Information technology literacy among Nigerian microbiology students and professionals

Education and research in the discipline of microbiology is set for change as a result of computers being used as teaching and learning tools. In order to catalyse this change in Nigeria, previous computer experience, knowledge and attitude to computers of Nigerian microbiology students and professionals was determined. Our results indicate the need to increase the awareness of use and potentials of computers in microbiological research and education.     

Oscillatory Threshold Logic

In the 1940s, the first generation of modern computers used vacuum tube oscillators as their principle components, however, with the development of the transistor, such oscillator based computers quickly became obsolete. As the demand for faster and lower power computers continues, transistors are themselves approaching their theoretical limit and emerging technologies must eventually supersede them. With the development of optical oscillators and Josephson junction technology, we are again presented with the possibility of using oscillators as the basic components of computers, and it is possible that the next generation of computers will be composed almost entirely of oscillatory devices. Here, we demonstrate how coupled threshold oscillators may be used to perform binary logic in a manner entirely consistent with modern computer architectures. We describe a variety of computational circuitry and demonstrate working oscillator models of both computation and memory.     

A crystallographic molecular lattice builder applied to model lipid bilayers

It is often desirable for noncrystallographers to generate graphical models of three-dimensional crystal structures based on published coordinates of the atoms that make up the crystallographic unit cells. This type of visualization is particularly important for small-molecule crystals, such as lipid crystals, where one may be interested in investigating interactions between the individual molecules in addition to their conformations. BILAYER BUILDER is a program that generates a portion of the entire crystal structure from the coordinates of the molecules in a single unit cell. It gives users of small desktop computers, such as the Apple Macintosh, the capability to generate and examine model crystal structures with a molecular graphics display program. BILAYER BUILDER stores the crystal coordinates in a Brookhaven Protein Data Bank file format for possible use in a variety of applications on many different computers. Initially, it was written for use with lipid crystals and bilayers but may be used for building an assortment of molecular crystals.     

Distributed computing in bioinformatics

This paper provides an overview of methods and current applications of distributed computing in bioinformatics. Distributed computing is a strategy of dividing a large workload among multiple computers to reduce processing time, or to make use of resources such as programs and databases that are not available on all computers. Participating computers may be connected either through a local high-speed network or through the Internet.     

Doctors' experience with handheld computers in clinical practice: qualitative study

Objective To examine doctors'' perspectives about their experiences with handheld computers in clinical practice.Design Qualitative study of eight focus groups consisting of doctors with diverse training and practice patterns.Setting Six practice settings across the United States and two additional focus group sessions held at a national meeting of general internists.Participants 54 doctors who did or did not use handheld computers.Results Doctors who used handheld computers in clinical practice seemed generally satisfied with them and reported diverse patterns of use. Users perceived that the devices helped them increase productivity and improve patient care. Barriers to use concerned the device itself and personal and perceptual constraints, with perceptual factors such as comfort with technology, preference for paper, and the impression that the devices are not easy to use somewhat difficult to overcome. Participants suggested that organisations can help promote handheld computers by providing advice on purchase, usage, training, and user support. Participants expressed concern about reliability and security of the device but were particularly concerned about dependency on the device and over-reliance as a substitute for clinical thinking.Conclusions Doctors expect handheld computers to become more useful, and most seem interested in leveraging (getting the most value from) their use. Key opportunities with handheld computers included their use as a stepping stone to build doctors'' comfort with other information technology and ehealth initiatives and providing point of care support that helps improve patient care.     

GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops

ABSTRACT: BACKGROUND: Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today's computing technology. FINDINGS: We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core computers. We show that GTfold predicts secondary structure in less time than UNAfold and RNAfold, without sacrificing accuracy, on machines with four or more cores. CONCLUSIONS: GTfold supports advances in RNA structural biology by reducing the timescales for secondary structure prediction. The difference will be particularly valuable to researchers working with lengthy RNA sequences, such as RNA viral genomes.     

A Probabilistic Model of Perception

The development of electronic computers has made it possible to transfer to them a number of the "intellectual" functions of man. At present such machines are being employed to model broader and broader regions of man's psychological activity. One of the most important problems in this connection is the building of "perceptive machines," such as reading machines, "the printing phonograph" and so forth. Perceptive machines are a necessary element in the development of automatic equipment to operate in complicated environments.     

Quantum computing: a new paradigm for ecology

A global technology arms race is underway to build evermore powerful and precise quantum computers. Quantum computers have the potential to tackle certain quantitative problems quicker than classical computers. The current focus of quantum computing is on pushing the boundaries of fundamental quantum information and commercial applications in industrial sectors, financial services, and other profit-led sectors, particularly where improvements in optimisation and sampling can improve increased economic return. We believe that ecologists could exploit the computational power of quantum computers because the statistical approaches commonly used in ecology already have proven pathways on quantum computers. Moreover, quantum computing could ultimately leapfrog our understanding of complex ecological systems, if the hardware, opportunity, and creativity of quantitative ecologists all align.     

The Computerization of Learning—Scientific Foundation

The computerization of secondary schools is proceeding along two lines. First there is the problem of teaching pupils to work with computers. Today this is regarded as a second literacy: all basic types of modern labor presuppose a person's ability to work with computers.     

Low dissipation computing in biological systems

Biological systems frequently need to solve many computationally hard decision and optimization problems. The solution of these problems by digital computers as presently understood requires exponentially large energy dissipation. This severely restricts the ability of digital computers to attack such problems. We shall show that only polynomial dissipation is required to solve these problems adequately by "physical annealing", as realized in the genetic system, making these problems tractable energetically.     

Using medical genetics applications to educate for computer competence.

This article proposes specific areas of computing competence and illustrates how these skills can be acquired as an integral part of the curriculum of medical genetics. Geneticists are at the forefront in the use of computers for medical care, because of the driving force of the Human Genome Project. Computer searching of international data bases is the most efficient method to keep current with the explosion in molecular genetics data and with its immediate relevance to clinical care. The use of computers in genetics education could go far beyond the use of computer-assisted instruction (CAI) to show how to use computer systems to assist with clinical decisions. The proposed basic computer skills can be obtained using genetics software. The six proposed skills include the use of (1) microcomputers, (2) productivity software, (3) CAI, patient simulations and specific application programs, (4) remote computers, (5) data bases and knowledge bases, and (6) computers to improve the clinical care of patients.     

Apps for angiosperms: the usability of mobile computers and printed field guides for UK wild flower and winter tree identification

We investigated usability of mobile computers and field guide books with adult botanical novices, for the identification of wildflowers and deciduous trees in winter. Identification accuracy was significantly higher for wildflowers using a mobile computer app than field guide books but significantly lower for deciduous trees. User preference followed a similar pattern. These results suggest that the identification method and its design are more important for a field guide than its presentation medium (electronic or printed). We discuss the relative advantages of the presentation media used and their value as engagement tools for botany.     

A user-friendly biological workstation

Learning methods developed by artificial intelligence research teams are very efficient for biological sequences analysis but they need running on large computers accessed by terminals. These computers are interfaced with standard displays involving long and unpleasant alphanumerical data handling. The "biological work station" is a personal computer with a color graphic screen providing a user-friendly interface for the artificial intelligence learning programs running on large computers. It provides to biologist a graphical convenient tool for sequence analysis built with efficient man-machine communication methods such as multiwindows, icons and mouse selection. It allows the biologist to edit and display sequences in an efficient and natural way, showing off directly on color pictures the data and the results of learning programs.     

Indispensable role of quantum theory in the brain dynamics

Recently, Tegmark pointed out that the superposition of ion states involved in the superposition of firing and resting states of a neuron quickly decohere. It undoubtedly indicates that neural networks cannot work as quantum computers, or computers taking advantage of coherent states. Does it also mean that the brain can be modeled as a neural network obeying classical physics? Here we show that it does not mean that the brain can be modeled as a neural network obeying classical physics. A brand new perspective in research of neural networks from quantum theoretical aspect is presented.     

Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations

G protein-coupled receptors (GPCRs) are a large, biomedically important family of proteins, and the recent explosion of new high-resolution structural information about them has provided an enormous opportunity for computational modeling to make major contributions. In particular, molecular dynamics simulations have become a driving factor in many areas of GPCR biophysics, improving our understanding of lipid-protein interaction, activation mechanisms, and internal hydration. Given that computers will continue to get faster and more structures will be solved, the importance of computational methods will only continue to grow, particularly as simulation research is more closely coupled to experiment.     

Interfacing electrochromic spectacles to computer IO ports

Many important properties of molecules depend on their precise three-dimensional (3D) structure. It is therefore useful to be able to view a molecule in 3D on a 2D computer screen when manipulating it. An inexpensive method for viewing in 3D using liquid crystal glasses and a PC is presented. The methodology used is easily extended to other computers and workstations.     

Personal access to sequence databases on personal computers.

A comprehensive package of software has been developed to access nucleic acid and protein sequence databases on stand-alone IBM personal computers. The software combines keyword search on the annotation fields of the data with pattern matching algorithms on the biological sequences. Sequences containing complex sites like promoters or kink sites can be identified as well as sequences that are similar to a query sequence. Protein sequences with particular patterns of amino acids such as hydrophobic regions can be identified as well. Considering the relatively inexpensive hard disks now available, personal computers have become a cost-effective alternative to mainframe processing for sequence databases.     

Sequence similarity (‘Homology’) searching for molecular biologists

Major types of sequence similarity searching (often, and incorrectly, called ‘homology’ searching) are reviewed and examples of each are presented. The features and limitations of each type of program, and individual implementations of each type are discussed. Two pairs of sequences are used as examples to show how implementations of each type differ in their results and their presentation. Both local and global alignment programs are examined, and the programs reviewed run on many different types of computer architectures, from laboratory computers such as the IBM PC, minicomputers such as the VAX, to large mainframe computers such as DEC-10/20 series.     

Screening protein and nucleic acid sequences against libraries of patterns.

We describe programs that can screen nucleic acid and protein sequences against libraries of motifs and patterns. Such comparisons are likely to play an important role in interpreting the function of sequences determined during large scale sequencing projects. In addition we report programs for converting the Prosite protein motif library into a form that is compatible with our searching programs. The programs work on VAX and SUN computers.