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spidmax="1027"/> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1"/> </o:shapelayout></xml><![endif]--> </head> <body bgcolor="#CCCCFF" lang=EN-US link=blue vlink=blue style='tab-interval: .5in'> <div class=WordSection1> <h3 align=center style='text-align:center'><span style='color:blue;letter-spacing: .75pt'>CS 384R (#53650), CSE 392 (#65334) </span><o:p></o:p></h3> <h3 align=center style='text-align:center'><span style='letter-spacing:.75pt'>SPRING 2013&nbsp;&nbsp;&nbsp;&nbsp; TTH 8:00  9:15am&nbsp;&nbsp;&nbsp; RLM 7.116</span></h3> <h3 align=center style='text-align:center'><span style='font-size:18.0pt; font-family:"Comic Sans MS";color:blue;letter-spacing:.75pt'>Geometric (Bio-) Modeling and Visualization</span> </h3> <p class=MsoNormal>&nbsp;</p> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:10.0pt;font-family:Times'><img width=362 height=223 id="_x0000_i1025" src="index_files/scaleImages.jpg"><br> (Top Row, left to right) Models of the HIV-Envelope Spike Multi-Protein; Electro-static potential (red = negative, blue = positive) via Poisson Boltzmann of the Machupo-Virus; Quality meshed models of a spiny Hippocampal dendrite (yellow) and axon (green);Visualization from a different view of the dendrite and axon, together with a slice of the ssTEM; (Bottom Row): Model of the inner workings of a cell with a collection of ribosomes and phage-29 at different stages of formation. <o:p></o:p></span></p> <p class=MsoNormal align=center style='text-align:center'><br> &nbsp; </p> <div align=center> <table class=MsoNormalTable border=1 cellpadding=0 width="50%" style='width:50.0%;mso-cellspacing:1.5pt;mso-yfti-tbllook:1184;mso-padding-alt: 0in 5.4pt 0in 5.4pt'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td width="13%" style='width:13.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>Name</span></b></p> </td> <td width="41%" style='width:41.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'><a href="http://www.cs.utexas.edu/users/bajaj/">Chandrajit Bajaj</a></span></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td width="13%" style='width:13.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>Office</span></b></p> </td> <td width="41%" style='width:41.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'><a href="http://www.utexas.edu/maps/main/buildings/ace.html">ACES </a>2.324</span></p> </td> </tr> <tr style='mso-yfti-irow:2'> <td width="13%" style='width:13.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>Email</span></b></p> </td> <td width="41%" style='width:41.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'><a href="mailto:bajaj@cs.utexas.edu">bajaj@cs.utexas.edu</a></span></p> </td> </tr> <tr style='mso-yfti-irow:3'> <td width="13%" style='width:13.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>Phone</span></b></p> </td> <td width="40%" style='width:40.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>512-471-8870</span></p> </td> </tr> <tr style='mso-yfti-irow:4;mso-yfti-lastrow:yes'> <td width="13%" style='width:13.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>Office hours</span></b></p> </td> <td width="40%" style='width:40.0%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Tue 1:00 - 4:00p or by appt. via <span style='color:blue'>bajaj@cs.utexas.edu</span></span></p> </td> </tr> </table> </div> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'>CS384R, CSE392 Course Outline</span></b></p> <p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span style='font-family:Tahoma'>The course will teach you the basic mathematics, algorithms, techniques and tools of geometric and physiological modeling and visualization with applications in the biomedical sciences and engineering. Bio-medical modeling (or Biomodeling) and visualization has roots in medical illustration and communication for the health sciences, with branches of application to mathematical modeling and computer simulation of artificial life. In this course we shall emphasize computational image processing, harmonic analysis, computational topology, computational geometry (algebraic and differential), group theory, polynomial spline approximations, computer graphics, data analysis, together with aesthetic choices involved in producing effective scientific animations. The emphasis shall be on spatial realism, and the programmatic use of multi-scale modeling, analysis and visualization to quantitatively depict &quot;how things work&quot; at the molecular,<span style="mso-spacerun:yes">  </span>and cellular scales.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span style='font-family:Tahoma'><br> Exercises on geometric and physiological modeling analysis and visualization at multiple scales, shall be drawn from virology (viral envelopes, capsids, proteins, nucleic acids), and neurology (brain, hippocampus, neuropil, axons, dendrites, glial cells, ion-channels, neurotransmitters), and their interactions (molecular energetics and force fields, molecular flexibility, synaptic transmission, synaptic spillover). </span></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'>Lecture Topics<o:p></o:p></span></b></p> <p><o:p>&nbsp;</o:p></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'>Mathematical Preliminaries: </span></b><span style='font-size:10.0pt;font-family:Times'>Linear algebra, Barycentric coordinates, Mean-value coordinates, Algebraic (polynomial) splines, Parametrization, Singularities, Differential forms,<span style="mso-spacerun:yes">  </span>Discrete exterior calculus, Motion groups, Radon and Fourier transforms<o:p></o:p></span></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></b></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'>Models: </span></b><span style='font-size:10.0pt;font-family:Times'>Surface and Volumetric representations,<span style="mso-spacerun:yes">  </span>Point-based, Clouds, Weighted Delaunay triangulations, Voronoi diagrams, Octrees, Complementary Space (Pockets, Tunnels, Voids)<o:p></o:p></span></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></b></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'>Maps:</span></b><span style='font-size:10.0pt;font-family:Times'> X-ray diffraction, Electron microscopy, CT/MRI,<span style="mso-spacerun:yes">  </span>Voxel<span style="mso-spacerun:yes">  </span>and Continuum Representations<o:p></o:p></span></p> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'>Images &amp; Maps: </span></b><span style='font-size:10.0pt;font-family:Times'>Forward and Inverse Problems,<span style="mso-spacerun:yes">  </span><span style="mso-spacerun:yes"> </span>Contrast Transfer Corrections, Symmetry and Anisotropy considerations, Compression<br> <br> <b style='mso-bidi-font-weight:normal'>Maps2Models: </b>Filtering, Contrast enhancement, Alignment, Classification, Symmetry detection, Static &amp; active Contouring,<span style="mso-spacerun:yes">  </span>Segmentation, Medial axis, Skeletonization,&nbsp; Clustering, Matching<br> <br> <b style='mso-bidi-font-weight:normal'>Models2Analytics I: </b>Point cloud and Cross-sectional Contour Reconstruction,<span style="mso-spacerun:yes">  </span>Surface and Volumetric finite element meshing,<span style="mso-spacerun:yes">  </span>Spline representations, Feature identification,<span style="mso-spacerun:yes">  </span>Symmetry detection, Shape segmentation, Matching &amp; Complementary Docking,<span style="mso-spacerun:yes">  </span>Flexibility, Multi-component Assemblies &amp; Reassembly,<span style="mso-spacerun:yes">  </span><br> <br> <b style='mso-bidi-font-weight:normal'>Models2Analytics II: </b>Bonded and non-bonded Molecular Energetics, Forces,<span style="mso-spacerun:yes">  </span>Poisson-Boltzmann Electrostatics, Poisson-Nernst Planck ElectroDiffusion,<span style="mso-spacerun:yes">  </span>Electric Cable Models, Numerical Quadrature, Cubature,<span style="mso-spacerun:yes">  </span>Fast Multipole Methods, fast Fourier techniques, Discrete differential operators, de-Rham Diagrams, Integral equations<br> <br> <b style='mso-bidi-font-weight:normal'>Analytics2Informatics/Visualization </b>: Differential/integral/Topological/Combinatorial Properties, Active sites, Hydrogen bond Networks, Branching structures, Packings &amp; Tilings, Contour trees, Comparative Structural analysis, Multi-dimensional Transfer Functions, Visible Surface and Volume rendering, Functions on Surface, Quantifying<span style="mso-spacerun:yes">  </span>Uncertainity<o:p></o:p></span></p> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span style='font-size:10.0pt;font-family:Times'>Case Studies:</span></b><span style='font-size:10.0pt;font-family:Times'> Molecular recognition, Electrical signaling amongst neurons.<o:p></o:p></span></p> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'>Grading</span></b></p> <p>You will be graded on periodic written homework assignments (60%), a research and/or programming project with a written report and final presentation (40%).</p> <p><o:p>&nbsp;</o:p></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'>Lectures</span></b><span style='font-family:"Comic Sans MS"'> <br> &nbsp; </span></p> <table class=MsoNormalTable border=1 cellpadding=0 width="100%" style='width:100.0%;mso-cellspacing:1.5pt;mso-yfti-tbllook:1184;mso-padding-alt: 0in 5.4pt 0in 5.4pt'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>DATE&nbsp;</span></b></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt'>LECTURES</span></b></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan 15 (T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec0.pdf"><span style="mso-spacerun:yes"> </span>Multiscale Imaging, Modeling, Informatics; Applications in Modeling Biology </a></span>(Computational Drug Design, Discovery; Neuronal Electrical Circuits: Form and Function)</p> </td> </tr> <tr style='mso-yfti-irow:2'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan 17 (TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec1.pdf"><span style="mso-spacerun:yes"> </span>Maps &amp; Models I: Image Representations, Modalities, Capturing Molecular and Cellular Form</a><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:3'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan 22 (T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec2.pdf">Maps &amp; Models II: Mesh Representations, Regular Triangulations, Power Diagrams, <o:p></o:p></a></span></p> <p class=MsoNormal><span style='font-size:10.0pt;mso-fareast-font-family: "Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:4'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan 24(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec3.pdf">Maps &amp; Models III: <span class=SpellE>Barycentric</span> Coordinates, Bernstein-Bezier Polynomials, Polynomial Splines</a></span><span style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-fareast-font-family: "Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:5'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan 29<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec4.pdf">Maps &amp; Models IV: Spline, Finite Element Representations of Molecular / Cellular Structure</a></span><span style='font-family:Cambria;mso-ascii-theme-font: minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font: minor-latin;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:6'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan 31 (TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec5.pdf">Images-&amp;-Maps I: The Forward Problem for Electron Microscopy, and Computed Tomography</a></span><span class=MsoHyperlink><o:p></o:p></span></p> <p class=MsoNormal><span style='font-family:Cambria;mso-ascii-theme-font: minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font: minor-latin;mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:7'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 5<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec6.pdf">Images-&amp;-Maps II: The Inverse Problem for Electron Microscopy, and Computed Tomography</a></span><span class=MsoHyperlink><o:p></o:p></span></p> <p class=MsoNormal><span style='font-family:Cambria;mso-ascii-theme-font: minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font: minor-latin;mso-bidi-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:8'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 7<span style="mso-spacerun:yes">  </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec7.pdf">Maps2Models I: Image Processing 2D and 3D</a></span><span style='font-family:Cambria; mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman"; mso-hansi-theme-font:minor-latin;mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:9'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 12<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec8.pdf">Maps2Models II: Geometry Processing, Molecular and Cellular Structure Elucidation</a></span></p> </td> </tr> <tr style='mso-yfti-irow:10'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 14<span style="mso-spacerun:yes">  </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec9.pdf">Maps2Models III: Geometry Processing, <span class=SpellE>Skeletonization</span>, Segmentation, Virus Ultrastructure, Reduced Neuronal Structures </a></span></p> </td> </tr> <tr style='mso-yfti-irow:11'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 19<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec10.pdf">Models2Analytics I: Point Cloud Reconstruction (Surface, Volumetric), Dynamic Packing Grids</a></span></p> </td> </tr> <tr style='mso-yfti-irow:12'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 21 (TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec11.pdf">Models2Analytics II: Cross-Sectional Contour Reconstruction (Surface, Volumetric)</a></span></p> </td> </tr> <tr style='mso-yfti-irow:13'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal>Feb 26<span style="mso-spacerun:yes">  </span><span style='font-size:13.5pt'>(T)</span><span style='font-size:11.0pt;font-family: "Lucida Console";color:blue'><o:p></o:p></span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec12.pdf">Models2Analytics III: Molecular Modeling: Hierarchical Structure Representations</a></span></p> </td> </tr> <tr style='mso-yfti-irow:14'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 28<span style="mso-spacerun:yes">  </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec13.pdf">Models2Analytics IV: Molecular Surfaces, Complementary Regions<span style="mso-spacerun:yes">  </span>Structural Bioinformatics</a></span></p> </td> </tr> <tr style='mso-yfti-irow:15'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 5<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec14.pdf">Models2Analytics V: Molecular Recognition: Complementary Docking<span style="mso-spacerun:yes">  </span>(Cartesian and Spherical Fast Fourier Methods)</a></span></p> </td> </tr> <tr style='mso-yfti-irow:16'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 7<span style="mso-spacerun:yes">  </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec15.pdf">Models2Analytics VI: Molecular Match &amp; Fit (Cartesian and Spherical Fast Fourier Methods) </a></span></p> </td> </tr> <tr style='mso-yfti-irow:17'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 19<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec16-17.pdf">Models2Analytics VII: Molecular Bonded &amp; Non-Bonded Energetics (Fast Algorithms)</a></span></p> <p class=MsoNormal><o:p>&nbsp;</o:p></p> </td> </tr> <tr style='mso-yfti-irow:18'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 21 (TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec16-17.pdf">Models2Analytics VIII: Molecular Solvation Energetics - Generalized Born, Dispersion, Poisson Boltzmann</a></span></p> </td> </tr> <tr style='mso-yfti-irow:19'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 26<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec18-19.pdf">Models2Analytics IX: Forces, Normal Mode Analysis and Molecular Dynamics</a></span></p> </td> </tr> <tr style='mso-yfti-irow:28'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 28<span style="mso-spacerun:yes">  </span>(TH)<o:p></o:p></span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec20-21.pdf">Models2Analytics X:Multi-Protein Docking, Molecular Assemblies, Tiling Theory &amp; a><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:27'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 2<span style="mso-spacerun:yes">  </span>(TH)<o:p></o:p></span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec22.pdf">Models2Analytics XI: Neuronal Form: Spatially Realistic Cellular Connectomics</a><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:20'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 4<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec23.pdf">Models2Analytics XII: Neuronal Electrophysiology A  Cable Models</a></span></p> </td> </tr> <tr style='mso-yfti-irow:21'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 9<span style="mso-spacerun:yes">  </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec24.pdf">Models2Analytics XIII: Neuronal Electrophysiology B - Electro-Diffusion</a></span></p> </td> </tr> <tr style='mso-yfti-irow:22'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 11<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec25.pdf">Models2Analytics XIV: Neuronal Electrophysiology C  Multi-scale Models</a></span></p> </td> </tr> <tr style='mso-yfti-irow:23'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 16<span style="mso-spacerun:yes">   </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec26.pdf">Analytics2Informatics I: Contouring, Contour Spectrum</a></span></p> </td> </tr> <tr style='mso-yfti-irow:24'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 18<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec27.pdf">Analytics2Informatics II: Topological Contour Trees, <span class=SpellE>Reeb</span> Graphs</a></span></p> </td> </tr> <tr style='mso-yfti-irow:25'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 23<span style="mso-spacerun:yes">  </span>(TH)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec28.pdf">Analytics2Informatics III: Comparative Structural Analysis</a></span></p> </td> </tr> <tr style='mso-yfti-irow:26'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 25<span style="mso-spacerun:yes">  </span>(T)<o:p></o:p></span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/lectures/GeoModViz-Lec29.pdf">Analytics2Informatics IV: Quantifying <span class=SpellE>Uncertainity</span>Verification &amp; Validation</a><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:29'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 30<span style="mso-spacerun:yes">  </span>(T)<o:p></o:p></span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'>FINAL PROJECT PRESENTATIONS <a href="http://www.cs.utexas.edu/~bajaj/cs384R2012/Projects/">Gallery</a></span></p> </td> </tr> <tr style='mso-yfti-irow:30;mso-yfti-lastrow:yes'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>May 2<span style="mso-spacerun:yes">  </span>(TH)<o:p></o:p></span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"; color:blue'>FINAL PROJECT PRESENTATIONS <a href="http://www.cs.utexas.edu/~bajaj/cs384R2012/Projects/">Gallery</a></span></p> </td> </tr> </table> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'>Exercises:</span></b><span style='font-family: "Comic Sans MS"'> <br> &nbsp; </span></p> <table class=MsoNormalTable border=1 cellpadding=0 width="100%" style='width:100.0%;mso-cellspacing:1.5pt;mso-yfti-tbllook:1184;mso-padding-alt: 0in 5.4pt 0in 5.4pt'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes;height:15.75pt'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Jan<span style="mso-spacerun:yes">  </span>22<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/exercise1.pdf">Exercise 1</a> Computer Science &amp; Mathematics Refresher <a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/hw1-sol.pdf">Solution 1 </a></span></p> </td> </tr> <tr style='mso-yfti-irow:1;height:15.75pt'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>Feb 5<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/exercise2.pdf">Exercise 2</a> Image Processing 2D &amp; 3D <a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/hw2-sol.pdf">Solution 2 </a></span></p> </td> </tr> <tr style='mso-yfti-irow:2;height:15.75pt'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 7<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/exercise3.pdf">Exercise 3</a> Geometry Processing 2D &amp; 3D<a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/hw3-sol.pdf">Solution 3</a><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:5;height:15.75pt'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>March 26<span style="mso-spacerun:yes">  </span>(T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/exercise4.pdf">Exercise 4</a> Quantitative Analysis, Informatics (Molecular and Cellular) <a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/exercises/hw4-sol.pdf">Solution 4</a></span></p> </td> </tr> <tr style='mso-yfti-irow:6;mso-yfti-lastrow:yes;height:15.75pt'> <td width="11%" style='width:11.58%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:13.5pt'>April 9 (T)</span></p> </td> <td width="87%" style='width:87.9%;padding:.75pt .75pt .75pt .75pt; height:15.75pt'> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Lucida Console"'>FINAL PROJECTS<span style="mso-spacerun:yes">  </span>ASSIGNED</span></p> </td> </tr> </table> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'>Primary Texts &amp; References<o:p></o:p></span></b></p> <p><span style='font-size:10.0pt;mso-fareast-font-family:"-ÿ3ÿ fg";mso-fareast-theme-font: minor-fareast'><o:p>&nbsp;</o:p></span></p> <ol style='margin-top:0in' start=1 type=1> <li class=MsoNormal style='mso-list:l4 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj. <i>Multi-scale BioImaging and Informatics, 2012</i> ()<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l4 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj. <i>Multi-scale BioModeling and Analysis, 2012</i> ()<o:p></o:p></span></li> </ol> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'>Background Mathematical, Modeling References<o:p></o:p></span></b></p> <ol style='margin-top:0in' start=1 type=1> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj. <i>Multi-scale Bio-Modeling and Visualization,</i> Chapters 2, 3, 4 (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/bio-viz.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj. <i>Computational Structural Bioinformatics II: Molecular Models.</i> Chapters 2, 3, 4 (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/mol-model.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj. <i>Computational Structural Bioinformatics II: Molecular Models.</i> Appendix (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/mol-model-appendix.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj, A. Gillette. <b>Polynomial Curves and Surfaces</b>, <i>Algebraic Spline Finite Elements ,</i> Chapter 1. (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/algebraicFEM-chap1.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj, A. Gillette. <b>Operations on Polynomial Curves and Surfaces</b>, <i>Algebraic Spline Finite Elements ,</i> Chapter 2. (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/algebraicFEM-chap2.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj, A. Gillette. <b>Piecewise Polynomial Curves and Surfaces</b>, <i>Algebraic Spline Finite Elements,</i> Chapter 3. (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/algebraicFEM-chap3.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj, A. Gillette. <b>Geometric Modeling</b>, <i>Algebraic Spline Finite Element ,</i> Chapter 4. (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/algebraicFEM-chap4.pdf">pdf</a>)<o:p></o:p></span></li> <li class=MsoNormal style='mso-list:l3 level1 lfo2;tab-stops:list .5in'><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: "Times New Roman"'>C. Bajaj, A. Gillette. <b>Derivatives and Integration</b>, <i>Algebraic Spline Finite Element,</i> Chapter 5. (<a href="http://www.cs.utexas.edu/~bajaj/cs384R10/reading/algebraicFEM-chap5.pdf">pdf</a>)<o:p></o:p></span></li> </ol> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'>Suggested Modeling, Analysis and Visualization Projects<o:p></o:p></span></b></p> <p><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></p> <p><span style='font-size:10.0pt;font-family:Times'>I Molecular Forces and Recognition<span style="mso-spacerun:yes">  </span>(Computational Drug Design and Discovery)<o:p></o:p></span></p> <p><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></p> <p><span style='font-size:10.0pt;font-family:Times'>II Neuronal Structure and Plasticity (Electrical Circuits in the Hippocampus: Form and Function)<o:p></o:p></span></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'>Modeling, Analysis and Visualization Software <o:p></o:p></span></b></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'><o:p>&nbsp;</o:p></span></b></p> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial Italic"; mso-fareast-font-family:"Times New Roman";color:black;background:white; mso-bidi-font-weight:bold'>Graphical User Tools</span><span style='font-size: 11.0pt;font-family:"Arial Italic";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> <ul type=disc> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l0 level1 lfo3;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/texmol.shtml"><i>TexMol</i></a>&nbsp;- Molecular modeling and visualization <o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l0 level1 lfo3;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/volrover.shtml"><i>VolRover</i></a>&nbsp;- Volumetric Image Processing and Visualization<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l0 level1 lfo3;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://cvcweb.ices.utexas.edu/cvcwp/?page_id=2089">VolRoverN</a> -<span style="mso-spacerun:yes">  </span>Spatial Realistic Modeling and Visualization of Neuronal Electrophysiology<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l0 level1 lfo3;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/LBIE.shtml"><i>LBIE</i></a>&nbsp;- Level Set Boundary-Interior-Exterior Meshing Tool.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l0 level1 lfo3;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/prism.shtml"><i>Prism</i></a>&nbsp;- Geometric modeling using dual form Hermite Algebraic Surface Elements.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l0 level1 lfo3;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/ganith.shtml"><i>GANITH</i></a>&nbsp; An Algebraic geometry toolkit.<o:p></o:p></span></li> </ul> <p class=MsoNormal><span style='font-size:11.0pt;font-family:"Arial Italic"; mso-fareast-font-family:"Times New Roman";color:black'><br> <span style='background:white;mso-bidi-font-weight:bold'>Software Libraries and Command-Line Utilities</span></span><span style='font-size:11.0pt;font-family: "Arial Italic";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> <ul type=disc> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/molsurf.shtml"><i>MolSurf</i></a>&nbsp;- Molecular surface generation and manipulation.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/molenergy.shtml"><i>MolEnergy</i></a>&nbsp;- Molecular energetics computation.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/DPG.shtml"><i>DPG</i></a>&nbsp;- Dynamic packing grids.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/SecondaryStructure.shtml"><i>SSEP</i></a>&nbsp;- Secondary structure elucidation package.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/Pocktunnel.shtml"><i>Pocket/Tunnel</i></a>&nbsp;- Protein pocket/tunnel extractor.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/QHM.shtml"><i>QHM</i></a>&nbsp;- Quality Quadrilateral/Hexahedral Mesh Generator. <a href="http://www.cs.utexas.edu/~bajaj/cvc/software/QTM.shtml"><i>QTM</i></a>&nbsp;- Quality Triangular/Tetrahedral Mesh Generator.<span style="mso-spacerun:yes">  </span><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/MMM.shtml"><i>MDM</i></a>&nbsp;- Multi-Domain Meshing.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l1 level1 lfo4;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/SurfVolRender.shtml"><i>GPU Renderer</i></a>&nbsp;- Surface/Volume Rendering Packages.<o:p></o:p></span></li> </ul> <p class=MsoNormal><span style='font-size:11.0pt;font-family:Arial;mso-fareast-font-family: "Times New Roman";color:black'><br> </span><span style='font-size:11.0pt;font-family:"Arial Italic";mso-fareast-font-family: "Times New Roman";color:black;background:white;mso-bidi-font-weight:bold'>Server Based Codes</span><span style='font-size:11.0pt;font-family:"Arial Italic"; mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> <ul type=disc> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l2 level1 lfo5;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/f2dock.shtml"><i>F2Dock</i></a>&nbsp;- Protein docking software.<o:p></o:p></span></li> <li class=MsoNormal style='color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt: auto;mso-list:l2 level1 lfo5;tab-stops:list .5in;background:white'><span style='font-size:10.5pt;font-family:Verdana;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman"'><a href="http://www.cs.utexas.edu/~bajaj/cvc/software/TRLIB.shtml"><i>TRLIB</i></a>&nbsp;- Texture-based Rendering Library.<o:p></o:p></span></li> </ul> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt; font-family:"Comic Sans MS"'>Additional Suggested Reading<o:p></o:p></span></b></p> <p><o:p>&nbsp;</o:p></p> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times'><a href="http://userweb.cs.utexas.edu/%7Ebajaj/cs384R2012/readinglist.html">Books &amp; Papers<span style="mso-spacerun:yes">  </span></a><o:p></o:p></span></p> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times'><o:p>&nbsp;</o:p></span></p> <p><b style='mso-bidi-font-weight:normal'><span style='font-size:13.5pt; font-family:"Comic Sans MS"'>Useful Links<o:p></o:p></span></b></p> <p><o:p>&nbsp;</o:p></p> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times'><a href="http://www.marcottelab.org/index.php/CH391L_2013">Other Relevant Course on Campus</a><o:p></o:p></span></p> <p><o:p>&nbsp;</o:p></p> <blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'> <p><a href="http://cvcweb.ices.utexas.edu/ccv/GroupMeetings">Group Meeting Schedule</a></p> </blockquote> <div id=bl-newtip> <p class=MsoNormal><span style='font-size:10.0pt;font-family:Times;mso-fareast-font-family: "-ÿ3ÿ fg";mso-fareast-theme-font:minor-fareast;display:none;mso-hide:all'><span style='mso-field-code:"HYPERLINK \0022http\:\/\/getglue\.com\/?s=w\0022 \\t \0022_blank\0022"'></span><o:p></o:p></span></p> </div> </div> </body> </html>