Data Storage Format Research Articles

Influence of Hot Carrier Diffusion on the Density Limitation of Optical Data Storage

Hot carrier diffusion (HCD) in Ge-Sb-Te phase change materials for re-writable optical data storage applications may limit the resolution of blue laser recording and cause additional cross-talk. As simulation studies show, the high optical excitation energy and small optical focus size characteristic of blue laser data storage formats lead to significant hot carrier diffusion prior to the energy transfer to the crystal lattice. As a consequence, the optical energy is deposited in an area larger than the laser spot size, leading to enhanced intertrack cross-talk and thermal cross-erase that reduces the quality of high-density optical storage. Therefore, the fundamental limit of resolution for re-writable optical storage systems is no longer determined by the laser focus size alone, but also by additional nonequilibrium HCD effects.

Database development in toxicogenomics: issues and efforts.

The marriage of toxicology and genomics has created not only opportunities but also novel informatics challenges. As with the larger field of gene expression analysis, toxicogenomics faces the problems of probe annotation and data comparison across different array platforms. Toxicogenomics studies are generally built on standard toxicology studies generating biological end point data, and as such, one goal of toxicogenomics is to detect relationships between changes in gene expression and in those biological parameters. These challenges are best addressed through data collection into a well-designed toxicogenomics database. A successful publicly accessible toxicogenomics database will serve as a repository for data sharing and as a resource for analysis, data mining, and discussion. It will offer a vehicle for harmonizing nomenclature and analytical approaches and serve as a reference for regulatory organizations to evaluate toxicogenomics data submitted as part of registrations. Such a database would capture the experimental context of in vivo studies with great fidelity such that the dynamics of the dose response could be probed statistically with confidence. This review presents the collaborative efforts between the European Molecular Biology Laboratory-European Bioinformatics Institute ArrayExpress, the International Life Sciences Institute Health and Environmental Science Institute, and the National Institute of Environmental Health Sciences National Center for Toxigenomics Chemical Effects in Biological Systems knowledge base. The goal of this collaboration is to establish public infrastructure on an international scale and examine other developments aimed at establishing toxicogenomics databases. In this review we discuss several issues common to such databases: the requirement for identifying minimal descriptors to represent the experiment, the demand for standardizing data storage and exchange formats, the challenge of creating standardized nomenclature and ontologies to describe biological data, the technical problems involved in data upload, the necessity of defining parameters that assess and record data quality, and the development of standardized analytical approaches.

Psrchive and psrfits: An Open Approach to Radio Pulsar Data Storage and Analysis

AbstractA new set of software applications and libraries for use in the archival and analysis of pulsar astronomical data is introduced. Known collectively as the psrchive scheme, the code was developed in parallel with a new data storage format called psrfits, which is based on the Flexible Image Transport System (FITS). Both of these projects utilise a modular, object-oriented design philosophy. psrchive is an open source development environment that incorporates an extensive range of c++ object classes and pre-built command line and graphical utilities. These deal transparently and simultaneously with multiple data storage formats, thereby enhancing data portability and facilitating the adoption of the psrfits file format. Here, data are stored in a series of modular header–data units that provide flexibility and scope for future expansion. As it is based on FITS, various standard libraries and applications may be used for data input, output, and visualisation. Both psrchive and psrfits are made publicly available to the academic community in the hope that this will promote their widespread use and acceptance.

The Bioperl toolkit: Perl modules for the life sciences.

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.

On an Integrated Approach for Optimizing Substrate Polymers for Future Optical Disc Requirements

The dynamic development of optical devices for the future blue laser digital versatile disk technology calls for a projection of the usability of the appropriate substrate polymer. As the new hardware (player) is usually not broadly available before market introduction of a new optical data storage format, a direct comparison of different substrate polymers for their usability is not possible. Computer simulation together with a thorough physical understanding of optical disk technology may present a useful tool first to model future optical drives and deduce critical disk requirements. These disk requirements have to be translated into quantitative polymer properties by a polymer physical model in a second step. Molecular modeling and structure property relations can then be used to propose promising monomer structures in a third step. Examples will be given in this presentation how with this strategy important open questions can be answered prior to the availability of future optical disk devices and chemical synthesis.

Updating XML

As XML has developed over the past few years, its role has expanded beyond its original domain as a semantics-preserving markup language for online documents, and it is now also the de facto format for interchanging data between heterogeneous systems. Data sources expert XML “views” over their data, and other system can directly import or query these views. As a result, there has been great interest in languages and systems for expressing queries over XML data, whether the XML is stored in a repository or generated as a view over some other data storage format. Clearly, in order to fully evolve XML into a universal data representation and sharing format, we must allow users to specify updates to XML documents and must develop techniques to process them efficiently. Update capabilities are important not only for modifying XML documents, but also for propagating changes through XML view and for expressing and transmitting changes to documents. This paper begins by proposing a set of basic update operations for both ordered and unordered XML data. We next describe extensions to the proposed standard XML query language, XQuery, to incorporate the update operations. We then consider alternative methods for implementing update operations when the XML data is mapped into a relational database. Finally, we describe an experimental evaluation of the alternative techniques for implementing our extensions.

Interfaces for data processing in surface analysis

As computer controlled instruments for surface analysis are in common use for many years, the problem of exchangeability of analytical data has attracted interest in the surface analysis community. More and more examples for the development of standarized data formats as the VAMAS format [1] and the Standard for Chromatography Data Communication from the AIA [2] have been published. There are a few attempts to establish standardized “data dictionaries” e.g. the parameter lists describing AES and XPS spectra pusblished in Surface Science Spectra [3, 4]. If several different analysis methods (such as AES, SAM, XPS, SIMS, STM, AFM, EPMA, …) are applied to the same sample, a quite independent and open approach is needed to be able to combine data of various instruments in a common data evaluation procedure. It could be the basic concept of real mutli-method analysis. The public domain software package MAXMIND has been developed, as only a standardized data exchange and storage format based on data dictionaries can guarantee a high level of independence of proprietary measurement systems.

Study on data storage format of a holographic optical disk

A systematic theory of holographic optical disk storage is developed. The recorded modes of addressing/tracking information on a holographic optical disk are discussed in detail, then the data storage format of a holographic optical disk is proposed. Parallel addressing techniques of the recorded images are analyzed.

A few words on bits & bytes: a tutorial on image and spectral processing for the novice

We are now in a position, in the world of microscopy and microanalysis, to record all of our data digitally and often, the first time that the data is printed out is when it is submitted for publication, although there are distinct possibilities that we shall soon be publishing electronically too. Digital image acquisition schemes are largely the realm of the microscope manufacturers, however, there are also a multitude of “homemade” acquisition systems in microscope laboratories around the world. Such a wide variety of systems leads to a wide variety of data storage formats. For example, a any one time there have been at least 6 manufacturers of X-ray Energy Dispersive Spectroscopy (XEDS) systems, each with their own proprietary data format, which, frequently, was not explained to the user. The philosophy was: “Our system is all you will ever need, so you don't need to know how the data is stored”.

Data structures for multi-sensor integration

This paper analyzes data organization requirements for multi-sensor information processing. It proposes solutions for both abstract data structures and storage formats. We formalize the concept of general sensor information and define a data structure able to support sensor information obtained by a wide spectrum of applications. The problem of off-line storage is studied and two different solutions are proposed. Finally, we comment on some guidelines for designing real-time applications under our approach.

High‐performance equation solvers and their impact on finite element analysis

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number od operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

The Human Genome Initiative—Do Databases Reflect Current Progress?

Mapping and sequencing the entire human genome in a timely fashion requires organization of all available resources to the common goal. Federal funding agencies have established individual genome centers that will focus on one or more chromosomes. Further, chromosome-specific workshops are being organized to permit individual centers, researchers, or groups to pool their results with other colleagues working on the same chromosome. The activities imply the following: (1) each chromosome community should have its own database; (2) the databases should permit inclusion of data from many different groups and give different map interpretations of the same chromosome region; and (3) similar formats for data storage and representation should be used across the databases to simplify data exchange and interpretation. However, no matter how sophisticated modern database management systems may be, they cannot realistically fulfill their responsibilities until all parties concerned are prepared to submit their data to centralized databases. To do this they need to be provided with adequate tools and incentives. Provision of the tools is the task of the database organizations. Provision of incentives is partly a question of adequate peer recognition for direct submission, partly a willingness to openly share information with the community at large, andmore » partly the need for funding organizations to insist on data sharing as a requisite for their continued support.« less

Standard generalized markup language: Why reference librarians should care

All of us in the library community are familiar with the impact of the MARC (machine‐readable cataloging) record on library operations. Whether we specialize in administrative, systems, public, or technical services, we recognize the MARC record as a standard data storage format that has made it easier to produce, store, and retrieve data. Few disagree that widespread adoption of the MARC record has enabled libraries to realize the full benefits of automation.

Proposed standard for image cytometry data files

A number of different types of computers running a variety of operating systems are presently used for the collection and analysis of image cytometry data. In order to facilitate the development of sharable data analysis programs, to allow for the transport of image cytometry data from one installation to another, and to provide a uniform and controlled means for including textual information in data files, this document describes a data storage format that is proposed as a standard for use in image cytometry. In this standard, data from an image measurement are stored in a minimum of two files. One file is written in ASCII to include information about the way the image data are written and optionally, information about the sample, experiment, equipment, etc. The image data are written separately into a binary file. This standard is proposed with the intention that it will be used internationally for the storage and handling of biomedical image cytometry data. The method of data storage described in this paper is similar to those methods published in American Association of Physicists in Medicine (AAPM) Report Number 10 and in ACR-NEMA Standards Publication Number 300-1985.

An introduction to the NSPCG software package

AbstractNSPCG is the most recent research‐oriented software package developed as part of the ITPACK Project at the Center for Numerical Analysis of The University of Texas at Austin. It is designed to solve large sparse systems of linear equations by a variety of different non‐symmetric preconditioned conjugate gradient methods. Several different sparse data storage schemes are available for storing the coefficient matrix of the linear system. Matrices with a wide range of structures from highly structured to completely unstructured can be accommodated. To limit memory requirements, the accelerators in the package can be called directly with the matrix stored in a user‐defined sparse data storage format (for example, from a particular application) by supplying some user‐written routines for certain matrix–vector operations.The main entry point into the package is through a single subroutine call. The various methods are accessed by using a particular naming convention for the first two parameters that in turn selects a preconditioner, an accelerator and a data storage scheme. Some of the basic preconditioners that are available are Jacobi, Incomplete LU Decomposition and Symmetric Successive Overrelaxation as well as block preconditioners. The user can select from a large collection of accelerators such as Conjugate Gradient (CG), Chebyshev (SI, for semi‐iterative), Generalized Minimal Residual (GMRES), Biconjugate Gradient Squared (BCGS) and many others. The package is modular so that almost any accelerator can be used with almost any preconditioner. One of the main purposes for the development of the package was to provide a common modular structure for research on iterative methods. The entire package is written in Fortran 77 with vectorization in mind for applications on supercomputers.

Optimal number of disc clock tracks for block-oriented rotating associative processors

Block-oriented rotating associative processors provide a highly cost-effective solution to the need for parallel processing of large volumes of data in information storage and retrieval applications. Such processors are implemented by incorporating some processing logic into each read/write head of a fixed-head (head-per-track) disc memory. With non-self-clocked data recording, which offers higher storage densities, the usual data storage format is to assign the fixed capacity dictated by the maximum bit density and the length of the innermost (shortest) track to all tracks, thus making it possible to use a single clock track for the synchronisation of read and write operations. In the paper, we note that with a single clock track about half of the total recording capacity of the disk surface is wasted. This leads to the proposal for dividing the tracks into groups, with one clock track for each group. It is shown that with optimal design, 90–95% of the useful disk capacity can be utilised. This represents a 70–90% improvement over the case of a single clock track and is achieved at virtually no extra cost.

Vector Computations for Sparse Linear Systems

We are interested in the development of algorithms, based on iterative methods, and software for the solution of large sparse systems of linear algebraic equations with emphasis on systems arising in the numerical solution of partial differential equations. The objective is to develop algorithms and software which are effective when used with a vector computer such as the Control Data CYBER 205 or the CRAY 1. A package of programs, known as ITPACK, has been developed for use on conventional, or scalar machines. A number of “short-range” modifications to ITPACK, including changes in the data storage format and changes in the programming, but not in the algorithms used, have been made and tested on a number of numerical examples. Preliminary work is described on “long-range” modifications which will involve extensive changes in the basic algorithms in order to achieve efficient vectorization.

Archiving and retrieval of data from the International Ultraviolet Explorer (IUE) mission

AbstractThe data base of IUE spectra available for dissemination to the scientific community presently contains approximately 22,000 separate images. Due to storage space and computer processing time limitations, it was decided to store the data on high density (6250 bpi) specially formatted tapes and to retrieve and reconvert them to the originally supplied format upon request. The archival/retrieval system for the data and an automatic data entry system for creation and maintenance of an indexing data base are described. Suggestions are made for the use of standard formats for future image data storage, retrieval and dissemination.

A new worldwide chronology of volcanic eruptions: (With a summary of historical ash-producing activity and some implications for climatic trends of the last one hundred years)

A chronological enumeration of volcanic eruptions from around the world is used to describe temporal and spatial variations in historical volcanism. Over 5000 eruptions from 907 active volcanoes of the world are classified on the basis of eruption type and scaled on the basis of relative magnitude of ejected material. The chronology extends from 2227 B.C. to 1969 A.D. but is most reliable after 1850 A.D. Advantages of the data set over other existing chronologies include a vastly increased sample size, a scheme for assessing the relative ash-producing magnitude of each eruption, and a computerized data-storage format. Preliminary application of the eruption chronology to global and hemispheric temperature trends for the period 1880–1969 demonstrates that episodes of frequent and intense ash-producing eruptions tend to be associated with periods of cooler hemispheric temperatures, while volcanically quiescent episodes tend to correspond with periods of hemispheric warming.

A computerized system for clinical microbiology.

A system of microbiology reporting by computer which is simple to operate and provides accurate, rapid reporting of laboratory results with provisions for permanent data storage, retrieval, and other programs is described. The system uses a coded, fixed data storage format, yet it is accessible to most hospitals since the equipment needed may be rented from commercial sources. It is ideally suited for contracting laboratories, geographically separate from the patient care area, but may also be used by multiple laboratories with teletype facilities available. The principal advantage of this system of reporting is the utilization of the fixed formatted data cards, allowing development of almost unlimited programs, for use with information held in the data bank.