http://wiki.biocellion.com/index.php?title=Cell_sorting&feed=atom&action=historyCell sorting - Revision history2024-03-29T09:05:17ZRevision history for this page on the wikiMediaWiki 1.27.0http://wiki.biocellion.com/index.php?title=Cell_sorting&diff=75&oldid=prevSimon Kahan at 02:48, 7 September 20142014-09-07T02:48:26Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:48, 7 September 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the Biocellion framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the Biocellion framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><center></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915|400}}</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915|400}}</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></center></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:74:newid:75 -->
</table>Simon Kahanhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=74&oldid=prevSimon Kahan at 01:57, 7 September 20142014-09-07T01:57:42Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:57, 7 September 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the Biocellion framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the Biocellion framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915|400<del class="diffchange diffchange-inline">|center</del>}}</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915|400}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:67:newid:74 -->
</table>Simon Kahanhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=67&oldid=prevFarzin at 02:54, 10 March 20142014-03-10T02:54:20Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:54, 10 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">== Cell sorting ==</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg, Malcolm S. (1963). Reconstruction of Tissues by Dissociated Cells. ''Science'', '''141''', no. 3579, 401-408.</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref>Zhang, L., Wang, Z., Sagotsky, J. A., and Deisboeck, T. S. (2009). Multiscale agent based cancer modeling. ''Journal of Mathematical Biology'', '''58'''(4-5), 545–559.</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg, Malcolm S. (1963). Reconstruction of Tissues by Dissociated Cells. ''Science'', '''141''', no. 3579, 401-408.</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref>Zhang, L., Wang, Z., Sagotsky, J. A., and Deisboeck, T. S. (2009). Multiscale agent based cancer modeling. ''Journal of Mathematical Biology'', '''58'''(4-5), 545–559.</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:66:newid:67 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=66&oldid=prevFarzin at 02:53, 10 March 20142014-03-10T02:53:43Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:53, 10 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td>
<td colspan="2" class="diff-lineno">Line 7:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the Biocellion framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the Biocellion framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915<ins class="diffchange diffchange-inline">|400|center</ins>}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:65:newid:66 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=65&oldid=prevFarzin at 02:52, 10 March 20142014-03-10T02:52:44Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:52, 10 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells<ref><del class="diffchange diffchange-inline">Zhang</del>, <del class="diffchange diffchange-inline">L., Wang, Z., Sagotsky, J. A., and Deisboeck, T. </del>S. (<del class="diffchange diffchange-inline">2009</del>). <del class="diffchange diffchange-inline">Multiscale agent based cancer modeling</del>. ''<del class="diffchange diffchange-inline">Journal of Mathematical Biology</del>'', '''<del class="diffchange diffchange-inline">58</del>'''<del class="diffchange diffchange-inline">(4</del>-<del class="diffchange diffchange-inline">5), 545–559</del>.</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref><del class="diffchange diffchange-inline">Steinberg</del>, <del class="diffchange diffchange-inline">Malcolm </del>S. (<del class="diffchange diffchange-inline">1963</del>). <del class="diffchange diffchange-inline">Reconstruction of Tissues by Dissociated Cells</del>. ''<del class="diffchange diffchange-inline">Science</del>'', '''<del class="diffchange diffchange-inline">141</del>''', <del class="diffchange diffchange-inline">no. 3579, 401-408</del>.</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref><ins class="diffchange diffchange-inline">Steinberg</ins>, <ins class="diffchange diffchange-inline">Malcolm </ins>S. (<ins class="diffchange diffchange-inline">1963</ins>). <ins class="diffchange diffchange-inline">Reconstruction of Tissues by Dissociated Cells</ins>. ''<ins class="diffchange diffchange-inline">Science</ins>'', '''<ins class="diffchange diffchange-inline">141</ins>'''<ins class="diffchange diffchange-inline">, no. 3579, 401</ins>-<ins class="diffchange diffchange-inline">408</ins>.</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref><ins class="diffchange diffchange-inline">Zhang, L., Wang, Z., Sagotsky, J. A., and Deisboeck</ins>, <ins class="diffchange diffchange-inline">T. </ins>S. (<ins class="diffchange diffchange-inline">2009</ins>). <ins class="diffchange diffchange-inline">Multiscale agent based cancer modeling</ins>. ''<ins class="diffchange diffchange-inline">Journal of Mathematical Biology</ins>'', '''<ins class="diffchange diffchange-inline">58</ins>'''<ins class="diffchange diffchange-inline">(4-5)</ins>, <ins class="diffchange diffchange-inline">545–559</ins>.</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:64:newid:65 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=64&oldid=prevFarzin: /* Cell sorting */2014-03-10T02:51:25Z<p><span dir="auto"><span class="autocomment">Cell sorting</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:51, 10 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"><ref>{{cite doi|10.1146/annurev.earth.33.092203.122621}}</ref> </del>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref><del class="diffchange diffchange-inline">Steinberg1963Reconstruction</del></ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref><del class="diffchange diffchange-inline">GG92</ref> <ref>Zhang2011Computer</del></ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells<ref><ins class="diffchange diffchange-inline">Zhang, L., Wang, Z., Sagotsky, J. A., and Deisboeck, T. S. (2009). Multiscale agent based cancer modeling. ''Journal of Mathematical Biology'', '''58'''(4-5), 545–559.</ins></ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref><ins class="diffchange diffchange-inline">Steinberg, Malcolm S. (1963). Reconstruction of Tissues by Dissociated Cells. ''Science'', '''141''', no. 3579, 401-408.</ins></ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l9" >Line 9:</td>
<td colspan="2" class="diff-lineno">Line 9:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><references></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><references> </references></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div></references></div></td><td colspan="2"> </td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:63:newid:64 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=63&oldid=prevFarzin: /* Cell sorting */2014-03-10T02:04:43Z<p><span dir="auto"><span class="autocomment">Cell sorting</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:04, 10 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg1963Reconstruction</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref>GG92</ref> <ref>Zhang2011Computer</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><ref>{{cite doi|10.1146/annurev.earth.33.092203.122621}}</ref> </ins>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg1963Reconstruction</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref>GG92</ref> <ref>Zhang2011Computer</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the <del class="diffchange diffchange-inline">\biocellion{} </del>framework has 756 lines---the empty model code template has 650 lines. <del class="diffchange diffchange-inline">[</del>Biocellion<del class="diffchange diffchange-inline">{www.biocellion.com}] </del>users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the <ins class="diffchange diffchange-inline">Biocellion </ins>framework has 756 lines---the empty model code template has 650 lines. Biocellion users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><references></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></references></ins></div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:62:newid:63 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=62&oldid=prevFarzin at 23:37, 9 March 20142014-03-09T23:37:29Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 23:37, 9 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the \biocellion{} framework has 756 lines---the empty model code template has 650 lines. <del class="diffchange diffchange-inline">\</del>biocellion<del class="diffchange diffchange-inline">{</del>} users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the \biocellion{} framework has 756 lines---the empty model code template has 650 lines. <ins class="diffchange diffchange-inline">[Biocellion{www.</ins>biocellion<ins class="diffchange diffchange-inline">.com</ins>}<ins class="diffchange diffchange-inline">] </ins>users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 ''&mu;<sub>m</sub>'' for 1.72 billion cells packed in a 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>''* 10 ''&mu;<sub>m</sub>'' region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:61:newid:62 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=61&oldid=prevFarzin at 23:36, 9 March 20142014-03-09T23:36:30Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 23:36, 9 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Cell sorting ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg1963Reconstruction</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns<del class="diffchange diffchange-inline">~</del><ref>GG92</ref> <ref>Zhang2011Computer</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg1963Reconstruction</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns <ref>GG92</ref> <ref>Zhang2011Computer</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:sorting.png|500px|center|Cell sorting]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:60:newid:61 -->
</table>Farzinhttp://wiki.biocellion.com/index.php?title=Cell_sorting&diff=60&oldid=prevFarzin at 23:35, 9 March 20142014-03-09T23:35:41Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 23:35, 9 March 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
<td colspan="2" class="diff-lineno">Line 3:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg1963Reconstruction</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns~<ref>GG92</ref> <ref>Zhang2011Computer</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Many multicellular patterns formed during morphogenesis and embryonic development arise because of differential adhesion among distinct types of disassociated cells <ref>Steinberg1963Reconstruction</ref>. Simulations of this process have demonstrated how changes in homotypic and heterotypic adhesion can result in many distinct macroscopic cellular arrangements including clumping, where homotypic cells aggregate, or mosaics where heterotypic cells alternate forming checkerboard-like patterns~<ref>GG92</ref> <ref>Zhang2011Computer</ref>. In our test model, two different cell types are defined with each cell mapped to a sphere of diameter 8 ''&mu;<sub>m</sub>''. If there is an overlap between two neighboring spheres, the two cells push each other to remove the overlap (cell-cell shoving). In this demonstration, if two non-overlapping cells of a same type are within 10 ''&mu;<sub>m</sub>'' they pull towards each other modelling stronger adhesion. If they are of different types there is no additional attractive force. The simulations demonstrate that such differential adhesion leads to cell sorting into homotypic aggregations from an initial random distribution.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[File:sorting.png|500px|center|Cell sorting]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the \biocellion{} framework has 756 lines---the empty model code template has 650 lines. \biocellion{} users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 <del class="diffchange diffchange-inline">$\</del>mu m<del class="diffchange diffchange-inline">$ </del>for 1.72 billion cells packed in a 10 <del class="diffchange diffchange-inline">$mm$ $\times$ </del>10 <del class="diffchange diffchange-inline">$mm$ $\times$ </del>10 <del class="diffchange diffchange-inline">$mm$ </del>region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The model code implemented using the \biocellion{} framework has 756 lines---the empty model code template has 650 lines. \biocellion{} users can simulate cell sorting using a cluster computer with just little more than 100 lines of coding. Evaluating pairwise interactions once for every cell pair within 10 <ins class="diffchange diffchange-inline">''&</ins>mu<ins class="diffchange diffchange-inline">;<sub></ins>m<ins class="diffchange diffchange-inline"></sub>'' </ins>for 1.72 billion cells packed in a 10 <ins class="diffchange diffchange-inline">''&mu;<sub>m</sub>''* </ins>10 <ins class="diffchange diffchange-inline">''&mu;<sub>m</sub>''* </ins>10 <ins class="diffchange diffchange-inline">''&mu;<sub>m</sub>'' </ins>region takes approximately 20 seconds using 32 compute nodes (each node has two AMD Opteron 6272 Interlago 2.1 GHz sockets).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>{{#ev:vimeo|88399915}}</div></td></tr>
<!-- diff cache key wikidb:diff:version:1.11a:oldid:57:newid:60 -->
</table>Farzin