From 2010.igem.org

	Home Team Colin Hoffman Jeremy Kemball Anna Kropornicka Bobak Hadidi Acknowledgements Team Profile Project BioMORTAR Website IMPtools Website IMPtools v1.0 Plasmid Designer Modeling Next Version Cooperation Press Newsletter Notebook Bootcamp Safety

• • • The notebook is organized into weeks. Click on the Saturday of each week to view that week's notebook entry

Weekly Lab Notebook

May 23 – May 29

Colin - At the beginning of the week, we hosted the iGEM regional convention, and we were able to meet other iGEM teams from around the Americas. It was very interesting to get to know other teams that we would be competing against this summer, and the convention went significantly better than expected.

Boot camp was also this week since it is the first week of the summer and the first week of full time iGEM. Everyone worked together to learn basic web programming with django, using a helpful, but long django tutorial. In between self-taught django lessons, we all took a look at last year's code for IMPtools to get an understanding of their previous work. Once we began to get a feel for the task ahead of us, we split the group into two, designating the task of improving IMPtools to one group, and coding the new project, the strain designer, in the other group. It seems that we have a long summer ahead of us.

Bobak - Migrating/Extracting imptools v1 code from Professor Bhalerao's server Setting up team development environment Setting up SVN Started BioMORTAR (strain designer step) development

Anna – We split up research and learned about ways to model cellular logic design, which would be a way to compute things within a cell, another area was metabolic pathways. We also looked up information about projects that were done by last year’s iGEM groups. The goal of the research was to be able to come up with a project idea. We read about and discussed aspects of metabolic pathway modeling. This entailed discussing Matlab’s Constraint-based reconstruction and analysis (COBRA) designed by Becker, et. Al. The components of COBRA are that it creates a flux balance analysis of a genome-scale metabolic reconstruction and models how a cell will growth based on different constraints. These constratins can be environmental or genetic manipulation.

Jeremy - I spent the first few days of this week reading the django tutorial, and most of the rest of this week integrating the RPAIR database into Imptools, partially because it needed to be done, but also because it allowed me to familiarize myself with the internal structure of Imptools. I also installed the necessary software to do dev work, including mysql, scipy, numpy, and biopython. Making mysql work with python through mysqldb was particularly frustrating, to the point where I considered dual-booting Ubuntu just to make setup easier.