Olin Johnson

A traveling salesman approach for predicting protein functions

BackgroundProtein-protein interaction information can be used to predict unknown protein functions and to help study biological pathways.ResultsHere we present a new approach utilizing the classic Traveling Salesman Problem to study the protein-protein interactions and to predict protein functions in budding yeast Saccharomyces cerevisiae. We apply the global optimization tool from combinatorial optimization algorithms to cluster the yeast proteins based on the global protein interaction information. We then use this clustering information to help us predict protein functions. We use our algorithm together with the direct neighbor algorithm [1] on characterized proteins and compare the prediction accuracy of the two methods. We show our algorithm can produce better predictions than the direct neighbor algorithm, which only considers the immediate neighbors of the query protein.ConclusionOur method is a promising one to be used as a general tool to predict functions of uncharacterized proteins and a successful sample of using computer science knowledge and algorithms to study biological problems.

Development and evaluation of indexed captioned searchable videos for STEM coursework

Videos of classroom lectures have proven to be a popular and versatile learning resource. This paper reports on videos featuring Indexing, Captioning, and Search capability (ICS Videos). The goal is to allow a user to rapidly search and access a topic of interest, a key shortcoming of the standard video format. A lecture is automatically divided into logical indexed video segments by analyzing video frames. Text is automatically identified with OCR technology enhanced with image transformations to drive keyword search. Captions can be added to videos. The ICS video player integrates indexing, search, and captioning in video playback and has been used by dozens of courses and 1000s of students. This paper reports on the development and evaluation of ICS videos framework and assessment of its value as an academic learning resource.

Tablet PC video based hybrid coursework in computer science: report from a pilot project

Online learning, defined broadly as recording and delivering classroom experience with technology, has tremendous potential. However, success to date has been very limited in science and engineering. We believe this is because traditional video recording is cumbersome and not suitable for technical lectures and removing live classroom interaction is detrimental to learning. Employing Tablet PCs with slide presentation software has made it simple and convenient to develop and record high quality lectures. We employ such videos in a hybrid model of coursework. All lectures are made available as online videos, but limited classroom interaction is an important component; the classroom is used for review of lecture material, examinations, demonstrations, tutorials, and hands-on sessions. The hybrid framework is particularly suitable for students with logistical difficulties, e.g., because of work schedule. This paper is an evaluation of the hybrid learning approach as applied to upper level computer science coursework. We report our experience in teaching a suite of hybrid courses at the University of Houston and discuss the detailed feedback we received from the students who participated in the courses.

PARADISE: an advanced featured parallel file system

Several important theoretical improvements to parallel I/O have been proposed in recent years. Support for many of these suggestions is still limited to theoretical models or simulations. PARADISE is an experimental parallel file system for distributed memory multiprocessors which attempts to integrate many of these proposals into a unified and working prototype. PARADISE includes such features as cooperative caching, alternative file access modes, tuned message passing and elements of disk-directed I/O. PARADISE is implemented in a hybrid fashion in which functionality is concentrated in local servers with additions in a user callable library. It assumes a Mach 3.0 microkernel based operating system with homogeneous processing elements. However, we believe that the approach used and the lessons learned can be easily extended to other homogeneous MPP environments.

A Vector Elastic Model for the Cyber 205

The research project reported in this paper is the result of a joint grant from Texaco and Control Data Corporation. The focus of this project was the development of a vectorized version of the two dimensional elastic forward modeling algorithm developed by Kosloff and Reshef (1982). The program was designed for the CDC CYBER 205, and implemented on Texaco’s installation. Timings obtained for Kosloff’s implementaion on the RCL VAX 11/780 with an attached FPS-100 array processor indicate that the vectorized version is approximately 900 times faster on a CYBER 205.

An overview of a MPI profiling environment for the NEC Cenju-3

This paper describes an ongoing effort to provide a profiling environment for MPI applications running on the NEC Cenju-3, an MPP research prototype. Highlights of these efforts include automatic management of dynamic trace buffers, efficient post-processing, and user-driven visualization support. Modern virtual memory support found in the Cenju-3 operating system provides automatic management of dynamic trace buffers. Parallelization provides post-processing efficiency. Researchers from an NSF Grand Challenge Application Group are guiding the development of the visualization tool.

Mapping 3‐D multi‐attribute data into HLS color space — Applications to Vinton Dome, LA

Seismic interpreters and processors encounter everincreasing volumes of seismic data each year. Processors are faced with analyzing common offset and azimuth volumes, acquisition azimuth volumes, time-lapse volumes, and multicomponent volumes. Processors also need to quality control traveltime, velocity, and subsurface illumination volumes. Interpreters are faced with cubes of AVO, coherence, spectral components, dip, azimuth, attenuation, and interval velocity. To partially address this challenge, we have exploited the HLS color model and developed a suite of compositing algorithms to display 2 or more of these cubes simultaneously into a single indexed color volume. Some of these ideas have been presented before, but have not been embraced by the commercial interpretation software community. We demonstrate the capabilities of such compositing algorithms in attribute analysis, seismic modeling, seismic processing, and seismic imaging applied to a prospect over Vinton Dome, LA.

Optimal scheduling policies for mixed scalar-vector multiprocessor supercomputers

A queuing network model is developed for multiprocessing supercomputer systems implemented on two heterogeneous processors, a scaler unit and a vector unit, which work concurrently on a single process. The model is analyzed theoretically for a representative case of model job mixes. It is found that the utilization of one of the two central service stations in the model can only be maximized at the expense of minimizing the utilization of the other central service station. The method of analysis adopted is the technique of variable aggregation based on nearly complete decomposability.<<ETX>>

Benchmark of the extended basic linear algebra subprograms on the NEC SX-2 supercomputer

The Basic Linear Algebra Subprograms (BLAS) covering most basic vector operations have been widely used in numerical applications including LINPACK. The Extended Basic Linear Algebra Subprograms (EBLAS) were developed recently as an extension to the strictly vector operations of the BLAS. The EBLAS, also known as Level-2 BLAS, are a set of subprograms that represent basic matrix-vector operations and were written to take advantage of the architecture of todays supercomputers.

A Computer Vision System For Understanding The Movement Of A Wave Field

Mathematical modeling of seismic phenomena is an important tool for producing synthetic wavefield snapshots as well as synthetic seismic traces. The generation of those models is mainly carried out as an aid for studying the propagation of a signal when it is transmitted through or reflected from a a given horizon. In fact, information regarding the geometry of the horizon and the nature of the materials, the contact of which gives rise to the horizon, are fundamental in geological exploration. The snapshots mentioned above form a sequence of images showing a two-dimensional representation of the wave field evolving into refracted and reflected waves during a given period of time. By analyzing the behavior of the reflected and refracted waves a human observer can extract parameters like velocity of the waves, geometry of the horizon, reflection and refraction parameters, and nature of the materials. This is an intelligent process which infers properties of objects by relating aspects of an apparently totally different nature (like a sequence of picture where arcs of circles are delineated). It is interesting to observe that it is possible for the human eye to classify the waves residing in each configuration, tracking them from an image to the successive one, giving finally, a synthetic description of the environment. Frequently a problem rises when reflected, refracted, and wrap-around waves form complex configurations. In these cases the distinction of the components of the wavefield becomes difficult. An automatic system, which is able to emulate the behaviour of a human observer analyzing a simple sequence of synthetic snapshots, is presented.