Team:BU Wellesley Software/Notebook/JanooNotebook
From 2011.igem.org
(Difference between revisions)
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<h1>Life = 42</h1> | <h1>Life = 42</h1> | ||
[[User:jtferns|jtferns]] | [[User:jtferns|jtferns]] | ||
+ | |||
+ | --[[User:Jtferns|Jtferns]] 15:47, 7 June 2011 (CDT) | ||
<h2>To-Do List</h2> | <h2>To-Do List</h2> | ||
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**<del>fix link-caption centering issue</del> | **<del>fix link-caption centering issue</del> | ||
*<del>read through kirigami/TB paper</del> | *<del>read through kirigami/TB paper</del> | ||
- | *read through Friedland abstract/paper | + | *<del>read through Friedland abstract/paper</del> [6/7/2011] |
<br> | <br> | ||
*<span style="color:navy">PuppetShow Thought Project</span> | *<span style="color:navy">PuppetShow Thought Project</span> | ||
**<del>read through Puppeteer/PuppetShow powerpoint</del> [6/7/2011] | **<del>read through Puppeteer/PuppetShow powerpoint</del> [6/7/2011] | ||
+ | ***PuppetShow takes some version of the protocol graph produced via the Assembly Planner | ||
+ | ****The relationships between parts within the protocol graphs are assumed to be labeled with protocol names | ||
+ | ****The PuppetShow itself should link the protocol names to libraries and help generate the necessary Puppeteer code | ||
**<del>read through Puppeteer/related abstract</del> [6/7/2011] | **<del>read through Puppeteer/related abstract</del> [6/7/2011] | ||
**<del>peruse GroovyScripter code/structure</del> | **<del>peruse GroovyScripter code/structure</del> | ||
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**figure out how to seamlessly integrate Python script-compiling within fluid GUI | **figure out how to seamlessly integrate Python script-compiling within fluid GUI | ||
**design aforementioned fluid GUI | **design aforementioned fluid GUI | ||
+ | |||
+ | ''Using the Clotho platform [4], we develop two | ||
+ | ''applications for specifying and executing biological protocols. | ||
+ | ''The Assembly Planner [5] is the end-point of an endto- | ||
+ | ''end design workflow [3] that produces an assembly plan | ||
+ | ''for synthetic biological devices, with each assembly step | ||
+ | ''annotated with the name of a biological protocol. Each | ||
+ | ''such protocol itself may be fully specified using another | ||
+ | ''Clotho application called PuppetShow, which provides an | ||
+ | ''environment for writing, testing, debugging, and executing | ||
+ | ''biological protocols.'' | ||
+ | --'''A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering''' | ||
<h2>The Backburner</h2> | <h2>The Backburner</h2> |
Revision as of 20:47, 7 June 2011
Life = 42
--Jtferns 15:47, 7 June 2011 (CDT)
To-Do List
read through Doug's Algorithm paper[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860133/]read through AssemblyManager coderead through ClothoHelp[http://wiki.bu.edu/ece-clotho/index.php/Main_Page]edit main page to allow for click-able imagesbreak main pagefix link-caption centering issue
read through kirigami/TB paperread through Friedland abstract/paper[6/7/2011]
- PuppetShow Thought Project
read through Puppeteer/PuppetShow powerpoint[6/7/2011]- PuppetShow takes some version of the protocol graph produced via the Assembly Planner
- The relationships between parts within the protocol graphs are assumed to be labeled with protocol names
- The PuppetShow itself should link the protocol names to libraries and help generate the necessary Puppeteer code
- PuppetShow takes some version of the protocol graph produced via the Assembly Planner
read through Puppeteer/related abstract[6/7/2011]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
Using the Clotho platform [4], we develop two applications for specifying and executing biological protocols. The Assembly Planner [5] is the end-point of an endto- end design workflow [3] that produces an assembly plan for synthetic biological devices, with each assembly step annotated with the name of a biological protocol. Each such protocol itself may be fully specified using another Clotho application called PuppetShow, which provides an environment for writing, testing, debugging, and executing biological protocols. --A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering
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
- How do we want to construct this graph?
- Does the user input an expression?
- Should we have an interactive GUI to help user create custom protocol graphs?