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PubMed1984

A common philosophy and FORTRAN 77 software package for implementing and searching sequence databases.

I present a common philosophy for implementing the EMBL and GENBANK (BBN-Los Alamos) nucleic acid sequence databases, as well as the National Biological Foundation (Dayhoff) protein sequence database. The associated FORTRAN 77 fully transportable software package includes: 1) modules for implementing each of these databases from the initial magnetic tape file, 2) modules performing a fast mnemonic access, 3) modules performing key-string access and allowing the definition of user-specific database subsets, 4) a common probe searching module allowing the stacking of multiple combined search requests over the databases. This software is particularly suitable for 32-bit mini/microcomputers but would eventually run on 16-bit computers.

Amino Acid Sequence↗

PubMed1993

Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe.

A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences in the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.

Algorithms↗

PubMed1998

p53 gene mutation: software and database.

A large number of different mutations in the p53 tumor suppressor gene have been identified in all types of cancer. As of October, 1997, this database (http:// perso.curie.fr/tsoussi ) contained >7500 mutations. Such a substantial increase since our previous reports should enable epidemiological analyses which were not previously possible. In order to analyse these new data, the UMD software has been improved. A new Web version of the UMD software enables online analysis of the database. The present report describes various improvements since the last release of the database.

Animals↗

PubMed1998

Marfan Database (third edition): new mutations and new routines for the software.

The Marfan database is a software that contains routines for the analysis of mutations identified in the FBN1 gene that encodes fibrillin-1. Mutations in this gene are associated not only with Marfan syndrome but also with a spectrum of overlapping disorders. The third version of the Marfan database contains 137 entries. The software has been modified to accommodate four new routines and is now accessible on the World Wide Web at http://www.umd.necker.fr

Computer Communication Networks↗

PubMed1998

Software and database for the analysis of mutations in the VHL gene.

VHL is a tumor suppressor gene localized on chromosome 3p25-26. Mutations of the VHL gene were described at first in the heritable von Hippel-Lindau disease and in the sporadic Renal Cell Carcinoma (RCC). More recently, VHL has also been shown to harbor mutations in mesothelioma and small cell lung carcinoma. To date more than 500 mutations have been identified. These mutations are mainly private with only one hot spot at codon 167 associated with pheochromocytoma. The germline mutations are essentially missense while somatic mutations include deletions, insertions and nonsense. To standardize the collection of these informations, facilitate the mutational analysis of the VHL gene and promote the genotype-phenotype analysis, a software package along with a computerized database have been created. The current database and the analysis software are accessible via the internet and world wide web interface at the URL:http://www.umd.necker.fr

Computer Communication Networks↗

PubMed2000

Octamer-primed sequencing technology: development of primer identification software.

Octamer sequencing technology (OST) is a primer-directed sequencing strategy in which an individual octamer primer is selected from a pre-synthesized octamer primer library and used to sequence a DNA fragment. However, selecting candidate primers from such a library is time consuming and can be a bottleneck in the sequencing process. To accelerate the sequencing process and to obtain high quality sequencing data, a computer program, electronic OST or eOST, was developed to automatically identify candidate primers from an octamer primer library. eOST integrates the base calling software PHRED to provide a quality assessment for target sequences and identifies potential primer binding sites located within a high quality target region. To increase the sequencing success rate, eOST includes a simple dynamic folding algorithm to automatically calculate the free energy and predict the secondary structure within the template in the vicinity of the octamer-binding site. Several parameters were found to be important, including base quality threshold, the window size of the template sequence segment, and the threshold [Delta] G value. OST, coupled with the eOST software, can be used to sequence short DNA fragments or in the finishing assembly stage of large-scale sequencing of genomic DNA.

Algorithms↗

PubMed2003

ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis.

To date, assembling comprehensive annotation information for all probe sets of any Affymetrix microarrays remains a time-consuming, error-prone and challenging task. ChipInfo is designed for retrieving annotation information from online databases such as NetAffx and Gene Ontology and organizing such information into easily interpretable tabular format outputs. As companion software to dChip and GoSurfer, ChipInfo enables users to independently update the information resource files of these software packages. It also has functions for computing related summary statistics of probe sets and Gene Ontology terms. ChipInfo is available at http://biosun1.harvard.edu/complab/chipinfo/.

DNA Probes↗

PubMed2004

siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.

siDirect (http://design.RNAi.jp/) is a web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi). Highly effective siRNA sequences are selected using novel guidelines that were established through an extensive study of the relationship between siRNA sequences and RNAi activity. Our efficient software avoids off-target gene silencing to enumerate potential cross-hybridization candidates that the widely used BLAST search may overlook. The website accepts an arbitrary sequence as input and quickly returns siRNA candidates, providing a wide scope of applications in mammalian RNAi, including systematic functional genomics and therapeutic gene silencing.

Algorithms↗

PubMed2006

ProKware: integrated software for presenting protein structural properties in protein tertiary structures.

Protein tertiary structure plays an essential role in deciphering protein functions, especially protein structural properties, including domains, active sites and post-translational modifications. These properties typically yield useful clues for understanding protein functions. This work presents an integrated software, named ProKware, that presents protein structural properties in protein tertiary structures, such as domains, functional sites, families, active sites, binding sites, post-translational modifications and domain-domain interaction. Using this web-based and Windows-based interface, users can manipulate and visualize three-dimensional protein structures, as well as the supported structural properties that are curated in the protein knowledge database. ProKware is an effective and convenient solution for investigating protein functions and structural relationships. This software can be accessed on the internet at http://ProKware.mbc.nctu.edu.tw/.

Binding Sites↗

PubMed2006

The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc).

Computational Biology↗

PubMed2000

The use of instructional technology in poultry science curricula in the United States and Canada: 1. Demographics of technology and software use.

This paper describes a study conducted in recognition of the increasingly widespread use of computers and the importance of exposure to instructional technologies in all aspects of poultry science curriculum. The study consisted of the distribution and analyses of two cross-sectional surveys to gather detailed information on the use of instructional technology (IT) in poultry science curricula in the US and Canada. One survey was sent to departments to obtain profiles of poultry science degree programs and the availability of IT and general support for its use. A second survey was designed to obtain individual profiles of faculty use of IT and attitudes toward the use of such technologies. Information presented in this paper includes basic demographics, estimates of survey validity, and a cross-section of instructional technologies used in poultry science education. The survey found that poultry science faculty reported higher levels of use for some instructional technologies than was expected from recent reports in the literature for higher education in general. Traditional technologies were widely used for instruction, but computers and the Internet were almost as popular. Reasons for the high levels of use may be due to an increasing user-friendliness of equipment and software applications, as well as the rapid acceptance over the past 2 yr of computers and Internet technologies among the general public. Involvement with IT projects appears to be changing from passive to active, consistent with faculty reports of high interest levels and active experimentation with technology and software.

Agriculture↗

PubMed2005

A software tool for increased efficiency in observer performance studies in radiology.

Observer performance studies are time-consuming tasks, both for the participating observers and for the scientists collecting and analysing the data. A possible way to optimise such studies is to perform them in a completely digital environment. A software tool-ViewDEX (Viewer for Digital Evaluation of X-ray images)-has been developed in Java, enabling it to function on almost any computer. ViewDEX is designed to handle several types of studies, such as visual grading analysis (VGA), image criteria scoring (ICS) and receiver operating characteristics (ROC). The results from each observer are saved in a log file, which can be exported for further analysis in, for example, a special software for analysing ROC results. By using ViewDEX for an ROC experiment, an evaluation rate of approximately 200 images per hour can be achieved, compared to approximately 25 images per hour using hard copy evaluation. The results are obtained within minutes of completion of the viewing. The risk of human errors in the process of data collection and analysis is also minimised. The viewer has been used in a major trial containing approximately 2700 images.

Computer Simulation↗

PubMed2006

A technical note about Phidel: a new software for evaluating magnetic induction field generated by power lines.

The Regional Environment Protection Agency of Friuli Venezia Giulia (ARPA FVG, Italy) has performed an analysis on existing software designed to calculate magnetic induction field generated by power lines. As far as the agency's requirements are concerned the tested programs display some difficulties in the immediate processing of electrical and geometrical data supplied by plant owners, and in certain cases turn out to be inadequate in representing complex configurations of power lines. Phidel, an innovative software, tackles and works out all the above-mentioned problems. Therefore, the obtained results, when compared with those of other programs, are the closest to experimental measurements. The output data can be employed both in the GIS and Excel environments, allowing the immediate overlaying of digital cartography and the determining of the 3 and 10 muT bands, in compliance with the Italian Decree of the President of the Council of Ministers of 8 July 2003.

Algorithms↗

PubMed2001

Pictures to print: a software scaffold to written literacy.

BACKGROUND: Successful school placements require effective written literacy skills. When a student has traumatic brain injury (TBI), written literacy instruction may need to be individualized and intense to facilitate optimal reintegration into the school program. Software products can provide a method that assists in creating the needed individualized, intense experiences. Written literacy-learning experiences span a continuum from preconventional messages expressed through pictures, to conventional printed expressions designed to convey meaning, to the literate writing needed to create stories and reports. DESIGN: This article is designed to familiarize rehabilitation and research professionals in TBI with the range of written literacy software and to stimulate clinical applications and research related to their use with students who have sustained a TBI.

Adolescent↗

PubMed2002

Interactive software automates personalized radiation safety plans for Na131I therapy.

NRC regulations have liberalized the criteria for release from control of patients administered radioactive materials but require written radiation safety instruction if another individual is expected to receive more than 1 mSv. This necessitates calculation of expected doses, even when the calculated maximum likely dose is well below the 5 mSv release criterion. NRC interpretations of the regulation provide the biokinetic model to be used to evaluate the release criterion for patients administered Na131I, but do not provide guidance as to either the specifics of minimizing the dose of others or the length of time restrictions should remain in effect. Interactive software has been developed to facilitate creation of radiation safety plans tailored to patients' expected interactions. Day-by-day and cumulative effective exposures at several separation distances, including sleeping, are presented in grid format in a graphic interface. In an interview session, the patient proposes daily contacts, which are entered separately for each individual by point-and-click operation. Total dose estimates are accumulated and modified while negotiating contact schedules, guided by suggested age-specific limits. The software produces printed radiation safety recommendations specific to the clinical, dosing, and social situations and reflective of the patient's choice of combinations of close contact with others. It has been used in treating more than 100 patients and has been found to be very useful and well received.

CD-I↗

PubMed1995

The Population Health Information System: data analysis and software.

This article describes the software developed in the process of creating the Population Health Information System. The software can be applied to a range of administrative data and provides standardized data on the health status and health care use of populations by generating population-based rates of discrete events. The standardized approach permits construction of a comprehensive, comparative picture for residents of defined geographic regions. The addition of a user friendly graphic interface will permit regional planners to do their own data analyses and allow out-of-province researchers to adopt the system for their own uses.

Community Health Planning↗

PubMedDate not supplied

Using software to direct test construction and improve test performance.

Over the past 5 years, a test analysis software program was developed and is being successfully used to modify faculty-constructed nursing tests administered to small classes. The interplay of instruction, students, and test items were variables considered while developing a practical, efficient program to produce test performance printouts designed to be used with little need for statistical interpretation. This test performance profile software is now available as freeware for individual nursing faculty.

Computer-Assisted Instruction↗

PubMed2003

Comparison of automatic quantification software for the measurement of ventricular volume and ejection fraction in gated myocardial perfusion SPECT.

The aim of this study was to compare the performance of three different software packages for the calculation of ejection fraction (EF) and end diastolic volume (EDV) from gated myocardial single photon emission computed tomography studies. Two hundred patients undergoing gated stress myocardial perfusion scans were analysed retrospectively. Patients were grouped as follows: small heart (n=31), normal perfusion scan (n=71), and scan with perfusion defects (n=98). EF and EDV were calculated for each using QGS (Cedars Sinai, Los Angeles, CA), 4D-MSPECT (University of Michigan, Ann Arbor, MI), and ECT (Emory University, Atlanta, GA). Bland-Altman plots, repeated measures ANOVA, and linear regression analysis were used to compare methods. Correlation coefficients between the methods for both EF and EDV were high, greater than 0.9. However, Bland-Altman plots revealed a large standard deviation of the difference between methods, preventing the confident estimate of the value of one method from an observation of another. Despite good correlation, the variance between methods was high. These algorithms behave differently, produce widely variable results from one another, and should not be used interchangeably. It may prove prudent for laboratories to independently validate the software algorithm that is chosen against a 'gold standard' using their own population.

Adolescent↗