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Team:Paris Saclay/Notebook/July/17
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=='''Lab work'''== | =='''Lab work'''== | ||
constructing | constructing | ||
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| + | =='''Modeling'''== | ||
| + | |||
| + | Meeting memo<br> | ||
| + | Meeting Date: 17/07/2013<br> | ||
| + | Meeting participants: Patrick Amar, Claire Toffano-Nioche, Abdou Mouhtare, Damir Damipator, Gabriel Gallin, Zhou Yi<br> | ||
| + | Recorder: Zhou Yi<br> | ||
| + | |||
| + | Hsim:<br> | ||
| + | -Hsim is created for bio-chemical reaction simulation, it demonstrates bio-chemical systems which the scientists are already known.<br> | ||
| + | |||
| + | -The molecules are simulated as spheres (in 2D or 3D). Initial positions and size of sphere are configurable.<br> | ||
| + | |||
| + | -example of a Hsim command:<br> | ||
| + | B + V -> R + V [probability]<br> | ||
| + | |||
| + | -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.<br> | ||
| + | |||
| + | -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.<br> | ||
| + | |||
| + | -Probability of success is associated with kinetics of reaction which depends on concentrations of molecules varying during the reaction.<br> | ||
| + | |||
| + | -Time unit is 100ms. So movement of spheres is discreet. | ||
| + | <br> | ||
| + | -Spheres move randomly but could follow some stochastic rules (like Brownian movement).<br> | ||
| + | |||
| + | Ethic about open source:<br> | ||
| + | -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.<br> | ||
| + | |||
<br> | <br> | ||
Revision as of 21:38, 9 September 2013
Notebook : July 17
Lab work
constructing
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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