# Glasgow/Drylab

### From 2007.igem.org

## Contents |

## Week 1

### 02/07

After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.

From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.

### 03/07

We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.

### 04/07

We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.

In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.

Our experiment was to extract plasmids from a number of different bacterial cultures.

### 05/07

blank

### 06/07

Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.

## Week 2

### 09/07

Our first step towards modelling a possible method for PHASE 1.

### 10/07

We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation. Toby 11:27, 11 July 2007 (EDT)

### 11/07

We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.

Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless!

### 12/07

A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB.

--Karolis 04:53, 13 July 2007 (EDT)

### 13/07

Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done it by Macieck.