http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Rolfheil&year=&month=2012.igem.org - User contributions [en]2020-09-20T15:49:41ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:NTNU_Trondheim/CriteriaTeam:NTNU Trondheim/Criteria2012-08-15T10:04:25Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
</div><br />
<br />
{| class="wikitable" id="planTable"<br />
! Medal<br />
! No. of criteria that must be met<br />
! Criteria<br />
! Approach<br />
! Status<br />
! Deadline<br />
|-<br />
|rowspan="5" |Bronze<br />
|rowspan="5"| All<br />
|Team registration <br />
|Registrer team<br />
|Done<br />
|31.03<br />
|-<br />
|Complete Judging form<br />
|Complete judging form<br />
|<br />
|26.09<br />
|-<br />
|Team Wiki<br />
|Keep team wiki updated<br />
|<br />
|26.09<br />
|-<br />
|Present a poster and a talk at the iGEM Jamboree<br />
|Make poster and prepare talk<br />
|<br />
|6.10 (Amsterdam) Also make project abstract (deadline: 03.09)<br />
|-<br />
|At least one new submitted and well-characterized standard BioBrick Part or Device. A new application of and outstanding documentation (quantitative data showing the Part’s/ Device’s function) of a previously existing BioBrick part in the “Experience” section of that BioBrick’s Registry entry also counts.<br />
|lld promoter, quick and dirty characterization, and characterization by RHIT. Characterization of interaction between P<sub>lld</sub> and LldR by optical tweezers. Lysis-characterization of P<sub>lld</sub> from ''Corynebacterium glutamicum''.<br />
|<br />
|Parts must be sent to Registry within 26.09<br />
|-<br />
|rowspan="2" |Silver<br />
|rowspan="2" |All<br />
|Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected<br />
|lld promoter, quick and dirty characterization, and characterization by RHIT. Characterization of interaction between P<sub>lld</sub> and LldR by optical tweezers. Lysis-characterization of P<sub>lld</sub> from ''Corynebacterium glutamicum''.<br />
|<br />
|Wiki freeze 26.09<br />
|-<br />
|Characterize the operation of at least one new BioBrick Part or Device and enter this information in the “Main Page” section of that Part’s/Device’s Registry entry.<br />
|P<sub>lld</sub> either from ''E.coli'' or from ''C.glutamicum''.<br />
|<br />
|Wiki freeze 26.09<br />
|-<br />
|rowspan="4"|Gold<br />
|rowspan="4"|1<br />
|Improve the function of an existing BioBrick Part or Device (created by another team or your own institution in a previous year) and enter this information in the Registry (in the “Experience” section of that BioBrick’s Registry entry), and don't forget to create a new registry page for the improved part.<br />
|Nina is on it!<br />
|<br />
|<br />
|-<br />
|The growth of the Registry depends on having a broad base of reliable parts. This is why the improvement of an existing part is just as important as the creation and documentation of a new part. An "improvement" is anything that improves the functionality and ease-of-use of a part, so that it is more likely to be used by the community. For instance: strengthening the expression of a part by mutating the DNA sequence; modifying one or a few parts in construct (Device) so that it performs its intended job better; improving a cloning or expression vector that can be easily used by the entire community; and of course, troubleshooting and fixing a part reported to be non-functional. Data from an experimental comparison between the original and improved part/ device is strongly recommended.<br />
|<br />
|<br />
|<br />
|-<br />
| Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.<br />
|Modell parts of RHiTs system stochastically.<br />
|Done<br />
|<br />
|-<br />
|Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
|Matchmaker<br />
|Done and link has benn sent out to other teams.<br />
|<br />
|-<br />
|}</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:35:19Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|-<br />
|Fus3PP + Ste12 &rarr; Fus3Ste12<br />
|18<br />
|Activation of Ste12 through complexation with Fus3<br />
|-<br />
|Fus3Ste12 &rarr; Fus3PP + Ste12<br />
|10<br />
|Deactivation of Ste12 by release of Fus3<br />
|-<br />
|Bar1 + Fus3Ste12 &rarr; aBar1 + Fus3Ste12<br />
|0.1<br />
|Activation of Bar1 enzyme<br />
|-<br />
|aBar1 &rarr; Bar1<br />
|0.1<br />
|Deactivation of Bar1<br />
|-<br />
|aBar1 &rarr; ø<br />
|0.01<br />
|Export of active Bar1<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''<br />
<br />
<br />
The initial amounts are given in the table below.<br />
<br />
{|border="1"<br />
|-<br />
!Species<br />
!Amount<br />
|-<br />
|Fus3<br />
|200<br />
|-<br />
|Fus3PP<br />
|0<br />
|-<br />
|Ste12<br />
|200<br />
|-<br />
|Fus3Ste12<br />
|0<br />
|-<br />
|Bar1<br />
|200<br />
|-<br />
|aBar1<br />
|0<br />
|}<br />
<br />
A .zip file of the model can be downloaded [[Media:NTNU_Trondheim_Yeast.zip|here]]. The original file is in .xml format and can be opened with the Cain software[http://cain.sourceforge.net].</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:32:05Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|-<br />
|Fus3PP + Ste12 &rarr; Fus3Ste12<br />
|18<br />
|Activation of Ste12 through complexation with Fus3<br />
|-<br />
|Fus3Ste12 &rarr; Fus3PP + Ste12<br />
|10<br />
|Deactivation of Ste12 by release of Fus3<br />
|-<br />
|Bar1 + Fus3Ste12 &rarr; aBar1 + Fus3Ste12<br />
|0.1<br />
|Activation of Bar1 enzyme<br />
|-<br />
|aBar1 &rarr; Bar1<br />
|0.1<br />
|Deactivation of Bar1<br />
|-<br />
|aBar1 &rarr; ø<br />
|0.01<br />
|Export of active Bar1<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''<br />
<br />
<br />
The initial amounts are given in the table below.<br />
<br />
{|border="1"<br />
|-<br />
!Species<br />
!Amount<br />
|-<br />
|Fus3<br />
|200<br />
|-<br />
|Fus3PP<br />
|0<br />
|-<br />
|Ste12<br />
|200<br />
|-<br />
|Fus3Ste12<br />
|0<br />
|-<br />
|Bar1<br />
|200<br />
|-<br />
|aBar1<br />
|0<br />
|}<br />
<br />
A .zip file of the full model can be downloaded [[Media:NTNU_Trondheim_Yeast.zip|here]].</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:30:49Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|-<br />
|Fus3PP + Ste12 &rarr; Fus3Ste12<br />
|18<br />
|Activation of Ste12 through complexation with Fus3<br />
|-<br />
|Fus3Ste12 &rarr; Fus3PP + Ste12<br />
|10<br />
|Deactivation of Ste12 by release of Fus3<br />
|-<br />
|Bar1 + Fus3Ste12 &rarr; aBar1 + Fus3Ste12<br />
|0.1<br />
|Activation of Bar1 enzyme<br />
|-<br />
|aBar1 &rarr; Bar1<br />
|0.1<br />
|Deactivation of Bar1<br />
|-<br />
|aBar1 &rarr; ø<br />
|0.01<br />
|Export of active Bar1<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''<br />
<br />
<br />
The initial amounts are given in the table below.<br />
<br />
{|border="1"<br />
|-<br />
!Species<br />
!Amount<br />
|-<br />
|Fus3<br />
|200<br />
|-<br />
|Fus3PP<br />
|0<br />
|-<br />
|Ste12<br />
|200<br />
|-<br />
|Fus3Ste12<br />
|0<br />
|-<br />
|Bar1<br />
|200<br />
|-<br />
|aBar1<br />
|0<br />
|}<br />
<br />
A .zip file of the full model can be downloaded [[Media:NTNU_Trondheim_yeast.zip|here]].</div>Rolfheilhttp://2012.igem.org/File:NTNU_Trondheim_Yeast.zipFile:NTNU Trondheim Yeast.zip2012-08-14T12:30:11Z<p>Rolfheil: .zip file of model of yeast reaction to alpha-pheromone</p>
<hr />
<div>.zip file of model of yeast reaction to alpha-pheromone</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:25:28Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|-<br />
|Fus3PP + Ste12 &rarr; Fus3Ste12<br />
|18<br />
|Activation of Ste12 through complexation with Fus3<br />
|-<br />
|Fus3Ste12 &rarr; Fus3PP + Ste12<br />
|10<br />
|Deactivation of Ste12 by release of Fus3<br />
|-<br />
|Bar1 + Fus3Ste12 &rarr; aBar1 + Fus3Ste12<br />
|0.1<br />
|Activation of Bar1 enzyme<br />
|-<br />
|aBar1 &rarr; Bar1<br />
|0.1<br />
|Deactivation of Bar1<br />
|-<br />
|aBar1 &rarr; ø<br />
|0.01<br />
|Export of active Bar1<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''<br />
<br />
<br />
The initial amounts are given in the table below.<br />
<br />
{|border="1"<br />
|-<br />
!Species<br />
!Amount<br />
|-<br />
|Fus3<br />
|200<br />
|-<br />
|Fus3PP<br />
|0<br />
|-<br />
|Ste12<br />
|200<br />
|-<br />
|Fus3Ste12<br />
|0<br />
|-<br />
|Bar1<br />
|200<br />
|-<br />
|aBar1<br />
|0<br />
|}<br />
<br />
A .zip file of the full model can be downloaded [[Media:NTNU_Trondheim_Yeast.zip|here]].</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:24:27Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|-<br />
|Fus3PP + Ste12 &rarr; Fus3Ste12<br />
|18<br />
|Activation of Ste12 through complexation with Fus3<br />
|-<br />
|Fus3Ste12 &rarr; Fus3PP + Ste12<br />
|10<br />
|Deactivation of Ste12 by release of Fus3<br />
|-<br />
|Bar1 + Fus3Ste12 &rarr; aBar1 + Fus3Ste12<br />
|0.1<br />
|Activation of Bar1 enzyme<br />
|-<br />
|aBar1 &rarr; Bar1<br />
|0.1<br />
|Deactivation of Bar1<br />
|-<br />
|aBar1 &rarr; ø<br />
|0.01<br />
|Export of active Bar1<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''<br />
<br />
<br />
The initial amounts are given in the table below.<br />
<br />
{|border="1"<br />
|-<br />
!Species<br />
!Amount<br />
|-<br />
|Fus3<br />
|200<br />
|-<br />
|Fus3PP<br />
|0<br />
|-<br />
|Ste12<br />
|200<br />
|-<br />
|Fus3Ste12<br />
|0<br />
|-<br />
|Bar1<br />
|200<br />
|-<br />
|aBar1<br />
|0<br />
|}</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:19:39Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|-<br />
|Fus3PP + Ste12 &rarr; Fus3Ste12<br />
|18<br />
|Activation of Ste12 through complexation with Fus3<br />
|-<br />
|Fus3Ste12 &rarr; Fus3PP + Ste12<br />
|10<br />
|Deactivation of Ste12 by release of Fus3<br />
|-<br />
|Bar1 + Fus3Ste12 &rarr; aBar1 + Fus3Ste12<br />
|0.1<br />
|Activation of Bar1 enzyme<br />
|-<br />
|aBar1 &rarr; Bar1<br />
|0.1<br />
|Deactivation of Bar1<br />
|-<br />
|aBar1 &rarr; ø<br />
|0.01<br />
|Export of active Bar1<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:11:19Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha; is the concentration of &alpha;-phermone in nM''</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:10:47Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha is the concentration of &alpha-phermone in nM''</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:10:14Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha;-pheromone; concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha;-pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha is the concentration of &alpha-phermone in nM''</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:09:14Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to &alpha; concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of &alpha; pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶) ''where &alpha is the concentration of &alpha-phermone in nM''</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:04:11Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|}<br />
''* The function for Fus3 activation is given by'' 200*&alpha;⁶/(&alpha;⁶ + 150⁶)</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T12:02:53Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function. Timesteps in the model are minutes.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|Deactivation of Fus3<br />
|}<br />
''* The function for Fus3 activation is given by'' <math>\alpha</math></div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:59:25Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. The parameters are taken from[http://dx.doi.org/10.1002/yea.1122 [1<nowiki>]</nowiki>] and are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function.<br />
<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|-<br />
|Fus3 &rarr; Fus3PP<br />
|*<br />
|Activation of Fus3<br />
|-<br />
|Fus3PP &rarr; Fus3<br />
|150<br />
|}</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:55:59Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. All reactions are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function.<br />
<br />
{|border="1"<br />
|-<br />
!Reaction<br />
!Propensity<br />
!Comment<br />
|}</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:54:19Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
The equations used in the model are given in the table below. All reactions are modelled using mass action solvers, except Fus3 &rarr; Fus3PP, which use a sigmoid function.</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:52:12Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:51:50Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|center|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:50:56Z<p>Rolfheil: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|center|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]</div>Rolfheilhttp://2012.igem.org/Team:NTNU_Trondheim/YeastTeam:NTNU Trondheim/Yeast2012-08-14T11:50:39Z<p>Rolfheil: /* Overview */</p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<br />
<span class="heading">Collaboration with RHiT; Yeast modelling<hr/></span><br />
<br />
__TOC__<br />
<br />
Our part of the collaboration with RHiT was helping them with stochastic modelling of the trigger system for mating in yeast. The full mechanism has been quite well studied, but it is very complicated[http://dx.doi.org/10.1002/yea.1122]. In RHiTs [[Team:RHIT/Modeling|model]], the final steps of the mechanism is activation of the Ste12 protein by the Fus3 enzyme. To simplify the model, production of Fus3 in the model was described by a sigmoid curve found in experiments[http://dx.doi.org/10.1038/nature08946] with respect to the concentration of alpha pheromone. Inactive Ste12 was quickly activated by the presence of Fus3, so the outcome of active Ste12 followed a similar sigmoid curve, giving the expected switch behaviour. The resulting plot is shown in Figure 1. Each point is the average of 100 trajectories with the error bars indicating one standard deviation.<br />
<br />
[[File:NTNU_Trondheim_YeastAlpha.png|thumb|center|450px|Figure 1. Amount of activated Ste12 at steady state as a response to alpha concentrations. Error bars show one standard deviation.]]</div>Rolfheil