http://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?action=history&feed=atom&title=BanghamLabSVNBanghamLabSVN - Revision history2026-05-03T16:58:59ZRevision history for this page on the wikiMediaWiki 1.43.8http://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6241&oldid=prevAndrewBangham at 10:49, 23 May 20132013-05-23T10:49:27Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: darkred">DArT_Toolshed</span>=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: darkred">DArT_Toolshed</span>=</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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 DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.<del style="font-weight: bold; text-decoration: none;">6 </del>GB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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 DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.<ins style="font-weight: bold; text-decoration: none;">36 </ins>GB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions. The physics and numerics are accessible but elsewhere. Stick in a breakpoint and step through algorithms to see how they work.<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions. The physics and numerics are accessible but elsewhere. Stick in a breakpoint and step through algorithms to see how they work.<br><br></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6240&oldid=prevAndrewBangham at 10:44, 23 May 20132013-05-23T10:44:51Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: darkred">DArT_Toolshed</span>=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=<span style="color: darkred">DArT_Toolshed</span>=</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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 DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 <del style="font-weight: bold; text-decoration: none;">MB </del>zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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 DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 <ins style="font-weight: bold; text-decoration: none;">GB </ins>zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions. The physics and numerics are accessible but elsewhere. Stick in a breakpoint and step through algorithms to see how they work.<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions. The physics and numerics are accessible but elsewhere. Stick in a breakpoint and step through algorithms to see how they work.<br><br></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6235&oldid=prevAndrewBangham at 07:57, 22 May 20132013-05-22T07:57:46Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 08:57, 22 May 2013</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions. The physics and numerics are accessible but elsewhere. Stick in a breakpoint <del style="font-weight: bold; text-decoration: none;">on </del>step through algorithms to see how they work.<br><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions. The physics and numerics are accessible but elsewhere. Stick in a breakpoint <ins style="font-weight: bold; text-decoration: none;">and </ins>step through algorithms to see how they work.<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. We use Windows, Mac OS and Linux.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. We use Windows, Mac OS and Linux.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br><br></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6234&oldid=prevAndrewBangham at 07:57, 22 May 20132013-05-22T07:57:17Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 08:57, 22 May 2013</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4">Line 4:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions.<br><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions<ins style="font-weight: bold; text-decoration: none;">. The physics and numerics are accessible but elsewhere. Stick in a breakpoint on step through algorithms to see how they work</ins>.<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. We use Windows, Mac OS and Linux.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. We use Windows, Mac OS and Linux.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br><br></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6233&oldid=prevAndrewBangham at 19:23, 21 May 20132013-05-21T19:23:17Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:23, 21 May 2013</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions.<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions.<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. We use Windows, Mac OS and Linux.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. We use Windows, Mac OS and Linux.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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;"><br><br></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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;">In keeping with Matlab conventions, most of our functions have help comments in the first few lines of the file. This means that Matlab itself indexes this file-level help automatically. To allow you to see the scope of our work, this help has been listed on the following pages.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6232&oldid=prevAndrewBangham at 19:17, 21 May 20132013-05-21T19:17:06Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:17, 21 May 2013</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>__NOTOC__</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>__NOTOC__</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software| Return to Software]]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software| Return to Software]]<br><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>=DArT_Toolshed=</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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;"><span style="color: darkred"></ins>DArT_Toolshed<ins style="font-weight: bold; text-decoration: none;"></span></ins>=</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6231&oldid=prevAndrewBangham at 19:15, 21 May 20132013-05-21T19:15:43Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:15, 21 May 2013</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions.<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. MTtbox is similar, biological models are succinctly coded into interaction functions.<br><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors<ins style="font-weight: bold; text-decoration: none;">. We use Windows, Mac OS and Linux</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6230&oldid=prevAndrewBangham at 19:14, 21 May 20132013-05-21T19:14:53Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. <br><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model<ins style="font-weight: bold; text-decoration: none;">. MTtbox is similar, biological models are succinctly coded into interaction functions</ins>.<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6229&oldid=prevAndrewBangham at 19:13, 21 May 20132013-05-21T19:13:37Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:13, 21 May 2013</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: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=DArT_Toolshed=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=DArT_Toolshed=</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''DArT_Toolbox_Download.zip''''' Revision 4699</span>]<br><br></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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;">Most of the software is written in Matlab. Exceptions include VolViewer which uses OpenGL extensively. <br><br></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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;">'''Why Matlab?''' The language suits our problems. For example, ''GFtbox'' - the reasoning goes like this. Tissue is represented by a thin 3D mesh. Growth factors levels vary spatially forming patterns, e.g. Fig. 1. Here there are two, ''A'' and ''B''. We might make the hypothesis that the growth rate is specified by ''A'' but partially inhibited by ''B'' (inhibited by an amount ''K''). This is a simple idea that can be expressed in Matlab equally simply by writing ''Growth=A .* inh(K, B)''. This is because variables ''A'' and ''B'' can represent vectors - in this case a level for each node in the mesh. We also define a general inhibition function (''inh''). It means that it is straightforward to convert our thoughts on the biology into a programmatic description of a computational model. <br><br></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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;">Moreover, the language is well documented with lots of convenient tools. In particular, Matlab has an extensive library of portable graphical user interface (GUI) functions - and this is convenient for producing tools to visualise the mesh and patterns of growth factors. </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td></tr>
</table>AndrewBanghamhttp://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=BanghamLabSVN&diff=6228&oldid=prevAndrewBangham at 19:08, 21 May 20132013-05-21T19:08:50Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:08, 21 May 2013</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: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software| Return to Software]]<br><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Software| Return to Software]]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=DArT_Toolshed=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=DArT_Toolshed=</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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 DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''<del style="font-weight: bold; text-decoration: none;">Leaves</del>''''' <del style="font-weight: bold; text-decoration: none;">Kuchen et al 2012</del></span>]<br><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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 DArT_Toolshed is a repository of software developed on BBSRC grant BB/F005555/1 ''A Multiscale Approach to Genes Growth and Geometry'' (a collaboration with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab]). A 0.6 MB zipped copy (21st May 2013) is available [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/DArT_Toolbox_Download.zip <span style="color: Gray">'''''<ins style="font-weight: bold; text-decoration: none;">DArT_Toolbox_Download.zip</ins>''''' <ins style="font-weight: bold; text-decoration: none;">Revision 4699</ins></span>]<br><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==[[Toolboxes file level help|<span style="color: Navy">Toolboxes: File level help</span>]] ==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total 2828 functions.</div></td></tr>
</table>AndrewBangham