Biomod/2011/Harvard/HarvarDNAnos:LabNotebook Shwinn

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Contents

Shwinn's Lab Notebook Page

Week 1

Day 1, (6/6/2011)

  • Introductory day, discussed different origami structure designs. I attempted to work on making a basic cylinder with CADNano, but to no luck. Eventually, my goal is to design and successfully build a middle-separating sphere(as seen here http://www.sciencemag.org/content/332/6027/342.full.html).

Day 2, (6/7/2011)

  • Attempted spherical origami (curved surface) design.

Day 3, (6/8/2011)

  • Continued attempts of spherical origami design.

Day 4, (6/9/2011)

  • Switched focus to an elliptical origami design.

Day 5, (6/10/2011)

  • Continued working on elliptical origami design before beginning work on creating python scripts for spherical coordinate conversion of bases (useful for Maya 3D).


Week 2

Day 6, (6/13/2011)

  • Continued working on python scripts, now expanding to creating algorithms for looking up caDNAno positions and mapping them to base orientation.

Day 7, (6/14/2011)

  • Continued working on python scripts.

Day 8, (6/16/2011)

  • Completed first draft of python scripts for both PositionLookUp.py as well as NearestSphCoordinates.py

Day 9, (6/17/2011)

  • Began working on implementing python scripts in Maya3D, the graphical interface through which the visualization would occur.


Week 3

Day 10, (6/20/2011)

  • Attempted running scripts in Maya3D through MEL editor. PySource was not recognized, so troubleshooting began.

Day 11, (6/21/2011)

  • While troubleshooting remained largely unsuccessful, went back and re-edited PositionLookUp.py and NearestSphCoordinates.py because my dictionary functions were displaying numerous syntax errors (lesson learned: be very careful about indentation in Python)

Day 12, (6/22/2011)

  • Began working on a new script, cargo.py, that would act as the class for handling any placement of cargo on the sphere (and would call on PositionLookUp.py and NearestSphCoordinates.py

Day 13, (6/23/2011)

  • Continued working on cargo.py and considered making a main script (main.py), from which all the other scripts would run. My only problem with this is that it takes away from the dynamic interface approach we are aiming for.

Week 4

Day 14, (6/28/2011)

  • Abandoned main.py since, as suspected, running a main method in the MEL editor would only execute SphereCAD commands once and then exit.

Day 15, (6/29/2011)

  • Turned attention back to Maya3D. Made significant progress on cargo.py, namely "drawing" nanoparticles in Maya3D. However, if the other two scripts won't run, this may all be for naught.

Day 16, (6/30/2011)

  • Continued working with Maya3D while trying to understand why scripts are not running.


Week 5

Day 17, (7/5/2011)

  • Continued working with Maya3D but still found no solution.

Day 18, (7/6/2011)

  • After days of troubleshooting I am ready to give up on Maya3D as the MEL editor just will not recognize my scripts even though they run fine in the Python IDLE.

Day 19, (7/7/2011)

  • Decided to give AutoCAD a try since Maya3D was not recognizing scripts. However, AutoCAD's reliance on BASIC commands is undesirable and the inability to toggle between two-dimensional and three-dimensional views is an issue like it was for Maya3D.


Week 6

Day 20, (7/12/2011)

  • Completely new plan of action. Whereas previously Maya3D and AutoCAD were the viable interface options, it has become clear that a standalone GUI that can show a 2-dimensional view of the caDNAno file as well as the 3-D sphere in an adjacent panel is necessary.
  • Searching for new packages for native Python GUI programming.

Day 21, (7/13/2011)

  • Began coding Sphere construction. It is more optimal to separate each sphere into 24 rings (and more realistic), so this will be an ongoing process for the next few weeks. Imported free_camera.py script for handling rotation of angle for viewing 3-D sphere.

Day 22, (7/14/2011)

  • Considered the zoom-in, camera, and other programming aspects necessary for user functionality. Started working through specific case examples of this in other programs to see how this can be adapted for the GUI.


Week 7

Day 23, (7/19/2011)

  • Implemented xlrd, the excel file reader, to replace custom code that was previously provided by Adam (this will streamline processing of future excel spreadsheets containing caDNAno data)

Day 24, (7/20/2011)

Day 25, (7/21/2011)

Week 8

Day 26, (7/26/2011)

Day 27, (7/27/2011)

Day 28, (7/28/2011)

Week 9

Day 29, (8/2/2011)

Day 30, (8/3/2011)

Day 31, (8/4/2011)

Week 10

Day 32, (8/9/2011)

Day 33, (8/10/2011)

Day 34, (8/11/2011)

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