"
Team:Newcastle/Modelling/Cell Fusion
From 2013.igem.org
| Line 2: | Line 2: | ||
=Cell Fusion= | =Cell Fusion= | ||
| - | The following simple simulation demonstrates the expected behaviour of fusion events of L-forms. The L-forms shown in this simulation are expressing one of the two different BioBricks [http://parts.igem.org/Part:BBa_K1185001 BBa_K1185001] and [http://parts.igem.org/Part:BBa_K1185002 BBa_K1185002] which tag the genome with green or red fluorescence respectively. This simulation also shows the predicted phenotypic result (the colours of the L-forms) following fusion. This simulation was coded in Java. | + | The following simple simulation demonstrates the expected behaviour of fusion events of L-forms. The L-forms shown in this simulation are simplified models expressing one of the two different BioBricks [http://parts.igem.org/Part:BBa_K1185001 BBa_K1185001] and [http://parts.igem.org/Part:BBa_K1185002 BBa_K1185002] which tag the genome with green or red fluorescence respectively. This simulation also shows the predicted phenotypic result (the colours of the L-forms) following fusion. This simulation was coded in Java. |
<html> | <html> | ||
| Line 19: | Line 19: | ||
<strong>Movement. </strong> | <strong>Movement. </strong> | ||
Every L-form has a random movement speed which is 1-6 pixels per game step. Furthermore they have movement direction, there are two variables which represent their | Every L-form has a random movement speed which is 1-6 pixels per game step. Furthermore they have movement direction, there are two variables which represent their | ||
| - | movement per step on x axis and y axis. On every simulation step a random number [-2,2] is generated which is then added to current speed. Also there | + | movement per step on x axis and y axis. On every simulation step a uniformally random number in the [-2,2] interval is generated which is then added to current speed. Also there |
| - | are speed limits so that L- | + | are speed limits so that L-forms cannot move faster than -6 pixels or 6 pixels on any axis. |
</p> | </p> | ||
<p> | <p> | ||
<strong>Division. </strong> | <strong>Division. </strong> | ||
| - | There is 1 | + | There is 1% chance per step that cell division will be triggered, provided there is at least one "unused" L-form entity. If this happens, then the three |
biggest(in radius) L-forms are selected, provided they are not already dividing. | biggest(in radius) L-forms are selected, provided they are not already dividing. | ||
</p> | </p> | ||
<p> | <p> | ||
<strong>L-Forms. </strong> | <strong>L-Forms. </strong> | ||
| - | Simulation starts with eleven L- | + | Simulation starts with eleven L-forms (5 red, 6 green), which have random radius of 10 to 20 pixels. |
</p> | </p> | ||
<p> | <p> | ||
| Line 37: | Line 37: | ||
<p> | <p> | ||
<strong>Collision.</strong> | <strong>Collision.</strong> | ||
| - | + | When two L-forms collide there is 50% chance that the bigger L-form will absorb the smaller one, otherwise they just bounce off. If absorption happens, we calculate smaller L-form's surface area and add it to the bigger L-form's surface area. The absorbed ball entity is marked as "unused" and moved | |
| - | + | ||
away from the screen. | away from the screen. | ||
</p> | </p> | ||
<p> | <p> | ||
<strong>Colour</strong> | <strong>Colour</strong> | ||
| - | + | Originally we start with RED and GREEN colours. When a collision happens, L-forms will keep the same colour, or if two different colours collide they will | |
become yellow. | become yellow. | ||
</p> | </p> | ||
| - | <p>If you want to see the code or run it, or even edit it in your local | + | <p>If you want to see the code or run it, or even edit it in your local Java environment, you can download the source code <a href="https://2013.igem.org/File:BareCillus_simulation.zip">here</a>. </p> |
</html> | </html> | ||
{{Team:Newcastle/Sponsors}} | {{Team:Newcastle/Sponsors}} | ||
Latest revision as of 14:31, 4 October 2013
Cell Fusion
The following simple simulation demonstrates the expected behaviour of fusion events of L-forms. The L-forms shown in this simulation are simplified models expressing one of the two different BioBricks [http://parts.igem.org/Part:BBa_K1185001 BBa_K1185001] and [http://parts.igem.org/Part:BBa_K1185002 BBa_K1185002] which tag the genome with green or red fluorescence respectively. This simulation also shows the predicted phenotypic result (the colours of the L-forms) following fusion. This simulation was coded in Java.
Simulation rules and parameters
Movement. Every L-form has a random movement speed which is 1-6 pixels per game step. Furthermore they have movement direction, there are two variables which represent their movement per step on x axis and y axis. On every simulation step a uniformally random number in the [-2,2] interval is generated which is then added to current speed. Also there are speed limits so that L-forms cannot move faster than -6 pixels or 6 pixels on any axis.
Division. There is 1% chance per step that cell division will be triggered, provided there is at least one "unused" L-form entity. If this happens, then the three biggest(in radius) L-forms are selected, provided they are not already dividing.
L-Forms. Simulation starts with eleven L-forms (5 red, 6 green), which have random radius of 10 to 20 pixels.
Location. All L-forms are randomly created on the screen.
Collision. When two L-forms collide there is 50% chance that the bigger L-form will absorb the smaller one, otherwise they just bounce off. If absorption happens, we calculate smaller L-form's surface area and add it to the bigger L-form's surface area. The absorbed ball entity is marked as "unused" and moved away from the screen.
Colour Originally we start with RED and GREEN colours. When a collision happens, L-forms will keep the same colour, or if two different colours collide they will become yellow.
If you want to see the code or run it, or even edit it in your local Java environment, you can download the source code here.
