Editors_Telecon_19_Mar_2015.xml

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    <title>Editors Telecon 19 Mar 2015</title>
    <id>1013</id>
    <revision>
      <id>3963</id>
      <timestamp>2015-04-22T15:39:25Z</timestamp>
      <contributor>
        <username>Cannin</username>
        <id>72</id>
      </contributor>
      <comment>March meeting notes</comment>
      <text xml:space="preserve">==Participants==
* 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 &quot;order&quot; 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.</text>
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