Scanning protein sequence databanks using a distributed processing workstation network

The programme pscan has been developed to distribute proteindatabank scans over a network of computers that share a commonfilesystem. pscan may be used in conjunction with most conventionalsequence comparison programmes with few modifications. In testruns using the Smith — Waterman dynamic programming algorithm,the time required to scan a 6858 sequence databank using a querysequence 740 residues long was reduced from 50 min for a singleprocessor, to 11 minutes for five processors. Accordingly, pscanprovides a low-cost, portable alternative to dedicated parallelprocessing computers. Received on August 27, 1990; accepted on September 25, 1990     

Algamica: revisions to a key-based computerized counting program for free-living,attached, and benthic algae

A computerized counting program for algae and other microscopic bodies, named Algamica, is presented here. This program is a revised version of the original computer counting program of Hamilton published in 1990. This DOS-based software can enumerate all types of microscopic algae (i.e. phytoplankton, periphyton, diatoms), for which adequate expression of results are provided. Automated calculations of densities, biovolumes, surface areas and carbon biomass are available at the termination of each sample count. A simple counter for other micro-organisms is also available. A comprehensive guide manual file has been added to allow for a friendly first contact with the program and its options. This software conforms to current enumeration methodology. This version is available for PC computers, from website Algamica.ibelgique.com. Minimum required memory is 200 KB.     

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.     

Cyberkids in Metropolitan America

Children have learning and problem-solving powers at least equal to those of adults. But children are in general disempowered and treated as inferior to adults. The availability of home computers from around 1980, and of internet and e-mail facilities from around 1990, created a window of freedom for those children who were allowed unmonitored access to computers, e-mail and the internet. Children who learned computer skills while they were still children became more proficient at these skills than adults who only began to acquire the same skills as adults. For a period of time, scientists well advanced in such fields as physics and aeronautics had to rely upon adolescents to fill their programming needs. In addition, during the early days of home-computing, around 1980, computer-territory was still relatively rough and virgin. The internet was unknown, computer games were unknown, and anyone who entered computer territory had to learn programming in order to derive any benefits from this territory. By the late 1990's, commercial interests had gained a strong foothold in computer territory, and any child or adult with zero skills could enter this territory as a consumer and derive information and entertainment from this territory, without acquiring the kinds of skills necessary to exercise any degree of control over the computer-based landscape. Still, computer science remains a new frontier, in that any person who has the skills to act on this frontier may achieve success, regardless of that person's age, social status, et cetera. The two greatest barriers to success are limitations on access to computers and the internet, and English-language knowledge. The latter barrier is falling. Inasmuch as ability to navigate and alter the landscape of computer territory is a source of great power, and inasmuch as children acquire such skills more quickly than adults, may we consider a new empowerment of children to be in the offing? Or will adults co-opt the instruments of power, and will children remain as pets and slaves of adults for the indefinite future?     

Web-based consumer health information: public access, digital division, and remainders

Public access Internet portals and decreasing costs of personal computers have created a growing consensus that unequal access to information, or a "digital divide," has largely disappeared for US consumers. A series of technology initiatives in the late 1990s were believed to have largely eliminated the divide. For healthcare patients, access to information is an essential part of the consumer-centric framework outlined in the recently proposed national health information initiative. Data from a recent study of health information-seeking behaviors on the Internet suggest that a "digitally underserved group" persists, effectively limiting the planned national health information infrastructure to wealthier Americans.     

LSTSQ: a module for reliable constrained and unconstrained nonlinear regression

A software module for nonlinear regression analysis, based onthe reliable Meyer—Roth algorithm (a modified damped leastsquare algorithm), is presented. It allows both constrainedand unconstrained optimization, and the use of a variety ofweighting methods. Virtually any nonlinear function can be fitted,including those with several nondependent variables. The packagehas been thoroughly tested, and is available in several commoncomputer languages (Pascal, Modula-2 and C). It is easy to use,and advanced knowledge of mathematics or computers is not essential.Standard test problems, and a fully working example of use onenzyme kinetics are included. Received on September 24, 1990; accepted on February 20, 1991     

Concentration of Access to Information and Communication Technologies in the Municipalities of the Brazilian Legal Amazon

This study fills demand for data on access and use of information and communication technologies (ICT) in the Brazilian legal Amazon, a region of localities with identical economic, political, and social problems. We use the 2010 Brazilian Demographic Census to compile data on urban and rural households (i) with computers and Internet access, (ii) with mobile phones, and (iii) with fixed phones. To compare the concentration of access to ICT in the municipalities of the Brazilian Amazon with other regions of Brazil, we use a concentration index to quantify the concentration of households in the following classes: with computers and Internet access, with mobile phones, with fixed phones, and no access. These data are analyzed along with municipal indicators on income, education, electricity, and population size. The results show that for urban households, the average concentration in the municipalities of the Amazon for computers and Internet access and for fixed phones is lower than in other regions of the country; meanwhile, that for no access and mobile phones is higher than in any other region. For rural households, the average concentration in the municipalities of the Amazon for computers and Internet access, mobile phones, and fixed phones is lower than in any other region of the country; meanwhile, that for no access is higher than in any other region. In addition, the study shows that education and income are determinants of inequality in accessing ICT in Brazilian municipalities and that the existence of electricity in rural households is directly associated with the ownership of ICT resources.     

gm: a practical tool for automating DNA sequence analysis

The gm (gene modeler) program automates the identification ofcandidate genes in anonymous, genomic DNA sequence data, gmaccepts sequence data, organism-specific consensus matricesand codon asymmetry tables, and a set of parameters as input;it returns a set of models describing the structures of candidategenes in the sequence and a corresponding set of predicted aminoacid sequences as output, gm is implemented in C, and has beentested on Sun, VAX, Sequent, MIPS and Cray computers. It iscapable of analyzing sequences of several kilobases containingmulti-exon genes in >1 min execution time on a Sun 4/60. Received on December 4, 1989; accepted on February 28, 1990     

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.     

A platform for biological sequence comparison on parallel computers

We have written two programs for searching biological sequencedatabases that run on Intel hypercube computers. PSCANLJB comparesa single sequence against a sequence library, and PCOMPLIB comparesall the entries in one sequence library against a second library.The programs provide a general framework for similarity searching;they include functions for reading in query sequences, searchparameters and library entries, and reporting the results ofa search. We have isolated the code for the specific functionthat calculates the similarity score between the query and librarysequence; alternative searching algorithms can be implementedby editing two files. We have implemented the rapid FASTA sequencecomparison algorithm and the more rigorous Smith — Watermanalgorithm within this framework. The PSCANLIB program on a 16node iPSC/2 80386-based hypercube can compare a 229 amino acidprotein sequence with a 3.4 million residue sequence libraryin {small tilde}16s with the FASTA algorithm. Using the Smith— Waterman algorithm, the same search takes 35 min. ThePCOMPUB program can compare a 0.8 millon amino acid proteinsequence library with itself in 5.3 min with FASTA on a third-generation32 node Intel iPSC/860 hypercube. Received on September 8, 1990; accepted on December 15, 1990     

Portable microcomputer software for nucleotide sequence analysis.

The most common types of nucleotide sequence data analyses and handling can be done more conveniently and inexpensively on microcomputers than on large time-sharing systems. We present a package of computer programs for the analysis of DNA and RNA sequence data which overcomes many of the limitations imposed by microcomputers, while offering most of the features of programs commonly available on large computers, including sequence numbering and translation, restriction site and homology searches with dot-matrix plots, nucleotide distribution analysis, and graphic display of data. Most of the programs were written in Standard Pascal (on an Apple II computer) to facilitate portability to other micro-, mini-, and and mainframe computers.     

A parallel workload model and its implications for processor allocation

We develop a workload model based on the observed behavior of parallel computers at the San Diego Supercomputer Center and the Cornell Theory Center. This model gives us insight into the performance of strategies for scheduling moldable jobs on space-sharing parallel computers. We find that Adaptive Static Partitioning (ASP), which has been reported to work well for other workloads, does not perform as well as strategies that adapt better to system load. The best of the strategies we consider is one that explicitly reduces allocations when load is high (a variation of Sevcik's (1989) A+ strategy). This revised version was published online in July 2006 with corrections to the Cover Date.     

Nutrition transition and dietary energy availability in Eastern Europe after the collapse of communism.

After the economic transition of the late 1980s and early 1990s there was a rapid increase in overweight and obesity in many countries of Eastern Europe. This article describes changing availability of dietary energy from major dietary components since the transition to free-market economic systems among Eastern European nations, using food balance data obtained at national level for the years 1990-92 and 2005 from the FAOSTAT-Nutrition database. Dietary energy available to the East European nations satellite to the former Soviet Union (henceforth, Eastern Europe) was greater than in the nations of the former Soviet Union. Among the latter, the Western nations of the former Soviet Union had greater dietary energy availability than the Eastern and Southern nations of the former Soviet Union. The higher energy availability in Eastern Europe relative to the nations of the former Soviet Union consists mostly of high-protein foods. There has been no significant change in overall dietary energy availability to any category of East European nation between 1990-1992 and 2005, indicating that, at the macro-level, increasing rates of obesity in Eastern European countries cannot be attributed to increased dietary energy availability. The most plausible macro-level explanations for the obesity patterns observed in East European nations are declines in physical activity, increased real income, and increased consumption of goods that contribute to physical activity decline: cars, televisions and computers.     

Computers in the surgery. The patient's view.

A postal survey sent to 350 patients from two rural practices confirmed that an appreciable minority of patients (17%) were opposed to doctors using computers. The questionnaire distributed had been carefully designed to identify their opposition more specifically. Most of the general concern was accounted for by the 91 patients (31%) who feared that confidentiality of information would be reduced. The sensitive nature of medical information alerts patients to the possibility of diminished security of records and obliges practices considering acquiring a computer to ensure that these fears are not realised. Smaller proportions of patients were found to oppose computers on other grounds--namely, impersonality, economy, and general anxiety.     

A case study of a shared/buy-in computing ecosystem

Many research institutions are deploying computing clusters based on a shared/buy-in paradigm. Such clusters combine shared computers, which are free to be used by all users, and buy-in computers, which are computers purchased by users for semi-exclusive use. The purpose of this paper is to characterize the typical behavior and performance of a shared/buy-in computing cluster, using data traces from the Shared Computing Cluster (SCC) at Boston University that runs under this paradigm as a case study. Among our main findings, we show that the semi-exclusive policy, which allows any SCC user to use idle buy-in resources for a limited time, increases the utilization of buy-in resources by 17.4%, thus significantly improving the performance of the system as a whole. We find that jobs allowed to run on idle buy-in resources arrive more frequently and run for a shorter time than other jobs. Finally, we identify the run time limit (i.e., the maximum time during which a job is allowed to use resources) and the type of parallel environment as two factors that have a significant impact on the different performance experienced by shared and buy-in jobs.     

CAMBIO: software for modelling and simulation of bioprocesses

CAMBIO, a software package devoted to bioprocess modelling,which runs on Apollo computers, is described. This softwareenables bioengineers to easily and interactively design appropriatemathematical models directly from their perception of the process.CAMBIO provides the user with a set of design symbols and mnemonicicons in order to interactively design a functional diagram.This diagram has to exhibit the most relevant components withtheir related interactions through biological and physico-chemicalreactions. Then, CAMBIO automatically generates the dynamicalmaterial balance equations of the process in the form of analgebraic-differential system by taking advantage of the knowledgeinvolved in the functional diagram. The model may be used forcontrol design purpose or completed by kinetics expressionswith a view to simulation. CAMBIO offers facilities to generatea simulation model (for coding of kinetics, introducing auxiliaryvariables, etc.). This model is automatically interfaced witha specialized simulation software which allows an immediatevisualization of the process dynamical behaviour under variousoperational conditions (possibly involving feedback controlstrategies). An example of an application dealing with yeastfermentation is given. Received on June 14, 1990; accepted on January 11, 1991     

Basic concepts of computer simulation of plant growth

The experimental study of plant growth and architecture requires two consecutive and complementary approaches. The first one is qualitative and botanical. Through this qualitative analysis, it is possible to divide a tree into botanically homogeneous subunits. The second one is quantitative. Modeling of the functioning of meristems based on stochastic processes has been carried out in the Laboratoire de Modelisation of CIRAD (1980 1990) in combination with extensive experimental work on temperate and tropical plants. Calculations involved in the tree simulations from field data are based on the probabilistic Monte Carlo method for the topological part and on analytical geometry for the morphological part. Data, such as length, angles, elasticities, tropism, are necessary for geometric construction of the plant. The growth model, together with the geometric calculations enables a random plant simulation in 3-D according to geometry for the morphological one. Computer graphics methods are then used to visualize the computed plant (perspective, colours, texture, shadows); they require special programs and graphic computers.     

Sharing digital micrographs and other data files between computers

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.     

Sharing digital micrographs and other data files between computers.

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.     

Sharing digital micrographs and other data files between computers

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.