Project:  Visualizing The Cell Do Its Thing

 

Prologue: Each living cell is an autonomous agent filled with complex and simple macro-molecules all towards three activities – eat, gossip, and reproduce.Do they not sound like an inner replicates of us all. And indeed they are. They metabolize sugars (eat) to carry out basic existential chores, communicate with other organisms and like-minded cells using signal transduction pathways, and of course reproduce through mitosis. Some brave souls lead by Prof. Marcus Covert simulated in silico the chores of the cell of a mean bacterium namely M. Genatlium. This living organism is only endowed with 500+ genes. Still, is an ominous task to computational simulate the cellular processes that transpire within each each cell.  WholeCellViz was developed to visually exploring and analyzing whole-cell simulations and provides 14 animated visualizations, including metabolic and chromosome maps of biology in action in a single cell of Mycoplasma genitalium. A plethora of data has been generated.  Now one has to visualize. The Covert Lab created a framework for visualization. Please peruse, ponder and then improve.

 

Resources: Please find

1.     Class slides here.

2.     I offer myself myself as a resource. Please consult with me frequently.

3.     Appeal to your instincts. Do not think of it as some hidden biological nonsense. Think of this mother lode of data that is all about temporal data.

4.     The simulation can be found in this paper.

5.     If interested, the code for simulation can be found here.

6.     The paper on visualization can be found here. 

7.     The code on visualization can be found here.

The Data:

 Please visit - https://simtk.org/project/xml/downloads.xml?group_id=714#package_id1307 and download the tutorial.  Some batch data is available for your consumption.

 

Deliverables:   The project should have all these components.

1.     Complete a user study as we discussed in laboratory assignment 4. Create a list of tasks, and have some peers examine the list.

2.     Next do one of two things

a.     Create a mockup (no coding) and complete a second user study as a focus group and demonstrate that there was an improvement. You will need to at least use 5 or more views of data.

b.     Or, using at least two views, create a new tool that incorporates the first user study. No second user study is needed to show improvement.

3.     Write a report.

4.     Finally, yes you need to submit code, a report (with results of the user study) and any material that is required to demonstrate the project. If you cannot show in person make sure you have slide-decks/videos, links to web sites, etc. And yes you make your deposit into a Carmen dropbox.