First Day Issues
These are ordered in the original sequence. The parenthesized numbers after the headings indicate priority, as decided at the time of the discussion.
- Empty set: do we need it? (1)
- Filled ellipse or not filled? (2)
- Semantics of state variables: several unspecified semantics (3)
- Shape of a complex & what's under the shape (multiple questions) (4)
- emek: do shapes have to touch inside? does topology indicate anything?
- Shape of compartments (4)
- can compartments can have any shape?
- emek: are we allowing nested compartments?
- emek: are membranes separate compartments?
- emek: there are neighborhood relationships -- are we going to draw them?
- Rectangular shape of gene (2)
- emek: what happens if several elements of one gene intersect with another? does the info get duplicated?
- stuart: would like to discuss examples of state transition vis-a-vis gene regulation
- Controlled vocabulary for macromolecule labels (1)
- nicolas: also for physical properties (1)
- Modulation, catalysis: use a circle? should catalysis even exist? (5)
- mirit: do we want all of them in SBGN L1?
- emek: also trigger and others
- also topic of shape of modulation & rescaling diagrams
- anatoly: should there be multiple shapes? or one shape for all? put smth inside the diamond?
- All boolean connectors: (5)
- emek: highly tied to modulation
- Module: shape, content, terminals (3)
- also: can a connector connect to a component inside the complex
- Hiroaki: discussing reduced notation (1)
- Rules for drawing layout (eg avoid overlap, etc.) (1)
- falk offers to prepare a list
- Do we want to incorporate annotation glyphs? (1)
- Do we want to discuss the languages used to implement SBGN? (0.5)
- Do we want to include generic entities in L1? (1)
- ralph: eg is event
- Entity-relationships: how to proceed? (1)
- mirit: must make sure to heed orthogonality goals
- Hiroaki: arrows? (1)