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Team:Paris Saclay/Notebook/July/17
From 2013.igem.org
Contents |
Notebook : July 17
Lab work
A - Aerobic/Anaerobic regulation system
Objective : obtaining Bba_K1155003, Bba_K1155007
1 - Electrophoresis of digestions of Bba_B0015, Bba_B0017, Bba_I732019 by EcoRI/PstI
Anaïs, Sheng
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Expected sizes :
- Bba_B0015 digested by EcoRI/PstI : ...
- Bba_B0017 digested by EcoRI/PstI : ...
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We obtain fragments at the right size. We will do a PCR of them. |
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Expected sizes :
- RBS-LacZ-term : ...
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We didn't obtain fragments at the right size. We will use Bba_I732017. |
Modeling
Meeting memo
Meeting Date: 17/07/2013
Meeting participants: Patrick Amar, Claire Toffano-Nioche, Abdou Mouhtare, Damir Damipator, Gabriel Gallin, Zhou Yi
Recorder: Zhou Yi
Hsim:
-Hsim is created for bio-chemical reaction simulation, it demonstrates bio-chemical systems which the scientists are already known.
-The molecules are simulated as spheres (in 2D or 3D). Initial positions and size of sphere are configurable.
-example of a Hsim command:
B + V -> R + V [probability]
-Molecules diffusion are simulated by movements of spheres, if the distance between two centers of the spheres is less than the sum of 2 radium, we consider that will lead to a collision.
-Computer takes a random sample and compare it to the probability which is specified in equation. If the value exceeds the threshold, we consider that the reaction takes place.
-Probability of success is associated with kinetics of reaction which depends on concentrations of molecules varying during the reaction.
-Time unit is 100ms. So movement of spheres is discreet.
-Spheres move randomly but could follow some stochastic rules (like Brownian movement).
Ethic about open source:
-Hsim is not an open source software, it belongs to the University of Paris Sud. However, it is a free software, we can download it free.
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