"
Team:Mexico-UNAM-CINVESTAV/Modeling/Simulations
From 2010.igem.org
m |
m |
||
| Line 3: | Line 3: | ||
== Cold shock response simulations == | == Cold shock response simulations == | ||
| - | Our model was implemented in the software tool CellDesigner 4.1. And the model file can be downloaded from [[MEXICO_UNAM_CINVESTAV_CspA_system.zip]] | + | Our model was implemented in the software tool CellDesigner 4.1. And the model file can be downloaded from [[https://2010.igem.org/Image:MEXICO_UNAM_CINVESTAV_CspA_system.zip here]] |
The estimation of the parameters has been a serious problem for the design of any model, and in our case we are not te exception. Unfortunately we were not able to obtain enough laboratory meditions and then our model is more an qualitative than quantitative approach. | The estimation of the parameters has been a serious problem for the design of any model, and in our case we are not te exception. Unfortunately we were not able to obtain enough laboratory meditions and then our model is more an qualitative than quantitative approach. | ||
Revision as of 17:05, 27 October 2010
Cold shock response simulations
Our model was implemented in the software tool CellDesigner 4.1. And the model file can be downloaded from [here]
The estimation of the parameters has been a serious problem for the design of any model, and in our case we are not te exception. Unfortunately we were not able to obtain enough laboratory meditions and then our model is more an qualitative than quantitative approach.
The main behavior that we tried to reproduce was the induction of the expression of the CspA protein during cold shock and later the adapted state of the cell where the synthesis of the cold shock proteins is low and the rate of the synthesis of the rest of the proteins stabilizes to certain level.
In the Simulations 1 and 2 is represented the qualitative response of the cold shock system. From time t=0 the level of the E. coli proteins decrease until enough CspA is present in the media. The amount of CspA grows until a E. coli proteins reach a maximum level and then decays to a stable one.
Visualization of the Antifreeze protein
Software references
- Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H., CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, 1:159-162, 2003 [doi:10.1016/S1478-5382(03)02370-9]
- Funahashi, A.; Matsuoka, Y.; Jouraku, A.; Morohashi, M.; Kikuchi, N.; Kitano, H."CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks" Proceedings of the IEEE Volume 96, Issue 8, Aug. 2008 Page(s):1254 - 1265 [doi 10.1109/JPROC.2008.925458]
 |
 |
 |
 |
