IGEM:IMPERIAL/2007/Dry Lab/Log

--Anthony Lazzaro 15:23, 3 September 2007 (EDT) Welcome to the Dry Lab Log ! Here you can see what work we've been doing in Modeling & Data Analysis in a Day to Day format.

Week 9

Monday 3rd September

We have recieved some data from the Testing team and need to do the following work on it for tomorrow

$$$$ Major Problems with Excel Sheets & staggering need to have a chat to lab team in morning not much work done tonight ! $$$$$

Data to be analysed:

1.Deg GFP @ 37 Degrees

• need to normalise with respect to control
• need to extract decay coeficient

2.Deg GFP @ 20

• needs more data
• need to nomalise
• need to extract decay coeficient

3.Plux 25 Degrees

• Normalise Data wrt control
• Lag time
• Rate of GFP synthesis
• Steady State value given initial concentration

4.Ptet 20 degrees

• Turning on of Promoter
• Normalise wrt to control to get rid of increase in day 2

5.PTET @ 37 Degrees

• Get Steady State Value / Maximum Value
• Use Deg from 1. to determine K

6.Calibration cuve

• Need more data not very useful at the moment

Tuesday 4th September

• Spoke with testing team and have decided have come up with a template for importing data from notepad to excel

• Spoke with testing team about wierd results and they are currently looking into it

• Wiki design needs some work: needs to have a graphic language and make it more visual

• Started Data Analysis today :
• Degradation: We focused mostly on this today and have done some simple log based calculations do determine delta
  • Deg 37: Deg doesn't need overlap we will treat each part, day 1 staggered & day 2, as seperate. Major concern is that 1st part of the data actually goes up, we have cut this from our data when analysing (testing team will find out why this happens)
  • Deg 20
• PTET 37 : Wierd Results - staggered data is lower than 1st - many theories
• PTET 20 : Same as above
• Plux 25: The initial data for this is very good but it is difficult to analyse
  • We have noted that 50nM should be closer to 100nM than 10nM. A possible explanation for this is cooperativity, the threshold for this could be between 50-100nM: looking at the F2620 characterisation we can see that the threshold occours at 10-100nM.
  • We think we should proceed by looking at the 1-10nM region more closely.
  • In terms of analysis we will leave this data for a while as it will be the most difficult to analyse

Wednesday 5th September

We have improved on log method in excel by trying out curve fitting methods using Least Squares approach implemented in matlab.

We have 3 curve fitting methods 2 using functions in matlab libraries and one built from scratch.

First Builds of all 3 show promise 2 return values in line with our log based calclations for Deg GFP @ 27 Degrees

Thursday 6th September

1.Wiki

• We will work on our portal page today
• We will look into creating a data analysis page to store all of our work

2.Curve Fitting

• M suggested improvements on our Curve Fitting Codes and we are trying to Implement them
  • J
  • B
  • A

3.Modeling Research

• V has advised that the results generated for PTET @ 20/37 degrees may in fact be accurate and mabye our models are wrong ! We are looking into this today

4.Normalisation

• M has given us a better normalisation method and we are tyring to implement it into our models / Analyses