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PubMed1990

Free molecular biological software available from the EMBL file server.

A new service provided by EMBL (EMBL Software File Server) is described that will make free molecular biology software available to anyone with computer network access. MS-DOS, Apple Macintosh and VAX/VMX are supported at the moment. The programs will be delivered by normal electronic mail; conversion mechanisms will transform binary files to ASCII to allow mail transfer. This service will also help authors to distribute their software conveniently.

Computer Communication Networks↗

PubMed1991

CAMBIO: software for modelling and simulation of bioprocesses.

CAMBIO, a software package devoted to bioprocess modelling, which runs on Apollo computers, is described. This software enables bioengineers to easily and interactively design appropriate mathematical models directly from their perception of the process. CAMBIO provides the user with a set of design symbols and mnemonic icons in order to interactively design a functional diagram. This diagram has to exhibit the most relevant components with their related interactions through biological and physico-chemical reactions. Then, CAMBIO automatically generates the dynamical material balance equations of the process in the form of an algebraic-differential system by taking advantage of the knowledge involved in the functional diagram. The model may be used for control design purpose or completed by kinetics expressions with a view to simulation. CAMBIO offers facilities to generate a simulation model (for coding of kinetics, introducing auxiliary variables, etc.). This model is automatically interfaced with a specialized simulation software which allows an immediate visualization of the process dynamical behaviour under various operational conditions (possibly involving feedback control strategies). An example of an application dealing with yeast fermentation is given.

Algorithms↗

PubMed2026

MultiDMPcaller: a one-stop software for detection and visualization of differentially methylated positions and regions.

MOTIVATION: Whole-genome bisulfite sequencing (WGBS/BS-Seq) is the gold standard for single-base resolution DNA methylome profiling. However, the diverse statistical models of existing computational methods lead to limited overlap between their results, highlighting the need for novel methods to detect differentially methylated positions (DMPs) and differentially methylated regions (DMRs). RESULTS: We developed MultiDMPcaller, an automated downstream methylome analysis software. It processes upstream outputs to profile DMPs, non-DMPs, DMRs, and context-specific (CpG/CHG/CHH) methylation status, alongside visualizing their chromosomal distribution and enrichment. The software features two key innovations: (i) an adaptive two-step P-value adjustment strategy based on organism-specific methylation patterns, with raw P-value ≤0.05 pre-filtering followed by false discovery rate (FDR) correction, to recover potential DMPs usually missed by standard FDR correction in plant CHG/CHH and animal CpG contexts; and (ii) a multiple pairwise comparison approach, which performs m × n pairwise comparisons for m control and n experimental replicates, followed by a voting system supporting both user-defined majority thresholds and model-based adaptive thresholds, to identify robust and reliable DMPs (with a stricter voting threshold exclusively for loci with low methylation differences) and DMRs. On real datasets from Arabidopsis, apple, and mouse, as well as simulated human datasets, MultiDMPcaller's results showed good agreement with those of other software, exhibiting high conservativeness and superior precision, which suggested a low false discovery proportion. AVAILABILITY AND IMPLEMENTATION: MultiDMPcaller is available at GitHub (https://github.com/jiantaoyuNWAFU/MultiDMPcaller) and via a web server (https://ciebioinfo.nwafu.edu.cn).

Software↗

PubMed1991

Mapping sequenced E.coli genes by computer: software, strategies and examples.

Methods are presented for organizing and integrating DNA sequence data, restriction maps, and genetic maps for the same organism but from a variety of sources (databases, publications, personal communications). Proper software tools are essential for successful organization of such diverse data into an ordered, cohesive body of information, and a suite of novel software to support this endeavor is described. Though these tools automate much of the task, a variety of strategies is needed to cope with recalcitrant cases. We describe such strategies and illustrate their application with numerous examples. These strategies have allowed us to order, analyze, and display over one megabase of E. coli DNA sequence information. The integration task often exposes inconsistencies in the available data, perhaps caused by strain polymorphisms or human oversight, necessitating the application of sound biological judgment. The examples illustrate both the level of expertise required of the database curator and the knowledge gained as apparent inconsistencies are resolved. The software and mapping methods are applicable to the study of any genome for which a high resolution restriction map is available. They were developed to support a weakly coordinated sequencing effort involving many laboratories, but would also be useful for highly orchestrated sequencing projects.

Base Sequence↗

PubMed1990

[Mental health in software engineers. II. Classification of occupational stressors, and relationship between occupational stressors and psychiatric disorders].

Occupational stressors and psychiatric disorders were studied in a sample of 101 male software engineers. Psychiatric diagnosis was based on DSM-III (Diagnostic and Statistical Manual of Mental Disorders, Third Edition). The results can be summarized as follows: 1) More than 30% of the subjects were not satisfied with their work. 2) Occupational stressors ascertained in the interview could be classified into "quantity of job," "quality of job," "role in organization," "relations with others," "work conditions," "career development," "reward," "organizational structure and climate," "low social support," and "lack of decision making." "quality of job" (35%), "quantity of job" (30%), and "role in organization" (33%) were the most common stressors for the subjects. 3) Among the occupational stressors, only "quantity of job" was significantly related to psychiatric disorders (p less than 0.05). The results suggest that many software engineers are not satisfied with their work and that "quantity of job" has the greatest influence on their mental health. Some measures should be taken to avoid potential health hazards, for the research findings indicate a relationship between occupational stressors and mental health in software engineers.

Adult↗

PubMed1990

Computerized literature reference system: use of an optical scanner and optical character recognition software.

A computerized reference system for radiology journal articles was developed by using an IBM-compatible personal computer with a hand-held optical scanner and optical character recognition software. This allows direct entry of scanned text from printed material into word processing or data-base files. Additionally, line diagrams and photographs of radiographs can be incorporated into these files. A text search and retrieval software program enables rapid searching for keywords in scanned documents. The hand scanner and software programs are commercially available, relatively inexpensive, and easily used. This permits construction of a personalized radiology literature file of readily accessible text and images requiring minimal typing or keystroke entry.

Electronic Data Processing↗

PubMedDate not supplied

Pulse shape analysis of RBC micropore flow via new software for the cell transit analyser (CTA).

The Cell Transit Analyser (CTA) provides a means to rapidly measure the deformability of large numbers of individual cells. It combines many of the advantages of micropipette studies with the simplicity and speed of filtrometry methods by measuring the duration of each resistive pulse generated as a cell passes through one of 30 identical micropores in a membrane. However, in our opinion, the potential of the system is limited by the microcomputer and software supplied for data analysis. We have therefore written new software for a more-powerful microcomputer to examine the shape of each resistive pulse rather than just the duration. Seven new parameters are derived, which provide additional information regarding the passage of cells through the pores. In particular, the contribution of the entry and exit phases of the cell transit are evident in the rise time and fall time of the pulses. The software is user-friendly and allows the analysis of each pulse to be reviewed, which aids understanding of the system and helps to avoid errors in interpreting the data.

Adult↗

PubMedDate not supplied

[Development of an integrated software program to analyze statistically the results of complex investigations in space biology and medicine].

A concept of implementing the problem-oriented statistical software based on an application of expert systems is presented. The shortcomings of existing statistical software for personal computers and trends of their improvements are analyzed. Recommendations on designing of statistical expert systems can be used by the statisticians, mathematicians, programmers and users not being professionals in these fields. Integrated statistical software will make it possible to perform additional retrospective analysis and to check up the large arrays of previously gained data and to obtain supplementary scientific information and to find new regularities in the previous experimental findings.

Aerospace Medicine↗

PubMed1992

[A software design for standard grayscale printout of China-made automatic static quantitative TBC visual field analyser].

A method of "TBC GRAPH" software design for standard grayscale printout of TBC static quantitative perimetry is introduced. The software is operated in IBM PC/XT or PC/AT compatible computer, using Chinese Character Disk Operating System (CCDOS) which has widespread users in China. Symbols were established by using CCDOS word--make function, and sectoral as well as symbolic matrix were made, which realized the standard grayscale printout. The software is recommended for use in ophthalmic clinic and education.

Humans↗

PubMed1992

A shell program for the design of PCR primers using genetics computer group (GCG) software (7.1) on VAX/VMS systems.

A number of software analysis packages for the design of PCR primers are available for PCs; however, software for users that depend on VAX/VMS operating systems is not available. By treating oligonucleotides as RNA molecules, I have designed an alternative means toward studying oligonucleotide interactions using software that is currently available from The Genetics Computer Group (GCG, Madison, WI). The oligonucleotide interactions with self and non-self are analyzed by the GCG FOLD program, a program which finds a secondary structure of minimum free energy for an RNA molecule. This approach allows the identification of self-priming primer pairs, and the interaction energies provide a guideline for the prediction of optimal PCR primers.

Base Sequence↗

PubMedDate not supplied

Quantifying the disease impact of alcohol with ARDI software.

Alcohol-Related Disease Impact (ARDI) Software has been developed for the Centers for Disease Control (CDC) to allow States to calculate mortality, years of potential life lost (YPLL), direct health-care costs, indirect morbidity and mortality costs, and nonhealth-sector costs associated with alcohol use and misuse. The mortality related measures--mortality, YPLL, and indirect mortality costs--are computed for 35 diagnoses related to alcohol use and misuse. A review of clinical research studies and injury surveillance studies was conducted to produce estimates of the alcohol-attributable fraction (AAF) for each diagnosis. For these measures, age-specific and age-adjusted rates are also calculated. Health care costs, morbidity costs, and nonhealth-sector costs are prorated from national studies to the State or locality. This multiple-measure approach to quantifying a health problem is termed "disease impact estimation." National estimates of the disease impact of alcohol use and misuse have been produced using ARDI software and State-specific estimates are in preparation. Designed to CDC specifications, ARDI is completely menu-driven and operates within Lotus 1-2-3 software as a set of linked spreadsheets. ARDI adapts national epidemiologic and health economics methods for use by State and local health agencies. ARDI produces data on the health consequences of alcohol use and misuse for use by locally based policymakers, public health professionals, and researchers, while permitting comparison and compilation of these data across jurisdictions.

Alcohol Drinking↗

PubMed1991

AuthorBase: a database of authoring systems software.

A working prototype database of authoring system software was developed as part of a study of authoring software conducted by the National Library of Medicine. The database and development issues ranging from the scope of the database to what information to document are described. The protype demonstrates that records of reasonable integrity can be derived from vendor supplied information as long as users understand the database is only an initial starting point in searching for authoring software and a resource for becoming generally familiar with the technology.

Authorship↗

PubMedDate not supplied

[Computer-assisted design in removable partial dentures. Expert system and software for framework tracing].

Stelligraph, a software program for designing the removable partial denture offers many possibilities in computer assisted technology. The design can be realized on any particular case, based on three different concepts. This software program can also provide on individual, manual and personalized design this offening complete freedom in the conception. This software program is an expert system in removable partial denture by providing the general practitioner with a rational design as well as clinical guidance for oral rehabilitation.

Denture Design↗

PubMedDate not supplied

Quantifying the disease impact of cigarette smoking with SAMMEC II software.

Smoking-Attributable Mortality, Morbidity, and Economic Costs Software, Release II (SAMMEC II) has been developed for the Office on Smoking and Health, Public Health Service, to permit rapid calculation of deaths, years of potential life lost, direct health-care costs, indirect mortality costs, and disability costs associated with cigarette smoking. For the mortality-related measures, age-specific and age-adjusted rates are also calculated. The pivotal epidemiologic measure in these calculations is the smoking-attributable fraction, and attributal risk measure. A multiple-measure approach (attributable mortality and economic costs) to quantifying a health problem is termed "disease impact estimation." Previously, national and State-specific estimates of smoking-attributable mortality and economic costs were calculated using SAMMEC software, the predecessor of SAMMEC II. SAMMEC II is completely menu-driven and operates within the Lotus 1-2-3 software as a set of linked spreadsheets. SAMMEC II adapts national epidemiologic methods for use by State and local health departments. Increased exposure of public health professionals to disease impact estimation techniques, as demonstrated by SAMMEC II, will lead to improvements in both methodology and the quality of smoking-related health data. The primary purpose of SAMMEC II, however, is to provide State or locality-specific data on the health consequences of smoking to policymakers and public health professionals in these jurisdictions.

Cost Allocation↗

PubMed1991

[Convenient and useful computer software for the anesthesiologist].

Convenient and useful computer software for the anesthesiologist to draw figures for presentation, or to perform statistical analysis were presented. Each software is selected in the condition that it does not need special optional hardware, and processes the data quickly even with an old type computer, and also that even a computer beginner can easily operate it. The presented software are as follows: 1) Silhouette (drawing figures), 2) NEO (drawing figures), 3) Graph note (drawing figures), 4) Chart up science (drawing figures), 5) Z's word JG (making slide manuscripts) and 6) Biostat (doing statistical analysis).

Anesthesiology↗

PubMed1979

Software development of the EMI head scanner.

A method has been developed to run the general purpose operating system RDOS on the same disc of the head scanner computer as is used for scanner software and data. This made it possible to develop additional software in high level programming language for image processing, based on original image data on the disc. All new images produced by the program are stored on the disc in the same format as the original images. This makes it possible to handle processed images exactly as the original ones and to do multiple operations. The following processing has been included in the program so far: subtraction, smoothing, density profiles, vertical reconstructions, magnification and labelling. A set of operator commands has been developed which are very similar to the ordinary commands for the scanner, which makes the program to appear being a direct extension of the standard scanner software.

Computers↗

PubMedDate not supplied

Characteristics of the software for computer applications in medicine.

The requirements of clinical medicine which have tended to make the design and implementation of software for hospital computer systems more difficult than that elsewhere, are discussed in this paper. Specific constraints on the software for selected computer-assisted activities in a hospital environment are examined in considerable depth. It is shown that since some of these activities have counterparts elsewhere, hospital computing can benefit from the accumulated experience in dealing with similiar problems in business and scientific environments. The argument is put forward that developing countries, with their characteristic problem of acute shortage of skilled manpower in both medicine and computing, should initially concentrate on applying computers to these activities alone. Furthermore, medical education in such countries should incorporate programmes relating to computer technology in general and the software aspects in particular.

Computers↗

PubMed1992

[Comparison of fingerprints using a personal computer and graphic software sold on market].

We compared the fingerprint images using a personal computer and a graphic software sold on market. The fingerprints of thumb of left hand recorded by pressing and rolling on paper were input in computer using image scanner. These two fingerprint images were overlapped by moving and rotation on the computer screen, and were fitted well. This result showed that the fingerprints recorded by any way from one person were fitted. Latent and accused's fingerprints were also input in computer using image scanner. These images were analyzed by the same procedure. These two fingerprints were part by unfitting. It was decided these two fingerprints were not derived from one person. We also considered the possibility that the latent fingerprint was the reversed one. Then, the image was reversed of its color on the screen of computer (black to white and white to black) and compared by the same procedure. In this experiment, two fingerprint images were not fitted in a part. This showed that the reversed fingerprint was also able to be analyzed by this procedure. For the comparison of fingerprints, this report showed the ability of the personal computer and software which can be obtained easily from market. Following the improvement of the hardware and software used in this examination in near future, the computerized identification of fingerprints like this study will become more accurate and convenient.

Computer Graphics↗