Compressing DNA sequence databases with coil

Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work

Spin-tunnel investigation of a 1/25-scale model of the General Dynamics F-16XL airplane

A spin-tunnel investigation of the spin and recovery characteristics of a 1/25-scale model to the General Dynamics F-16XL aircraft was conducted in the Langley Spin Tunnel. Tests included erect and inverted spins at various symmetric and asymmetric loading conditions. The required size of an emergency spin-recovery parachute was determined

Study to determine potential flight applications and human factors design guidelines for voice recognition and synthesis systems

A study was conducted to determine potential commercial aircraft flight deck applications and implementation guidelines for voice recognition and synthesis. At first, a survey of voice recognition and synthesis technology was undertaken to develop a working knowledge base. Then, numerous potential aircraft and simulator flight deck voice applications were identified and each proposed application was rated on a number of criteria in order to achieve an overall payoff rating. The potential voice recognition applications fell into five general categories: programming, interrogation, data entry, switch and mode selection, and continuous/time-critical action control. The ratings of the first three categories showed the most promise of being beneficial to flight deck operations. Possible applications of voice synthesis systems were categorized as automatic or pilot selectable and many were rated as being potentially beneficial. In addition, voice system implementation guidelines and pertinent performance criteria are proposed. Finally, the findings of this study are compared with those made in a recent NASA study of a 1995 transport concept

Optimal Compression of Floating-point Astronomical Images Without Significant Loss of Information

We describe a compression method for floating-point astronomical images that gives compression ratios of 6 -- 10 while still preserving the scientifically important information in the image. The pixel values are first preprocessed by quantizing them into scaled integer intensity levels, which removes some of the uncompressible noise in the image. The integers are then losslessly compressed using the fast and efficient Rice algorithm and stored in a portable FITS format file. Quantizing an image more coarsely gives greater image compression, but it also increases the noise and degrades the precision of the photometric and astrometric measurements in the quantized image. Dithering the pixel values during the quantization process can greatly improve the precision of measurements in the images. This is especially important if the analysis algorithm relies on the mode or the median which would be similarly quantized if the pixel values are not dithered. We perform a series of experiments on both synthetic and real astronomical CCD images to quantitatively demonstrate that the magnitudes and positions of stars in the quantized images can be measured with the predicted amount of precision. In order to encourage wider use of these image compression methods, we have made available a pair of general-purpose image compression programs, called fpack and funpack, which can be used to compress any FITS format image.Comment: Accepted PAS

A study of the vibration responses of shells and plates to fluctuating pressure environments

Vibration responses of cylindrical shells and plates to acoustic excitatio

Lossless Astronomical Image Compression and the Effects of Noise

We compare a variety of lossless image compression methods on a large sample of astronomical images and show how the compression ratios and speeds of the algorithms are affected by the amount of noise in the images. In the ideal case where the image pixel values have a random Gaussian distribution, the equivalent number of uncompressible noise bits per pixel is given by Nbits =log2(sigma * sqrt(12)) and the lossless compression ratio is given by R = BITPIX / Nbits + K where BITPIX is the bit length of the pixel values and K is a measure of the efficiency of the compression algorithm. We perform image compression tests on a large sample of integer astronomical CCD images using the GZIP compression program and using a newer FITS tiled-image compression method that currently supports 4 compression algorithms: Rice, Hcompress, PLIO, and GZIP. Overall, the Rice compression algorithm strikes the best balance of compression and computational efficiency; it is 2--3 times faster and produces about 1.4 times greater compression than GZIP. The Rice algorithm produces 75%--90% (depending on the amount of noise in the image) as much compression as an ideal algorithm with K = 0. The image compression and uncompression utility programs used in this study (called fpack and funpack) are publicly available from the HEASARC web site. A simple command-line interface may be used to compress or uncompress any FITS image file.Comment: 20 pages, 9 figures, to be published in PAS

Investigation of dual polarization laser modulation

Dual polarization lasers for wideband optical communication

An evaluation of alternative techniques for estimating county population in a six-state area

County population statistics in Arkansas, Iowa, Kansas, Missouri, Nebraska, and Oklahoma for industry, government, and educatio

Mesoscale variability of free tropospheric humidity near San Nicolas Island during FIRE

Humidity variability at the top of the marine boundary layer (MBL) and in the free troposphere was examined using a variety of measurements taken on and around San Nicolas Island (SNI) during the FIRE IFO in July, 1987. Doppler wind profiler reflectivity recorded at two minute time resolution has provided the most continuous record and detail of small scale humidity fluctuations. Rawinsonde data were available from both an island site and the research vessel Point Sur. The information extractable from these sources is somewhat limited due to the frequency of launches (3 to 4/day at SNI and 6/day on the Point Sur). Some additional data were available from instrumented aircraft although scheduling flights in the neighborhood of the island was difficult due to restrictions on the air space. Other relevant data were collected at SNI near the radar and rawinsonde launch sites. A continuous record of cloud base altitude was logged by a ceilometer. Doppler acoustic sounder (sodar) reflectivity data provided a good record of inversion height. The sodar also monitored turbulent temperature fluctuations in the MBL. A small ground station recorded hourly averages of solar irradiance and downward longwave irradiance. The analysis in progress of the various data sets for two adjacent two day periods from 11 July to 14 July is described. The earlier period was chosen because the marine inversion was unusually high and there was increased frequency of rawinsonde launches at SNI. The later period was chosen because of the significant descent with time of an elevated inversion indicated by the radar data. Throughout the four day period, but especially in the first half, the turbulent humidity structure calculated from Doppler radar reflectivity shows excellent agreement with humidity profiles evaluated from rawinsonde data

Oxygen Absorption in Cooling Flows

The inhomogeneous cooling flow scenario predicts the existence of large quantities of gas in massive elliptical galaxies, groups, and clusters that have cooled and dropped out of the flow. Using spatially resolved, deprojected X-ray spectra from the ROSAT PSPC we have detected strong absorption over energies ~0.4-0.8 keV intrinsic to the central ~1 arcmin of the galaxy, NGC 1399, the group, NGC 5044, and the cluster, A1795. These systems have amongst the largest nearby cooling flows in their respective classes and low Galactic columns. Since no excess absorption is indicated for energies below ~0.4 keV the most reasonable model for the absorber is warm, collisionally ionized gas with T=10^{5-6} K where ionized states of oxygen provide most of the absorption. Attributing the absorption only to ionized gas reconciles the large columns of cold H and He inferred from Einstein and ASCA with the lack of such columns inferred from ROSAT, and also is consistent with the negligible atomic and molecular H inferred from HI, and CO observations of cooling flows. The prediction of warm ionized gas as the product of mass drop-out in these and other cooling flows can be verified by Chandra, XMM, and ASTRO-E.Comment: 4 pages (2 figures), Accepted for publication in ApJ Letters, no significant changes from previous submitted versio