Notes of Modeling

Before July

Team members in modeling have get to know so much about the general knowledge of synthetic biology and related knowledge such as the biochemistry and the microbiology. We have learned and communicate with other team members through communication.

The First Week of July

We have communicated with last year’s TU iGEM fellows in charge of modeling immediately after the division of labors. Many important suggestions are impart by them. They also helped us with the time schedule of the modeling part.

The Second Week of July

We have studied the team of 2010 Slovenia whose team is very helpful especially in modeling. After detailed study and communication, we came to contact with one of the most important software in iGEM modeling that is the Simbiology toolbox in MATLAB. We have also practiced some real examples of Simbiology, the detailed discussion with each other have enhanced our understanding of modeling in Simbiology.

The Third Week of July

This week we have read several important articles about orthogonal ribosome. After thoroughly discussion with other team members, we get to know the inner principle of orthogonal ribosome and how to design the sequence of orthogonal RBS. Combined with what we have already known about this years’ project, we have also discussed with the people who are in charge of the wet lab to seek for appropriate tasks of modeling. Finally, we have also determined one task.

The Fourth Week of July

In this week, we are primarily seeking for related knowledge of the task, for example the ribosome binding intensity is directly related to the protein expression amount, and we have study the use of RBS calculator. We have also practice to use this online tool to calculate the related delta Gibbs free energy and relative protein expression level. What is more, we also learned Vienna and the Nupack to assist our modeling.

The First Week of August

This week we have calculated out the orthogonality of our experimental states, which goes the same with the result of the wet lab. We also calculated the relative protein expression level of the three states.

The Second Week of August

Seeking for appropriate perspective and problem to establish our modeling work, we have a good idea is to study how the gene pollution transferred within the environment. So we searched a lot of papers about genetic pollution and find an inspiring idea Bass Model which give us a spark to describe the genetic pollution.

The Third Week of August

With the basic equation in Bass Model, we are still searching papers and trying to apply this model into the real conditions. We have considered the disappearing of plasmid, the changing number of bacteria under ideal and real condition. We also considered the spatial diffusion of the equation and many other future work details.

The Fourth Week of August

We have also talked with the team member who are in charge of the human practice to search for new point to provide tasks for modeling, after thoroughly discussion, we have are surprisingly to find there are many points to be modeled. So we have searched important articles about the related problems, especially those related to AHP method.

The Fifth Week of August

We have learned and tried the detailed calculation step of AHP and establish a model for the solution of general modeling. After that, we also designed our questionnaire to represent collect the data of our calculation and modeling.

The First Week of September

This week we have distributed our questionnaires to many people, and we also collect data from these questionnaires and did the related calculation work. We also analyzed the result.

The Second Week of September

We have also established the model to describe the process of advertisement.

The Third Week of September

We are collecting all the data and calculation result and writing the analysis. All the wiki related content are all written by us.

The Fourth Week of September

We are assisting all the other people with the work of our project including powerpoint, wiki and videos.