Cellml.org - Meeting Minutes 8 April 2004

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Meeting Minutes 8 April 2004

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Author:
          Autumn Cuellar (Bioengineering Institute, University of Auckland)
Collaborators:
          Shane Blackett (Bioengineering Institute, University of Auckland)
          David Bullivant (Bioengineering Institute, University of Auckland)
          Matt Halstead (Bioengineering Institute, University of Auckland)
          Poul Nielsen (Bioengineering Institute, University of Auckland)
          David Nickerson (Bioengineering Institute, University of Auckland)
          Carey Stevens (ZEST Technology Group Ltd )

Tools mailing list (Matt). Andrew (our sys admin) can do everything fine inside bioengineering network. He is checking out why it's not working outside of the network.
Shane: “Can someone explain to me the purpose of the separate CellML discussion mailing list and tools discussion mailing list?” Matt: “The Tools mailing list was conceived for the 4th year project students. It's intended for specific tool-related discussions. The CellML discussion mailing list is for the language specifications and general discussions.”
Stephanie's Content MathML editor (Poul). Gave a copy to Catherine. Said she'd work on a distribution for other interested users. Autumn, e-mail her for a copy to put on the website.
Road Map. Shane, who was not present at last week's discussion, was asked for his feedback. Shane said he didn't see listed as one of the tools we want to develop a repository that people can interact with, one in which everyone can check out models, modify, then commit. Matt pointed out Section 1.2 (bullet 1). Poul suggests that we discuss:
- What kind of limitations do we want to set on the interaction?
- What tools should we be writing to facilitate this interaction?
Matt thinks that if we try to add all this to the Road Map, we'll end up with a book. Shane agrees, but also thinks we need to say a bit more about it.
Shane has only had a cursory look at the Road Map and will give more feedback when he's had more time.
Carey asks if we will also prioritize the tasks in the Road Map. Matt says yes, that's the next step, adding some sort of timeline. The timeline will only be for the concrete tasks set forth in the Road Map. We also need to take into consideration what resources we have and need.
Shane and Matt: The anatomy ontologies as a replacement of AnatML should also be on the task list. [As a sidenote to Section 1.2 Shane mentioned that Srdan is now putting SwissPROT links in (for an example see http://www.bioeng.auckland.ac.nz/physiome/ontologies/immune_system/proteins.php). I think the eventual plan is to use the Protein DataBase's protein coordinates in CMGui to get pretty pictures of the proteins.]
Discussion with Sheffield group (Poul). We spoke to the Sheffield group about how they can extend ModelML for epithelial tissue modelling two days ago (see Meeting Minutes). They were especially interested in FieldML as a possible geometric representation of tissue and cell.