Hackathon2005

This is just a brainstorming session right now. We can prioritize discussion and ideas for projects later.

• Discuss the difference between node hide and delete concepts -> Goal: get conceptual clarity and a plan to document/implement any necessary changes based on this. Also select/deselect vs. flag/unflag

• Improve conceptual clarity and better document the core and graph model - Is the root graph a multigraph or a graph? Is the root graph directed, undirected or mixed? How about graph perspective? Can nodes or edges be duplicated? etc.
• Discuss switching to a numbered node system instead of the current node ID as a string system
  • This may be required for some graph editing use cases (having nodes with no name yet) and two nodes with the same name.
• Discussion of undo manager
• Prioritize subsystems for refactoring
• Discuss new documentation options e.g. wiki based, which can be translated to PDF and Java help.
• Plan core code cleanup - removing old libraries, old classes, clean up of package structure
• How can we package code so it is easier for developers to load - we have a problem with core plugin and library code being in too many places.
• Clarify and document the difference between core and non-core and decide on policies for making future decisions on this.

• Review community development process and core coding conventions, etc -> goal is to increase quality of our codebase and application

• Discuss user interface standardization issues (Benno brought this up 2 years ago)

• MetaNodes

• Discussion of how to handle "compound" node types -- e.g. complexes, families (sets) (related to MetaNodes above...) (Note: I'd like to make this a high priority for discussion. Alex Pico of the GenMAPP project will be participating in the Hackathon and can go into considerable depth on the requirements for these constructs. It would be very useful to have this discussion while we have the opportunity to pick Alex's brain).

• Discuss new rendering engine that Nerius is building
• Simplifying file formats and implementing the save session feature. Does .sif need to have two ways to specify interactions? Do we need GML if we have a save session file?

HACKATHON NOTES: File formats

Current types of file formats in Cytoscape: * sif, network, i/o * gml, network, i/o * noa, attr, i/o * eda, attr, i/o * expression, TP, i/o * .onto, .anno, .syno, .obo (BioDataServer) * GO .onto, .anno, .syno, (Kei)

Issues on each file format: * expression file: should be a noa file * GO: information gets loaded onto runtime memory, not reasonable for big species,(different topic: databases)

Action items: * Test Rowan's file format for attributes

• Do we need to standardize context menus for nodes and edges or is the current model fine? It seems to be working fine, but will it scale? One reason for standardizing in the core is that the current model uses Piccolo and that may be replaced.
• Please add your discussion points here.