Graduate Special Topics in Computer Science

NOTE: for descriptions of standard graduate computer science courses, see Graduate Course Descriptions.

G22.3033 Advanced Multimedia

This course will cover a variety of advanced topics in multimedia design, with emphasis on techniques for creation of interactivity, and on networked multimedia. Topics to be covered will include: the HTML-JavaScript-Java software complex as a vehicle for multimedia production. Comparisons with Lingo and Director. Potential improvements to HTML. VRML as a possible 3D replacement of the 2D graphics of Director. Bandwidth considerations. New graphic concepts, including the 'Pad' zoomable interface. Text searching. Morphing.

G22.3033 Internet & Intranet Protocols & Applications

Prerequisite: Data Communication and Network Design (G22.2262) or equivalent or permission of the instructor obtained via email to artg@cs.nyu.edu.

Internet and Intranet Protocols and Applications studies the world's most widely used application level network protocols and software systems. They are primarily client/server systems, with modifications and enhancements to improve performance, such as caching and replication, and security, such as firewalls.

We study protocols, such as HTTP, NNTP and SMTP. We discuss the design of client and server software, such as Web browsers and servers. We study the design of network systems, such as corporate intranets.

In examining these systems, we consider the technical challenges faced by their designers, including issues such as system performance, and network architecture and management.

Two programming projects will enhance the learning experience: write a UDP ECHO client and the core of a caching HTTP/1.1 proxy server.

G22.3033 Real Time Computing

Prerequisites: G22.2110 and either G22.2250 or practical knowledge of operating systems

Definition of real-time programming, and examples of important real-time applications. Approaches for construction of real-time programs including formal models (such as Mascot), formal analysis techniques (such as rate monotonic analysis), and design prinicipes. Programming language constructs for support of real-time programming. Specialized support hardware. Techniques for testing, maintaining, verifying and validating real-time programs.

G22.3033 Special Topics in Mathematical Biology: Computational Genomics

The genome contained within a human cell is very large and complex. It holds all of the genetic information necessary for its creation and function encoded with a total of six feet of DNA. The goals of the Human Genome Initiative (HGI), as framed by the National Institutes of Health and the Department of Energy, are to generate a complete map, containing well-defined markers, and to sequence the entire human genome within the next seven, or less years. The sequencing aspects of this project will have to deal with approximately 3 billion base pairs. A large number of genes (70,000-100,000) will be identified and characterized in terms of biochemical, developmental, and clinical criteria. Additionally, the development of approaches to globally, and quantitatively, characterize message (RNA transcripts, which direct synthesis of specific proteins) will also play a major role in virtually every aspect of biological, pharmaceutical and clinical research.

The science of computational genomics and bio-informatics have been created out of this massive sea of sequence data and the need to establish functionality of genes largely based on similarities discerned at the level of the DNA code; bypassing the need for extensive biochemical characterization.

This emerging subfield relies on some classical and many novel mathematical, statistical and algorithmic ideas that are essential to accomplish this task. This course deals with mainly these mathematical and computational approaches. The course is self contained, developing the biological, statistical, probabilistic and algorithmic tools and techniques along the way.

The following topics will be covered: Introduction & history, some molecular biology: DNA, transfer RNA and protein sequence, biochemistry, restriction maps, DDP (Double Digestion Problem): complexity and algorithms, cloning and clone libraries, physical genome maps (oceans, islands and anchors): Lander-Waterman statistics, sequence assembly, alignment of two and multiple sequences, Lander-Waterman Statistics and applications to sequence alignment, RNA secondary structure, optical mapping and map-based sequence assembly, research problems.

This course will focus on the important aspects of security on the web and on the Internet. The Internet refers to the infrastructure - the underlying protocols and routing. The web refers to the applications that run on the Internet. The course will address the following questions: What is a secure system? How is one designed, and how are vulnerabilities discovered? What are the effects of system vulerabilities, and how may they be minimized? We will look at browsers, web servers, and communication protocols on the Internet. Grading will be based on a midterm and final exam and some programming assignments.

G22.3033 Internet & Web Security

This course will focus on the important aspects of security on the web and on the Internet. The Internet refers to the infrastructure - the underlying protocols and routing. The web refers to the applications that run on the Internet. The course will address the following questions: What is a secure system? How is one designed, and how are vulnerabilities discovered? What are the effects of system vulerabilities, and how may they be minimized? We will look at browsers, web servers, and communication protocols on the Internet. Grading will be based on a midterm and final exam and some programming assignments.

G22.3033 Special Topics in Computational Computational Geometry: Random Graphs

Course material is designed to be selfcontained; although it uses ideas from probability, discrete math, and theoretical computer science, no particular background will be assumed. The core of the material is what is called the Probabilistic Method - a method of proving the existence of objects pioneered by the late Paul Erdos. This course will complement the material in the course "Randomized Algorithms" taught by Richard Cole.

G22.3033 Molecular Modeling

Introduction to biomolecular modeling and simulation, including portein and nucleic acid structure and dynamics (minitutorial); modeling aproaches (quantum and molectular mechanics, molecular dynamics, Monte Carlo); force fields (functional construction, variability, evaluation tricks of the trade); molecular visualization & simulation (introduction to the INSIGHT package); selected toipcs (protein folding, RNA folding, DNA dynamics, structural and functional genomics).

The intended audience for this chemistry course, cross-listed in the Computer Science Department, is advanced undergraduates and graduate students from chemistry, biology, physics, mathematics, computer science and neuroscience), as well as graduate students in biomedical science.

Textbook: "Understanding Molecular Simulations. From Algorithms to Applications" by Daan Frenkel and Berend Smit (Academic Press, 1996). The book will not be rigourously followed and supplemented by articles, additional books, web sites, and professor's notes.


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