Team:EPF-Lausanne/Modeling/BioreactorSim

From 2012.igem.org

(Difference between revisions)
Line 36: Line 36:
  <label class="control-label" for="radius">Bioreactor Radius</label>
  <label class="control-label" for="radius">Bioreactor Radius</label>
  <div class="controls">
  <div class="controls">
-
<input placeholder="Radius in meters" class="input-xlarge" type="text" id="radius">
+
<input placeholder="Radius in meters (0.5)" class="input-xlarge" type="text" id="radius">
<p class="help-block">This defines the size of the bioreactor. This can be anything from a few centimeters to a few meters (depends on the production scale).</p>
<p class="help-block">This defines the size of the bioreactor. This can be anything from a few centimeters to a few meters (depends on the production scale).</p>
  </div>
  </div>
Line 44: Line 44:
  <!-- Text input-->
  <!-- Text input-->
-
  <label class="control-label" for="power">Light power</label>
+
  <label class="control-label" for="power">Total Light power</label>
  <div class="controls">
  <div class="controls">
-
<input placeholder="The power of the lights in W/m" class="input-xlarge" type="text" id="power">
+
<input placeholder="The power of the lights in W/m (120)" class="input-xlarge" type="text" id="power">
-
<p class="help-block">As the model of the bioreactor is an infinite cylinder with infinite lighting strips, the light intensity needs of each strip needs to be defined in Watts per meter. A sample value is 10 Watts (a strip of normal LEDs)</p>
+
<p class="help-block">As the model of the bioreactor is an infinite cylinder with infinite lighting strips, the light intensity needs of all strip needs to be defined in Watts per meter. This power will be uniformly distributed among the lights.</p>
  </div>
  </div>
</div>
</div>
Line 61: Line 61:
</label>
</label>
  </span>
  </span>
-
  <input class="span10" placeholder="Reflectivity" id="reflectiveAmount" type="text">
+
  <input class="span2" placeholder="Reflectivity (0.9)" id="reflectiveAmount" type="text">
</div>
</div>
<p class="help-block">The bioreactor can have reflective walls which will keep more of the light inside of the bioreactor. Typical values for the frequencies we're working with are 0.9 (for aluminium and silver) and 0.4 (for gold)</p>
<p class="help-block">The bioreactor can have reflective walls which will keep more of the light inside of the bioreactor. Typical values for the frequencies we're working with are 0.9 (for aluminium and silver) and 0.4 (for gold)</p>
Line 71: Line 71:
  <label class="control-label" for="absorbance">Absorbance</label>
  <label class="control-label" for="absorbance">Absorbance</label>
  <div class="controls">
  <div class="controls">
-
<input placeholder="Absorbance of 1mm of culture" class="input-xlarge" type="text" id="absorbance">
+
<input placeholder="Absorbance of 1mm of culture (0.01)" class="input-xlarge" type="text" id="absorbance">
<p class="help-block">This value determines how much of the light is absorbed by the culture. Typical values can range from 0.01-0.04.</p>
<p class="help-block">This value determines how much of the light is absorbed by the culture. Typical values can range from 0.01-0.04.</p>
  </div>
  </div>
-
</div><div class="control-group">
+
</div>
<div class="control-group">
<div class="control-group">
Line 86: Line 86:
</label>
</label>
  </span>
  </span>
-
  <input class="span10" placeholder="Light Angle (in degrees)" id="lightAngle" type="text">
+
  <input class="span2" placeholder="Light Angle (in degrees) (20)" id="lightAngle" type="text">
</div>
</div>
<p class="help-block">The lights can be uniform (same amount of light in all directions) or directed (light will come out of in a small angle).</p>
<p class="help-block">The lights can be uniform (same amount of light in all directions) or directed (light will come out of in a small angle).</p>
Line 96: Line 96:
  <label class="control-label" for="rays">Rays per Lightsource</label>
  <label class="control-label" for="rays">Rays per Lightsource</label>
  <div class="controls">
  <div class="controls">
-
<input placeholder="The amount of rays shot per light (100)" class="input-xlarge" type="text" id="rays">
+
<input placeholder="The amount of rays shot per light (50)" class="input-xlarge" type="text" id="rays">
<p class="help-block">This simulator works by shooting rays out of each light source. The more rays are used, the longer the simulation will take, but the better the result will be.</p>
<p class="help-block">This simulator works by shooting rays out of each light source. The more rays are used, the longer the simulation will take, but the better the result will be.</p>
  </div>
  </div>
Line 114: Line 114:
  <label class="control-label" for="nLights">Number of Lights</label>
  <label class="control-label" for="nLights">Number of Lights</label>
  <div class="controls">
  <div class="controls">
-
<input placeholder="The number of lights (4)" class="input-xlarge" type="text" id="nLights">
+
<input placeholder="The number of lights (16)" class="input-xlarge" type="text" id="nLights">
<p class="help-block">Number of Lights in the system. The more lights, the better and the more uniform the lighting. Will increase the computation time.</p>
<p class="help-block">Number of Lights in the system. The more lights, the better and the more uniform the lighting. Will increase the computation time.</p>
 +
  </div>
 +
</div>
 +
 +
<div class="control-group">
 +
  <!-- Text input-->
 +
  <label class="control-label" for="nRings">Number of Rings</label>
 +
  <div class="controls">
 +
<input placeholder="The number of rings (2)" class="input-xlarge" type="text" id="nRings">
 +
<p class="help-block">Number of rings of Lights in the system. This just changes the distribution of the lights.</p>
  </div>
  </div>
</div>
</div>
<div class="control-group" id="runButtonWrapper">
<div class="control-group" id="runButtonWrapper">
-
  <label class="control-label"></label>
+
  <label class="control-label"> </label>
  <!-- Button -->
  <!-- Button -->
Line 129: Line 138:
<div class="control-group" id="cancelButtonWrapper" style="display: none;">
<div class="control-group" id="cancelButtonWrapper" style="display: none;">
-
  <label class="control-label"></label>
+
  <label class="control-label"> </label>
  <!-- Button -->
  <!-- Button -->
Line 158: Line 167:
  <label class="control-label">Image</label>
  <label class="control-label">Image</label>
  <div class="controls">
  <div class="controls">
-
             <canvas width="400" height="400" id="output"></canvas>
+
             <canvas width="400" height="400" id="output"> </canvas>
-
             <div class="help-block">Shows the light intensity in a slice of the bioreactor. This image uses the jet colormap. Red = saturated, yellow/green = partially saturated, blue = not enough lighting.</div>
+
             <div class="help-block">Shows the light intensity in a slice of the bioreactor. This image uses the jet colormap. Red = saturated, green = partially saturated, blue = low/no lighting.</div>
  </div>
  </div>
</div>
</div>

Revision as of 22:29, 20 September 2012


We chose to represent the bioreactor as an infinitely long cylinder. This allows us to consider the problem in two dimensions, yet should stay realistic (the bioreactor will normally be at least twice longer than its radius, this model should quite accurately represent what's happening in the middle). From literature [cite!], we know that LovTAP saturates at 200W/cm^2 (note: lower intensities should still work, as saturation isn't necessary, we just want a significant proportion to be activated, but this should keep things easier to calculate).

The results are displaed in a picture at the bottom of the page. Everything that is dark red is fully saturated, but everything between red and green should be enough. The places where the picture is blue represent parts that aren't illuminated enough. However, as the activated LOV-domain has a half-life of 30-40s (and our protein's half-life should be quite close to this), and the bioreactor is orbitally shaken (which results in chaotic movement, meaning every cell has a quasi-uniform probability of coming anywhere in the bioreactor), the only thing that matters is that the coverage is high enough (note: high enough depends on several parameters such as the shaker speed).

Please play with our tool! (If you're unsure about the settings, just click run to use sane defaults).

This page uses Web Workers to avoid freezing the page while performing its calculations. Please update your browser to use this simulator.
Please check if all values in the forms are correct (all fields are filled, numbers are numbers, etc...).
Bioreactor Lighting Simulator

This defines the size of the bioreactor. This can be anything from a few centimeters to a few meters (depends on the production scale).

As the model of the bioreactor is an infinite cylinder with infinite lighting strips, the light intensity needs of all strip needs to be defined in Watts per meter. This power will be uniformly distributed among the lights.

The bioreactor can have reflective walls which will keep more of the light inside of the bioreactor. Typical values for the frequencies we're working with are 0.9 (for aluminium and silver) and 0.4 (for gold)

This value determines how much of the light is absorbed by the culture. Typical values can range from 0.01-0.04.

The lights can be uniform (same amount of light in all directions) or directed (light will come out of in a small angle).

This simulator works by shooting rays out of each light source. The more rays are used, the longer the simulation will take, but the better the result will be.

Resolution of the simulation. Higher resolutions need more rays per lightsource to be accurate.

Number of Lights in the system. The more lights, the better and the more uniform the lighting. Will increase the computation time.

Number of rings of Lights in the system. This just changes the distribution of the lights.

Results
?%
Shows the light intensity in a slice of the bioreactor. This image uses the jet colormap. Red = saturated, green = partially saturated, blue = low/no lighting.
At any point in time, ?% of the cells are saturated in light (as the cells are shaken around the orbital shaker and the LOV domain has a long half-time, they don't need to be constantly saturated).
?% of the light was lost (absorbed by the walls or escaped through a transparent wall).


Wiki Links

Important pages

Pages

Retrieved from "http://2012.igem.org/Team:EPF-Lausanne/Modeling/BioreactorSim"