, stereotypes, spatial arrangement. HM: Can hybrid diagrams be created in XML? AL: There are validation difficulties TC: What is the interaction between elements in the multiple notations?

AL: I expect that SBOL wants the whole to be considered in a singular manner as well as the components. RH: Multiple activities from a single activity

HM: Conversed with Kevin and Chris Myers there is a need to support all the symbols in SBOL AL: What is the semantics of a spatial arrangement interaction? SM: May be difficult to express because of the activity node semantics AL: Can PD be used instead of AF? HM: It may be possible but it would complicate the semantics

TC: Semantics in PD is just as complicated AL: What in PD makes it hard? SM: Topological concept doesn't exist in PD either only the idea of a compartment SM: Nucleic acid was not the best solution to start with

AL: What about as a simplifcation using a single construct in a nucleic acid feature HM: No each feature is separate. Can we just add "order" as the semantics for spatial arrangement?

TC: Problems for describing SBOL: 1) define the spatial relationship, 2) stereotypes, 3) hybrid maps HM: We need the more AF examples from Kevin HM: We can schedule a call with SBOL in early April with example that the other editors contribute to

RH: Is DNA components the only thing that SBOL is concerned about? HM: Yes. RH: Can inter-compartment concepts able to be represented in SBOL?

APIs Needed by SBOL: Python

AL: What are the options for libSBGN in Python? PyXB seems like one TC: Martijn's solution creates classes, but is not working; Rostock wants to try PyXB.

Topic: HARMONY 2015

HM: Cannot go, will be go Biocuration 2015 RH: Cannot go, will not go to HARMONY or Biocuration 2015 HM: Can be available on Skype on April 20-21st during HARMONY, best during afternoon. AL: Projects that I can work on: Python bindings and perhaps, working on SBGNViz.js HM: A goal should be to release new specifications SM: Anatoly may be trying to go to HARMONY SM: AL send Anatoly an email about ER HM: We need to coordinate SBOL and SBGN specification breakouts

Topic: Reactome SBGNML Export

AL: Any progress on SBGNML from Reactome? RH: Original developer gone. I will need to look it pre-SAB meeting RH: On the fly generation of SBGNML. AL/TC: Could you send sample of SBGNML files generated from Reactome if available RH: Will update next week

Topic: ICSB

HM: Will give an update at ICSB about SBGN

Topic: Funding for Travel

HM: NSF grant was not accepted RH: OICR grant is available in Canada, which would include travel to Toronto travel and accomodations, if the meeting has a medical basis RH: HM could you send me the grant to see if any of it is applicable?

Topic: SBGN Competition

HM: Do it this year? SM: If someone has the available time HM: The basic process is send emails for advertisements, collect results, put up website, collect voting; there was the idea of putting up categories. RH: Will take on the competition. What should be the prizes? Books, Amazon gift cards are possibilities. 3 prizes: 1) best map, 2) best resource, 3) best tool? HM: We may be able to pay from remaining NSF funds; will find out out the remaining funds. The goal is to announce now and decide the winners before COMBINE. RH: OICR funding may also provide funding for a similar competition next year.

Topic: Next Meeting

HM: It should be in the middle of April, before HARMONY, but after in meeting with SBOL.

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