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From 2011.igem.org

Life = 42

jtferns

To-Do List

• read through Doug's Algorithm paper [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860133/]
• read through AssemblyManager code
• read through ClothoHelp [http://wiki.bu.edu/ece-clotho/index.php/Main_Page]
  • edit main page to allow for click-able images
  • break main page
  • fix link-caption centering issue
• read through kirigami/TB paper
• read through Friedland abstract/paper

• PuppetShow Thought Project
  • read through Puppeteer/PuppetShow powerpoint
  • read through Puppeteer/related abstract
  • peruse GroovyScripter code/structure
    • attempt to mimic GUI and incorporate Python-parsing?
  • figure out how to seamlessly integrate Python script-compiling within fluid GUI
  • design aforementioned fluid GUI

The Backburner

• Protocol Graphs Thought Project
  • Ideally, we should have a protocol graph that would be a generic form of managing an arbitrary combination of protocols.
  • The protocol graph should contain vertices, which are either operands or protocols/operations.
  • The graph should also connect operands to protocols.
  • Given access to a library of protocol specifications, one should be able to give an expression or an explicit protocol graph for parsing purposes.
  • One should be able to use PuppetShow (see powerpoint) to create an implicit protocol graph.
  • One should be able to reconfigure protocol graphs for optimization, etc.
  • Questions
    1. How do we want to construct this graph?
    2. Does the user input an expression?
    3. Should we have an interactive GUI to help user create custom protocol graphs?