Andrew T. Phillips

Coupled optimization in protein docking

Here, we introduce a new approach to macromolecular docking which combines the continuous global optimization algorithm CGU [6, 21] with the grid-based conformational search engine DOT [23]. We also detail the use of this method to dock acetylcholine into the fasciculin-acetylcholinesterase complex. Fasciculin blocks access to the long, narrow pathway leading to the active site, which is located in the interior of the acetylcholinesterase. For this reason, flnding the location computationally is rather non-trivial. We not only successfully identifled the optimal docking conflguration, but were able to do so in a matter of hours.

Implementing CC2001: a breadth-first introductory course for a just-in-time curriculum design

A first course in computer science that loosely follows the Computing Curricula 2001 report is described. This course blends theory and practice, highlights algorithm design, introduces a modest amount of imperative programming, and uses an Internet algorithmics theme to tie the topics together and keep the course both challenging and interesting to those with and without previous computing experience.

Seven design rules for teaching students sound encapsulation and abstraction of object properties and member data

Because encapsulation is a difficult concept for students to implement correctly, we propose a set of seven software design rules to be used as an aid for teaching the appropriate design and use of encapsulation of object properties.

Comparing the template method and strategy design patterns in a genetic algorithm application

We present a genetic algorithm software project that serves to give students direct experience with choosing among multiple potentially applicable design patterns. We carefully constructed this project to illustrate the power of design patterns in supporting encapsulation while at the same time providing a single context in which to compare and contrast similar design pattern alternatives.

Implementing object equivalence in Java using the template method design pattern

A standard practice in object-oriented programming is to implement an operation, called equals in Java, for testing the equality of two objects. The equals method should be defined for every new Java class, but because of the intricacies of inheritance, casting, and dynamic typing, equals is often quite difficult to write correctly. And unfortunately many textbooks present flawed implementations of this operation. In this paper, we present a semantically correct technique for testing object equivalence, a technique that simultaneously brings together important mathematical foundations (equivalence relations), practical programming issues (inheritance, casting, dynamic typing), and sound software design (design patterns) in a natural and compelling way. While Java is used to demonstrate how the semantic flaws are corrected and the design improved using our techniques, the design is general enough that it will be clear how the same ideas could easily be extended to other languages such as C++.

Energy Landscape Projections of Molecular Potential Functions

Key problems in computational biology, including protein and RNA folding and drug docking, involve conformational searching over multidimensional potential surfaces with very large numbers of local minima. This paper shows how statistics provided by the CGU global optimization algorithm can be used to characterize and interpret these topographies using a 2-dimensional landscape projection.

A portable computer security workshop

We have developed a computer security workshop designed to instruct post-secondary instructors who want to start a course or laboratory exercise sequence in computer security. This workshop has also been used to provide computer security education to IT professionals and students. It is effective in communicating basic computer security principles as well as an understanding of some of the significant tools and techniques in this area. Evaluations of the workshop have been very positive; we will offer the workshop locally, regionally, and nationally in the next year. The materials from this workshop are available at http://clics.cs.uwec.edu/workshopmaterials.htm.

Undergraduate computational science and engineering programs and courses

This 90-minute panel session will discuss recent and future developments in incorporating Computational Science and Engineering into the undergraduate curriculum. There is a companion session devoted to tools and techniques and so the focus here is on programs and courses.The panelists will demonstrate a clear uniformity of purpose but a wide variety of approaches to increasing the CSE experience of undergraduates in different types of schools.The schools represented vary from large state universities to small private liberal arts colleges and a medium-sized school with a strong engineering bias.The approaches adopted also differ. There are complete programs built largely from existing courses, specific courses that are added to established programs to allow a student to follow an emphasis in CSE. The introduction of CSE into existing programs through faculty advice and education has also been successful.Yet other approaches represented among the panelists are the introduction of multi-disciplinary team-taught project-based courses as a springboard for growing an undergraduate CSE program including undergraduate research projects. The incremental use of small add-on courses to supplement conventional mathematics offerings with some CSE content has also been used successfully.Another approach represented on the panel is the use of a particular vehicle --- in this case graphics and visualization --- to introduce key ideas of CSE into regular parts of the curriculum.The unifying theme of the panel --- the desire to improve undergraduate CSE education will be evident throughout. By presenting a wide variety of approaches to achieve this end, it is hoped that any audience participants who wish to create a CSE thread in their own programs will find some ideas to help them. Some of the practical and political issues will also be discussed in the various contexts.The program for the panel would allow each panelist a maximum of 10 minutes to outline their programs and approaches. The remaining 30 (or more) minutes would then be reserved for general discussion and questions and contributions from the audience.

Highlighting programming language issues using mixed language programming nn Maple and C

Three examples using mixed language programming in Maple and C are provided for the express purpose of highlighting, in a practical way, various issues normally discussed in a traditional programming languages class only as theoretical concepts. The three examples highlight concepts in parameter passing techniques, storage order choices, native machine types and sizes, and the handling of single and multi-dimensional arrays when dealing with legacy code.

Exploring security vulnerabilities by exploiting buffer overflow using the MIPS ISA

By exploiting a well known security vulnerability in many C library implementations, it is possible for an unprivileged user to gain unrestricted system privileges. With an understanding of how the process execution stack is allocated and managed during process execution, a user can override the return address of a C library routine and thereby resume execution at a different address where a set of malicious functions can be invoked [1]. This is known as the buffer overflow exploit. With buffer overflow as the underlying theme, an example will be described using C and the MIPS assembly language that simultaneously exposes students to issues in computer security, operating systems concepts such as memory management and function invocation/return, and the MIPS instruction set architecture.