Student Abstracts: Computer Science at PNNL

Motion Control of the 0.8-m Telescope at Rattlesnake Mountain Observatory. CULLEN ANDREWS (Eastern Washington University, Cheney, WA 99004) KEN SWANSON (Pacific Northwest National Laboratory, Richland, WA 99352) .
Rattlesnake Mountain Observatory is an astronomical observatory that is not currently used for research. Located on top of Rattlesnake Mountain northwest of Richland, WA, it is not a very accessible place. Work is now being done to automate the 0.8-m telescope and dome, so that local high school students will eventually have remote access to it via the Internet. Gaining adequate motion control of the telescope is currently the most immediate goal. Optical encoders on the hour angle and declination axes were used to measure output velocities over a range of input velocities sent to the control unit of the two servomotors. It was found that the velocity resolution--the smallest increment by which velocity can be changed--was 0.225 arc seconds per second. It turns out that this is because motor velocities are limited to integer values of motor encoder counts per second. This is insufficient for tracking stars during a prolonged photographic exposure. Velocity resolution of 10^-3 arc seconds per second or better is needed. A program is needed that will change motor velocity over time in order to stay within 1 arc second of the target. Increasing the gear ratio between the servomotors and telescope would improve velocity resolution, but not enough to completely solve the problem. Future projects at the observatory include calibration of the axis encoders and communication between the main computer and the dome control units.

Learning Java. MICHELLE BEGAY (South Mountain Community College, Phoenix, AZ 85014) RYAN HOHIMER (Pacific Northwest National Laboratory, Richland, WA 99352) .
Upon arriving, I didn't have any experience with computer programming. However, after ten weeks, I have learned about the terminology that is associated with Java. This is the code language that is used on the Image Science and Technology (ISAT) initiative's visualization software.

Coding a Water Budget Model in C++. STEVEN CERVENY (Case Western Reserve University, Cleveland, OH 44106) PHIL MEYER (Pacific Northwest National Laboratory, Richland, WA 99352) .
The near-surface water budget is useful for estimating groundwater recharge and contaminant transport from soil contamination. Solution of the time-dependent water budget under a set of simplifying simulations has been completed. This code is currently written in a combination of Fortran and Mathcad, but was desired in C++ to provide wider distribution and improve its ease of use. Other benefits include substantially quicker runtime, a standalone executable, greatly expanded graphing abilities, ability to read-in constants from file, enhanced error checking, increased modularization of code, and software evolution towards a completely command-line operated Monte Carlo simulation version. Recoding and testing was completed with sufficient time remaining to develop a Windows-based GUI (graphical user interface) yielding a professional software package that can be widely used for a broad range of implementations.

MUSTPAC. KRISTI DRAGOO (University of Washington, Seattle, WA 98105) LAURA MS CURTIS (Pacific Northwest National Laboratory, Richland, WA 99352) .
MUSTPAC stands for Medical UltraSound Three-dimensional, Portable with Advanced Communications. The MUSTPAC system was designed to expand ultrasound data into a 3-dimensional image, which can be transmitted to another location for diagnosis. Any ultrasound technician that has knowledge of basic anatomy can use the MUSTPAC system. It is entailed of attaching the MUSTPAC system to any standard ultrasound machine, sweeping the probe over the area to be scanned, and the MUSTPAC system will produce a three-dimensional image that can be stored on the system. This scan can then be transmitted to another location anywhere in the world in a matter of minutes for diagnosis purposes. This summer, I performed various tests on the MUSTPAC system as well as prepared the data to submit for FDA 510(k) approval. My tests included, calculating the percentage error from the image produced by the MUSTPAC system. I did this by scanning a calibration phantom, took measurements from the 3-dimensional image produced and compared the measurement to what the actual figure should have been. My data came out to have a percentage error of less than 5% in each category. In addition, I wrote supporting documents that included a flowchart and hardware outline. I also designed and implemented the creation of the MUSTPAC web page by using the program Macromedia Dreamweaver 4. The web page consists of MUSTPAC's general information, its history and current trial runs, as well as a short movie that shows how MUSTPAC works. This web page will be available to our clients as well as the general public at http://aims.pnl.gov:2080/mustpac/.

Columbia River Recreational Survey 2001: Human Health Risk Assessment. FRANCES MELENDEZ (Columbia Basin Colllege, Richland, WA 99352) AMORET BUNN (Pacific Northwest National Laboratory, Richland, WA 99352) .
The United States Department of Energy (DOE) has become concerned about the environment and resultant effect on human health near the Columbia River. DOE scientists have relied on the principles of risk assessment in their evaluation of its surroundings and the affects on individual and community health. One way to help evaluate their concerns for the environment is by collecting information using recreational surveys. The aims of these surveys are to help describe the potential threat that toxic contaminants may have on both the environment and human health. Remedial solutions, such as facilitating future clean up and the prevention of toxic contaminants from affecting the Columbia River, can be maintained using the risk-based information form these surveys.

Upgrading the Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES). Jeanne Dagenette Nowlin (Big Bend Community College, Moses Lake, Washington 98837) Mitchell A. Pelton (Pacific Northwest National Laboratory, Richland, Washington 99355). . JEANNE NOWLIN (Big Bend Community College, Moses Lake, WA 98837) MITCHELL PELTON (Pacific Northwest National Laboratory, Richland, WA 99352) .
The U.S. Department of Energy (DOE) and the U.S. Environmental Protection Agency (EPA) have regulatory programs pertaining to potential-risk environmental contaminants. They demand sound scientific methods of performing in-depth assessments over a variety of conditions. Many computer tools being similar, DOE and EPA logically concluded to collaborate in the development of computer applications that could mesh their software and experience towards standardization. Early efforts were difficult to modify and were concerned with a single medium. Battelle staff at Pacific Northwest National Laboratory (PNNL) undertook the challenge to create a platform that would allow users to input data in their own format and to link that data to other modules (such as receptors), and thus came about Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES). FRAMES has a user-friendly interface. It deals only with how data is transferred between modules and, therefore, the user can track contaminants through different media of the environment and view textually or graphically the results of exposure in time and concentration as well as human health risks. FRAMES utilizes established stand-alone programs such as Multimedia Environmental Pollutant Assessment System (MEPAS), a physics-based modeler. Its numerous versions demonstrate the necessity of any computer application to either undergo constant upgrading or become obsolete, as well as reflecting sensitivity to user feedback and requirements. FRAMES is presently undergoing tremendous coding changes that will radically alter the way it handles information, as well as opening itself to a broader spectrum of users.

CCI Abstract EMSL Computer Support. DET PHIOUPHANH (Columbia Basin College, Pasco, WA 99301) SCOTT CAMPBELL (Pacific Northwest National Laboratory, Richland, WA 99352) .
The main objective for the EMSL Computer Support Team is to provide computer and software support for the many scientists and administrative assistants. In addition we also help handle all audio/visual support. A few examples are putting up projectors and checking the sound setups for presentations in conference rooms or the Battelle Auditorium. When a problem occurs and the users needs some assistance, they fill out a request form and send it to our support queue. Various requests are then claimed by members of our staff, indicated by having their initials by the request in the queue program. After the request for service has been fulfilled, a brief description of the what was done is attached to the request and then closed. Users can also view the queue via the web. My mentor is Scott Campbell. He has been a very encouraging. My duties with the support team are minimal right now, but as I learn more I'm able to handle problems on my own, rather than serving as an assistant to others. I assist the other students mostly (Paul and Tim L.) They too take time to teach me how to handle the responsibilities of this job. Other helpful members of the computer support team include: Boyd and Mike, who handle Mac issues, Cheryl, who handles conference room scheduling and network account setup, Nick, our Audio/Visual support guru, and Tim C., our local Unix support expert. They all are very informative and supportive. My CCI experience with this staff has been well absorbed, but fun more than anything else.

Remote Sensing and Circulation Modeling: Willapa Bay, WA. BENJAMIN ROONEY (Central Washington University, Ellensburg, WA 98926) KAREN STEINMAUS (Pacific Northwest National Laboratory, Richland, WA 99352) .
The purpose of this study is to investigate the coupling of high resolution remotely sensed images with circulation and transport modeling in the marine environment. The transport of carbon-containing material from the river environment to the coastal environment may be a critical component of Earth's carbon cycle and may also be significantly impacted by subtle long-term changes in the regional climate.

Computer Modeling of Belief Formation. JAMES SLOUGHTER (Gonzaga University, Spokane, WA 99258) A. LYNN FRANKLIN (Pacific Northwest National Laboratory, Richland, WA 99352) .
The theory of explanatory coherence as put forth by Paul Thagard has the potential to be widened in scope so as to be useful as a predictor of public opinion and response. A computer model of the theory, similar in function to Thagard's ECHO program, was begun with the potential to be modified to allow for additional factors unaccounted for in Thagard's model. The scope of who could be modeled was expanded. Plans were made to model factors such as existing biases, order of information presentation, and emphasis of information. Strategies were developed to isolate the influences of individual propositions within a belief system. Once completed, the new program could be a useful tool in predicting public response to information without needing to present the information to the public. This could allow for improved public relations, and could provide a means for the user to be more immediately responsive to the public's needs and concerns.

Development of an Automated Microfluidic System for DNA Collection, Amplification, and Detection. . BRIAN YOXALL (Harvey Mudd College, Claremont, CA 91711) CINDY BRUCKNER-LEA (Pacific Northwest National Laboratory, Richland, WA 99352) .
The project was focused on developing and testing software for an automated Pathogen Detection System. The Pathogen Detection System has three primary components. The cell concentration component captures bacterial cells onto magnetic beads. The cell lysis and DNA amplification component consists of a temperature-controlled chamber for lysing cells (during heating) and amplifying DNA using polymerase chain reaction (PCR) or strand displacement amplification (SDA). The DNA detection component consists of laser induced florescence detection. The three components create a flexible platform that can be used for pathogen detection in liquid samples, in applications from health monitoring to laboratory research. Recent development of the system has included creating software for controlling the components and developing procedures to automate processes on the system. Software was created in "C" using Labwindows/CVI from National Instruments and provides independent process strings to prevent data loss and instrument interference. Additionally, it is easily adaptable to different types of instruments and different component configurations, and it provides real-time data output in graphs and numbers. Future developments of the system will include on-line DNA detection during DNA amplification and improved capture and release methods for the magnetic beads during cell concentration.