https://doyle.caltech.edu/index.php?action=history&feed=atom&title=Modeling_Biological_Systems 2026-05-11T04:11:54Z Revision history for this page on the wiki MediaWiki 1.44.2 https://doyle.caltech.edu/index.php?title=Modeling_Biological_Systems&diff=3164&oldid=prev 2010-02-18T22:16:21Z

<p><span class="autocomment">Slides</span></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 22:16, 18 February 2010</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;"><br></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;"><br></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>== Slides ==</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>== Slides ==</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;"></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;">*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/RecapFeb09.pptx  Architecture and Layering in Biology]</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;">*[http://www.cds.caltech.edu/~doyle/213/MinimalCell.pptx Minimal Cell Model]</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;"><br></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;"><br></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>== Reading ==</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>== Reading ==</div></td></tr> <!-- diff cache key acs_math_mw_144-doyle_:diff:1.41:old-3136:rev-3164:php=table --> </table>

Vanessa https://doyle.caltech.edu/index.php?title=Modeling_Biological_Systems&diff=3136&oldid=prev 2010-02-17T19:26:08Z

<p><span class="autocomment">Reading</span></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 19:26, 17 February 2010</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l6">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</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;"><br></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;"><br></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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf &lt;i&gt;Rule-Based Modeling of Biochemical Systems with BioNetGen&lt;/i&gt;, Faeder, Blinov and Hlavacek]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf &lt;i&gt;Rule-Based Modeling of Biochemical Systems with BioNetGen&lt;/i&gt;, Faeder, Blinov and Hlavacek]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf <ins style="font-weight: bold; text-decoration: none;">&lt;i&gt;</ins>Simulation of large-scale rule-based models<ins style="font-weight: bold; text-decoration: none;">&lt;/i&gt;</ins>, Colvin et al.]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf <ins style="font-weight: bold; text-decoration: none;">&lt;i&gt;</ins>The Complexity of Cell Signaling and the Need for a New Mechanics<ins style="font-weight: bold; text-decoration: none;">&lt;/i&gt;</ins>, Hlavacek and Faeder]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf <ins style="font-weight: bold; text-decoration: none;">&lt;i&gt;</ins>Rules for Modeling Signal-Transduction Systems<ins style="font-weight: bold; text-decoration: none;">&lt;/i&gt;</ins>, Hlavacek et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf <ins style="font-weight: bold; text-decoration: none;">&lt;i&gt;</ins>Mathematical and Computational Models of Immune-Receptor Signalling<ins style="font-weight: bold; text-decoration: none;">&lt;/i&gt;</ins>, Goldstein et al.]</div></td></tr> <!-- diff cache key acs_math_mw_144-doyle_:diff:1.41:old-3135:rev-3136:php=table --> </table>

Vanessa https://doyle.caltech.edu/index.php?title=Modeling_Biological_Systems&diff=3135&oldid=prev 2010-02-17T19:25:23Z

<p><span class="autocomment">Reading</span></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 19:25, 17 February 2010</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: #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>== Reading ==</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>== Reading ==</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;"><br></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;"><br></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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf &lt;i&gt;Rule-Based Modeling of Biochemical Systems with BioNetGen&lt;<del style="font-weight: bold; text-decoration: none;">\</del>i&gt;, Faeder, Blinov and Hlavacek]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf &lt;i&gt;Rule-Based Modeling of Biochemical Systems with BioNetGen&lt;<ins style="font-weight: bold; text-decoration: none;">/</ins>i&gt;, Faeder, Blinov and Hlavacek]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]</div></td></tr> <!-- diff cache key acs_math_mw_144-doyle_:diff:1.41:old-3134:rev-3135:php=table --> </table>

Vanessa https://doyle.caltech.edu/index.php?title=Modeling_Biological_Systems&diff=3134&oldid=prev 2010-02-17T19:25:12Z

<p><span class="autocomment">Reading</span></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 19:25, 17 February 2010</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: #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>== Reading ==</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>== Reading ==</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;"><br></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;"><br></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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf Rule-Based Modeling of Biochemical Systems with BioNetGen, Faeder, Blinov and Hlavacek]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf <ins style="font-weight: bold; text-decoration: none;">&lt;i&gt;</ins>Rule-Based Modeling of Biochemical Systems with BioNetGen<ins style="font-weight: bold; text-decoration: none;">&lt;\i&gt;</ins>, Faeder, Blinov and Hlavacek]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder]</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>* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]</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>*[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]</div></td></tr> <!-- diff cache key acs_math_mw_144-doyle_:diff:1.41:old-3133:rev-3134:php=table --> </table>

Vanessa https://doyle.caltech.edu/index.php?title=Modeling_Biological_Systems&diff=3133&oldid=prev 2010-02-17T19:24:30Z

<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 19:24, 17 February 2010</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: #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;"><br></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;"><br></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>== Reading ==</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>== Reading ==</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>*[<del style="font-weight: bold; text-decoration: none;">[Media</del>:<del style="font-weight: bold; text-decoration: none;">GlycolysisACCFinal</del>.pdf <del style="font-weight: bold; text-decoration: none;">| Linear Control Analysis </del>of <del style="font-weight: bold; text-decoration: none;">the Autocatalytic Glycolysis System</del>, <del style="font-weight: bold; text-decoration: none;">Chandra</del>, <del style="font-weight: bold; text-decoration: none;">Buzi</del>, <del style="font-weight: bold; text-decoration: none;">Doyle</del>]]</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> </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>*[[<del style="font-weight: bold; text-decoration: none;">Media</del>:<del style="font-weight: bold; text-decoration: none;">RedBloodCellsGlycolysis</del>.pdf <del style="font-weight: bold; text-decoration: none;">| Assembly </del>and <del style="font-weight: bold; text-decoration: none;">Regulation </del>of <del style="font-weight: bold; text-decoration: none;">a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane</del>, <del style="font-weight: bold; text-decoration: none;">Campanella </del>et al<del style="font-weight: bold; text-decoration: none;">]</del>]</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;">http</ins>:<ins style="font-weight: bold; text-decoration: none;">//www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009</ins>.pdf <ins style="font-weight: bold; text-decoration: none;">Rule-Based Modeling </ins>of <ins style="font-weight: bold; text-decoration: none;">Biochemical Systems with BioNetGen</ins>, <ins style="font-weight: bold; text-decoration: none;">Faeder</ins>, <ins style="font-weight: bold; text-decoration: none;">Blinov and Hlavacek]</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;">* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models</ins>, <ins style="font-weight: bold; text-decoration: none;">Colvin et al.</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;">* [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder</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;">http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]</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;">*</ins>[<ins style="font-weight: bold; text-decoration: none;">http</ins>:<ins style="font-weight: bold; text-decoration: none;">//www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published</ins>.pdf <ins style="font-weight: bold; text-decoration: none;">Mathematical </ins>and <ins style="font-weight: bold; text-decoration: none;">Computational Models </ins>of <ins style="font-weight: bold; text-decoration: none;">Immune-Receptor Signalling</ins>, <ins style="font-weight: bold; text-decoration: none;">Goldstein </ins>et al<ins style="font-weight: bold; text-decoration: none;">.</ins>]</div></td></tr> <!-- diff cache key acs_math_mw_144-doyle_:diff:1.41:old-3132:rev-3133:php=table --> </table>

Vanessa https://doyle.caltech.edu/index.php?title=Modeling_Biological_Systems&diff=3132&oldid=prev 2010-02-17T19:23:14Z

<p></p> <p><b>New page</b></p><div>== Topics ==<br /> <br /> == Slides ==<br /> <br /> == Reading ==<br /> *[[Media:GlycolysisACCFinal.pdf | Linear Control Analysis of the Autocatalytic Glycolysis System, Chandra, Buzi, Doyle]]<br /> *[[Media:RedBloodCellsGlycolysis.pdf | Assembly and Regulation of a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane, Campanella et al]]</div>

Vanessa