School of Computational Science

Course List

Course number Title and Description

ISC 3313 Introduction to Scientific Computing
This course introduces the student to the science of computations. Algorithms for standard problems in computational science are presented. The basics of an object-oriented programming language are taught to facilitate the student's implementation of algorithms.

ISC 4933 Selected Topics In Computational Science
Study selected computational science topics that are not covered by existing courses

ISC 5224 Introduction to Bioinformatics
Bioinformatics is an emerging discipline that provides a quantitative framework for understanding how the genomic sequence and its variations affect the phenotype. This course is designed both for biologists and biochemists seeking to improve quantitative data interpretation skills, and for mathematicians, computer scientists and other quantitative scientists seeking to learn more about computational biology. Laboratory exercises are designed to reinforce the classroom learning.

ISC 5225 Molecular Dynamics: Algorithms and Applications
Comprehensive introduction to molecular dynamics simulation algorithms and their corresponding applications in molecular sciences.

ISC 5226 Numerical Methods for Earth and Environmental Sciences
Application of numerical methods to the solution of scientific problems for earth and environmental sciences.

ISC 5227 Survey of Numerical Partial Differential Equations
This course provides an overview of the most common methods used for numerical partial differential equations. These include techniques such as finite differences, finite volumes, finite elements, discontinuous Galerkin, boundary integral methods, and pseudospectral methods.

ISC 5228 Markov Chain Monte Carlo Simulations
Covered are statistical foundations of Monte Carlo (MC) and Markov Chain Monte Carlo (MCMC) simulations, applications of MC and MCMC simulations, which may range from social sciences to statistical physics models, statistical analysis of autocorrelated MCMC data, and parallel computing for MCMC simulations.

ISC 5229 Multiscale Modeling of Materials
Mathematical and algorithmic basis for atomic scale, mesoscale and continuum scale modeling approaches in materials science, emphasizing the atomic-to-continuum connection, statistical approaches and homogenization problems in continuum modeling of heterogeneous materials. Concrete examples will be used to explain the basic ideas, and the students will pursue projects in which they apply the concepts discussed in lectures.

ISC 5305 Scientific Programming
Object oriented coding in C++, Java, Fortran 90 with applications to scientific programming. Discussion of class hierarchies, pointers, function and operator overloading, and portability. Examples include computational grids and multidimensional arrays.

ISC 5306 Programming Skills for Computation Biology and Bioinformatics
This course provides a basic programming background sufficient to begin a career in computational molecular biology and bioinformatics. It is also useful for those who want to develop their own programs for simulation or analysis in ecology, evolutionary biology, genetics or molecular biology. The Java language is used as a platform for presenting the concepts of data types, structures, flow control, and input/output. Programming assignments will be biologically oriented. In addition to Java, scripting languages such as Python or Perl will be presented for the control of batch processes, file filtering, and simple data analysis.

ISC 5307 Scientific Visualization
This course will cover the theory and practice of scientific visualization. Students will learn how to use state-of-the-art visualization toolkits as well as to create their own visualization tools. Students will learn to represent both 2-D and 3-D data sets and learn how to evaluate the effectiveness of their visualizations.

ISC 5315 Applied Computational Science I
This course provides students with high performance computational tools necessary to investigate problems arising in science and engineering with an emphasis on combining them to accomplish more complex tasks. A combination of course work and lab work will provide the proper blend of theory and practice with problems culled from the applied sciences. Topics include numerical solution to ODEs and PDEs, data handling, interpolation and approximation, and visualization.

ISC 5316 Applied Computational Science II
This course provides students with high performance computational tools necessary to investigate problems arising in science and engineering with an emphasis on combining them to accomplish more complex tasks. A combination of course work and lab work will provide the proper blend of theory and practice with problems culled from the applied sciences. Topics include mesh generation, stochastic methods, basic parallel algorithms and programming, numerical optimization, and nonlinear solvers.

ISC 5317 Computational evolutionary biology
This course presents computational methods for evolutionary inferences. Presentation includes the underlying models, the algorithms that analyze models, and the creation of software to carry out the analysis.

ISC 5318 High-Performance Computing
This course is an introductory course on high-performance computing. High-performance computing refers to the use of (parallel) supercomputers and computer clusters, and everything from software to hardware to speed up computations. Students will learn how to write faster code that is highly optimized for modern multi-core processors and clusters, using modern software development tools and performance analyzers, specialized algorithms, parallelization strategies, and advanced parallel programming constructs.

ISC 5906 Directed Individual Study In Computational Science
Study on a selected topic as designated by the student and the directing professor.

ISC 5907 Directed Individual Study In Computational Science
Study on a selected topic as designated by the student and the directing professor.

ISC 5934 Introductory Seminar on Research In Computational Science
A series of lectures given by faculty on the research being conducted by School of Computational Science

ISC 5935 Selected Topics In Computational Science
Study selected research topics that are not covered by existing courses

ISC 5936 Numerical Methods for Stochastic Differential Equations
This course provides students with basic knowledge of applied and numerical mathematics useful for scientific and engineering modelling, guided by some problems in applications. In particular, it focuses on the numerical solution of stochastic differential equations and Monte Carlo methods. A combination of theory and lab work will build up the student's intuition and give him more insight useful for applications.

ISC 5939 Advanced Graduate Student Seminar In Computational Science
A series of lectures given by faculty, students or outside scholars on research and research methods related to Computational Science.

ISC 5948 Graduate Internship In Computational Science
Supervised internship individually arranged to accommodate professional development

ISC 5975 Thesis

ISC 6981 Dissertation

ISC 8964 Doctoral Qualifying Examination

ISC 8965 Doctoral Preliminary Examination

ISC 8977 Master's Thesis Defense

ISC 8982 Defense of Dissertation

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Course List

Course number	Title and Description
ISC 3313	Introduction to Scientific Computing This course introduces the student to the science of computations. Algorithms for standard problems in computational science are presented. The basics of an object-oriented programming language are taught to facilitate the student's implementation of algorithms.
ISC 4933	Selected Topics In Computational Science Study selected computational science topics that are not covered by existing courses
ISC 5224	Introduction to Bioinformatics Bioinformatics is an emerging discipline that provides a quantitative framework for understanding how the genomic sequence and its variations affect the phenotype. This course is designed both for biologists and biochemists seeking to improve quantitative data interpretation skills, and for mathematicians, computer scientists and other quantitative scientists seeking to learn more about computational biology. Laboratory exercises are designed to reinforce the classroom learning.
ISC 5225	Molecular Dynamics: Algorithms and Applications Comprehensive introduction to molecular dynamics simulation algorithms and their corresponding applications in molecular sciences.
ISC 5226	Numerical Methods for Earth and Environmental Sciences Application of numerical methods to the solution of scientific problems for earth and environmental sciences.
ISC 5227	Survey of Numerical Partial Differential Equations This course provides an overview of the most common methods used for numerical partial differential equations. These include techniques such as finite differences, finite volumes, finite elements, discontinuous Galerkin, boundary integral methods, and pseudospectral methods.
ISC 5228	Markov Chain Monte Carlo Simulations Covered are statistical foundations of Monte Carlo (MC) and Markov Chain Monte Carlo (MCMC) simulations, applications of MC and MCMC simulations, which may range from social sciences to statistical physics models, statistical analysis of autocorrelated MCMC data, and parallel computing for MCMC simulations.
ISC 5229	Multiscale Modeling of Materials Mathematical and algorithmic basis for atomic scale, mesoscale and continuum scale modeling approaches in materials science, emphasizing the atomic-to-continuum connection, statistical approaches and homogenization problems in continuum modeling of heterogeneous materials. Concrete examples will be used to explain the basic ideas, and the students will pursue projects in which they apply the concepts discussed in lectures.
ISC 5305	Scientific Programming Object oriented coding in C++, Java, Fortran 90 with applications to scientific programming. Discussion of class hierarchies, pointers, function and operator overloading, and portability. Examples include computational grids and multidimensional arrays.
ISC 5306	Programming Skills for Computation Biology and Bioinformatics This course provides a basic programming background sufficient to begin a career in computational molecular biology and bioinformatics. It is also useful for those who want to develop their own programs for simulation or analysis in ecology, evolutionary biology, genetics or molecular biology. The Java language is used as a platform for presenting the concepts of data types, structures, flow control, and input/output. Programming assignments will be biologically oriented. In addition to Java, scripting languages such as Python or Perl will be presented for the control of batch processes, file filtering, and simple data analysis.
ISC 5307	Scientific Visualization This course will cover the theory and practice of scientific visualization. Students will learn how to use state-of-the-art visualization toolkits as well as to create their own visualization tools. Students will learn to represent both 2-D and 3-D data sets and learn how to evaluate the effectiveness of their visualizations.
ISC 5315	Applied Computational Science I This course provides students with high performance computational tools necessary to investigate problems arising in science and engineering with an emphasis on combining them to accomplish more complex tasks. A combination of course work and lab work will provide the proper blend of theory and practice with problems culled from the applied sciences. Topics include numerical solution to ODEs and PDEs, data handling, interpolation and approximation, and visualization.
ISC 5316	Applied Computational Science II This course provides students with high performance computational tools necessary to investigate problems arising in science and engineering with an emphasis on combining them to accomplish more complex tasks. A combination of course work and lab work will provide the proper blend of theory and practice with problems culled from the applied sciences. Topics include mesh generation, stochastic methods, basic parallel algorithms and programming, numerical optimization, and nonlinear solvers.
ISC 5317	Computational evolutionary biology This course presents computational methods for evolutionary inferences. Presentation includes the underlying models, the algorithms that analyze models, and the creation of software to carry out the analysis.
ISC 5318	High-Performance Computing This course is an introductory course on high-performance computing. High-performance computing refers to the use of (parallel) supercomputers and computer clusters, and everything from software to hardware to speed up computations. Students will learn how to write faster code that is highly optimized for modern multi-core processors and clusters, using modern software development tools and performance analyzers, specialized algorithms, parallelization strategies, and advanced parallel programming constructs.
ISC 5906	Directed Individual Study In Computational Science Study on a selected topic as designated by the student and the directing professor.
ISC 5907	Directed Individual Study In Computational Science Study on a selected topic as designated by the student and the directing professor.
ISC 5934	Introductory Seminar on Research In Computational Science A series of lectures given by faculty on the research being conducted by School of Computational Science
ISC 5935	Selected Topics In Computational Science Study selected research topics that are not covered by existing courses
ISC 5936	Numerical Methods for Stochastic Differential Equations This course provides students with basic knowledge of applied and numerical mathematics useful for scientific and engineering modelling, guided by some problems in applications. In particular, it focuses on the numerical solution of stochastic differential equations and Monte Carlo methods. A combination of theory and lab work will build up the student's intuition and give him more insight useful for applications.
ISC 5939	Advanced Graduate Student Seminar In Computational Science A series of lectures given by faculty, students or outside scholars on research and research methods related to Computational Science.
ISC 5948	Graduate Internship In Computational Science Supervised internship individually arranged to accommodate professional development
ISC 5975	Thesis
ISC 6981	Dissertation
ISC 8964	Doctoral Qualifying Examination
ISC 8965	Doctoral Preliminary Examination
ISC 8977	Master's Thesis Defense
ISC 8982	Defense of Dissertation