Computational Team Lab Notebook - Kathy Sirui Liu

Timeline

Week of 5/31/2011

Summary BU/Wellesley Synthetic Biology Bootcamp

Members of the BU/Wellesley iGEM come together and work on their "Hello World!" application in Clotho.

5/31-6/1: Team introductions; we learned the basics of CAD and basics of molecular biology and genetics.
6/2: We started learning the basics of Clotho, as well as more basic biology, focusing on the structure of a transcriptional unit. We split into teams and started exploring the format of Clotho.
6/3: Time to get into more details: How is TB involved in our research? Suma gave a brief powerpoint presentation on the global effects of TB, and an overview on the transcriptional regulation of TB. Also Traci talked to us more about the basics, such as the definition of a Biobrick, and objectives of the iGEM competition. Also, she gave an overview outline on wetlab protocol for this summer. Swapnil talked about how invertases work, and what would be a simple algorithm for computing potential permutations.

The comp team now has a good idea of what our goals are for the summer. Michelle and I will focus on observing the wet lab environment to see how a tangible user interface would potentially help research in a bioengineering lab. We may talk to more people later on in the summer about certain features to improve on G-nomeSurfer, and adjust our goals based on the needs of the wetlab.

Week of 6/6/2011

Summary:End of training; beginning of Wet-Lab Observations and Background Research

6/8: 1st lab meeting at BU with the wet-lab. Michelle and I spent a couple of hours in the wet-lab observing the wet-lab team. We took notes on the organization of the lab, team interactions, and where HCI tools would come best into.
There were a couple of questions we had in mind:

 o How useful would publications be when the team is starting to do research?  Would they need a lot of background reading?  
 o What potential sources would they go to for publications?  Would they prefer PubMed, GoogleScholar, or some other specific database?

Found out that publications are not the main focus at the moment. They need to first learn about the equipment in the lab, and also how the Registry of Standard Biological Parts works.

6/9: 1st HCI lab meeting at Wellesley- there was a general brainstorming session on BLAST visualization. After doing some background research on existing BLAST visualization, I divided the designs into categories based on linear vs. circular format, color scheme, and content organization. The circular BLAST visualizations are interesting, and we'll look more into GView and CGViewer. The team will keep the designs in m ind when considering how to design the paper prototype for the widget.
Work for the rest of the week: I need to start fiddling with Geneious, to see the pros/cons of the design. What are aspects that are great that may inspire the next generation of G-nome Surfer? What are some things that won't work on a Tangible User Interface? We need to first undersatnd the basic functions of Geneious before we know what to tweak about G-nome Surfer.
Some members of the team are starting to develop the Extended Desktop; How do we envision this being used?

Week of 6/12/2011

Summary: Started designing widget; continued with wet-lab observations; devising a plan for BLAST visualization

Team:BU Wellesley Software/Notebook/SiruiNotebook

From 2011.igem.org

Computational Team Lab Notebook - Kathy Sirui Liu

Contents

Timeline

Week of 5/31/2011

Week of 6/6/2011

Week of 6/12/2011

Week of 6/19/2011

Week of 7/4/2011

Week of 7/11/2011

Week of 7/18/2011

Week of 7/25/2011

Week of 8/1/2011

Week of 8/8/2011

Week of 8/15/2011

Week of 9/5/2011

Week of 9/12/2011

Week of 9/19/2011

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