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Team:Newcastle/Notebook/calendar
From 2013.igem.org
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Modelling Exercise. Identifying components and species of subtilin biosynthesis pathway. We also sketched down some potential logo ideas and created a shortlist of favorites. | Modelling Exercise. Identifying components and species of subtilin biosynthesis pathway. We also sketched down some potential logo ideas and created a shortlist of favorites. | ||
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In the afternoon we learned about the differences and similarities between stochastic and deterministic modeling. We also used rule based modeling such as RuleBender and BioNetGen. We changed the parameters and rates of reaction and observed the effects. | In the afternoon we learned about the differences and similarities between stochastic and deterministic modeling. We also used rule based modeling such as RuleBender and BioNetGen. We changed the parameters and rates of reaction and observed the effects. | ||
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Contents |
6
10
Titles
- First Day of Training
Details
Morning
We started a discussion of our sub-project, doing some research into project presentation: wiki layout, t-shirt design and possible team logos. We looked at precedents for inspirational ideas.
Afternoon
Learn about Computational Modelling and BioBrick concepts. Decided to start with biophysical modelling of the lipid membrane of Bacillus subtilis and modelling of lipid synthetic pathway. Later in the day, we had a team meeting to discuss aims and progress of our work.
11
Modelling Training
- Modelling Training
Details
Morning
Modelling Exercise. Identifying components and species of subtilin biosynthesis pathway. We also sketched down some potential logo ideas and created a shortlist of favorites.
Afternoon
In the afternoon we learned about the differences and similarities between stochastic and deterministic modeling. We also used rule based modeling such as RuleBender and BioNetGen. We changed the parameters and rates of reaction and observed the effects.
6
13
Basic Lab Skills 1
- Basic Lab Skills 1
Details
Morning
On our first day of lab, we were briefed on various lab health and safety policies to ensure we maintained a safe working environment. We were then led by our supervisor on a tour around the lab to inform us about the layout. Once we have familiarised with everything, we officially started our first lab session.
We started by callibrating our pipettes and learning how to operate them, then we were shown how to innoculate bacteria to a liquid culture. Finally, before we took a break, we prepared bacteria streak plates.
Afternoon
In the afternoon, we extracted GFP and RFP bricks from the iGEM 2013 biobrick plate and transformed it into competent Escherichia coli cells. These procedures were performed using the following protocols (). Then plate those cells onto LB with chloramphenicol selection marker plates.
6
14
Basic Lab Skills 2
- Basic Lab Skills 2
Details
Morning
When we first arrived in the lab, we were all excited to check on our plates to see if anything grew. The RFP plates showed a lot of collonies, while the GFP plates did not work as expected. The next thing we did was too view the plates under the fluorescent inverted microscope.
Afternoon
We had an introductory lecture on basic molecular biology and biobrick design. It was particullarly helpful for the non-biologist of the team.
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6
17
Basic Lab Skills 3
- Basic Lab Skills 3
Details
Morning
The first thing we did was to transfer collonies of bacteria into LB. Then we extracted the plasmids via (plasmid prep) protocol, and check the concentration of plasmids through the use of nanodrop spectrophotometry. Next,we prepared 1% Agarose and whilst waiting for it to set we performed a single digest with (Xbal or Pstl) and double digest with both restriction digest. Finally, we load our samples to the gel in addition with DNA ladder and control.
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