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PubMed2005

A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

Interest in the assignment and frequency analysis of haplotypes in samples of unrelated individuals has increased immeasurably as a result of the emphasis placed on haplotype analyses by, for example, the International HapMap Project and related initiatives. Although there are many available computer programs for haplotype analysis applicable to samples of unrelated individuals, many of these programs have limitations and/or very specific uses. In this paper, the key features of available haplotype analysis software for use with unrelated individuals, as well as pooled DNA samples from unrelated individuals, are summarised. Programs for haplotype analysis were identified through keyword searches on PUBMED and various internet search engines, a review of citations from retrieved papers and personal communications, up to June 2004. Priority was given to functioning computer programs, rather than theoretical models and methods. The available software was considered in light of a number of factors: the algorithm(s) used, algorithm accuracy, assumptions, the accommodation of genotyping error, implementation of hypothesis testing, handling of missing data, software characteristics and web-based implementations. Review papers comparing specific methods and programs are also summarised. Forty-six haplotyping programs were identified and reviewed. The programs were divided into two groups: those designed for individual genotype data (a total of 43 programs) and those designed for use with pooled DNA samples (a total of three programs). The accuracy of programs using various criteria are assessed and the programs are categorised and discussed in light of: algorithm and method, accuracy, assumptions, genotyping error, hypothesis testing, missing data, software characteristics and web implementation. Many available programs have limitations (eg some cannot accommodate missing data) and/or are designed with specific tasks in mind (eg estimating haplotype frequencies rather than assigning most likely haplotypes to individuals). It is concluded that the selection of an appropriate haplotyping program for analysis purposes should be guided by what is known about the accuracy of estimation, as well as by the limitations and assumptions built into a program.

Algorithms↗

PubMed2005

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.

Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a semi-automated footprinting analysis software package that achieves accurate gel quantification while reducing the time to analyze a gel from several hours to 15 min or less. The increase in analysis speed is achieved through a graphical user interface that implements a novel methodology for lane and band assignment, called "gel rectification," and an optimized band deconvolution algorithm. The SAFA software yields results that are consistent with published methodologies and reduces the investigator-dependent variability compared to less automated methods. These software developments simplify the analysis procedure for a footprinting gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories that otherwise might not have considered their use. Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu.

Algorithms↗

PubMed2003

One library's experience with review and selection of chat software for reference.

When Michigan State University (MSU) Libraries decided to make the foray into virtual reference, the first thing that needed to be done was to decide on the software to use. This article discusses the process used including the items considered essential (deal-breakers) for software to make the first cut, what other features needed to be included, and what features would be useful but were not critical. A literature review of some useful current articles on virtual reference is included. The vendor and software ultimately selected was not one of the original vendors; how MSU Libraries was able to evaluate and select Docutek is presented. A matrix for software comparison is included in the appendix.

Academic Medical Centers↗

PubMed2006

Performance of drug-drug interaction software for personal digital assistants.

BACKGROUND: Personal digital assistants (PDAs) allow healthcare professionals to check for potential drug-drug interactions (DDIs) at the point of care, reducing the need to consult traditional references. However, PDAs can only be as effective as the software programs they use. OBJECTIVE: To examine the ability of DDI software programs manufactured for Palm OS-compatible PDAs in detecting clinically important DDIs. METHODS: Eight PDA software programs were assessed for sensitivity, specificity, and positive and negative predictive values for 16 well-documented DDIs contained within 6 simulated patient profiles. RESULTS: Sensitivity of the software programs ranged from 0.81 to 1.0, specificity ranged from 0.52 to 1.0, positive predictive values ranged from 0.62 to 1.0, and negative predictive values ranged from 0.88 to 1.0. Five programs scored perfect sensitivity scores: DrugIx, ePocrates Rx, ePocrates Rx Pro, Lexi-Interact, and the Tarascon pocket Pharmacopoeia. Of these, the ePocrates programs scored the highest in specificity (0.9), while Lexi-Interact and the Tarascon pocket Pharmacopoeia scored considerably lower (0.52). MosbyIx was the only program to score a 1.0 in specificity; however, its sensitivity was just 0.81. CONCLUSIONS: ePocrates Rx and ePocrates Rx Pro scored greater than or equal to 90% in regard to both sensitivity and specificity, making them the most reliable in detecting the clinically relevant interactions studied without the distraction of detecting those of no clinical significance. In addition, ePocrates Rx is updated regularly and is easily accessible on the Internet at no cost.

Computers, Handheld↗

PubMed2024

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗

PubMed2007

Web-based primer design software for genome-scale genotyping by pyrosequencing.

Design of locus-specific primers for use during genetic analysis requires combining information from multiple sources and can be a time-consuming process when validating large numbers of assays. Data warehousing of genomic DNA sequences and genetic variations when coupled with software applications for optimizing the generation of locus-specific primers can increase the efficiency of assay development. Selection of oligonucleotide primers for PCR and Pyrosequencing (SOP3) software allows user-directed queries of warehoused data collected from the human and mouse genome sequencing projects. The software automates collection of DNA sequence flanking single-nucleotide polymorphisms (SNPs) as well as the incorporation of locus-associated functional information, such as whether the SNP occurs in an exon, intron, or untranslated region. SOP3 software accepts three types of user-directed input consisting of gene locus symbols, SNP reference sequence numbers, or chromosomal physical location. For human polymorphisms, SOP3 incorporates haplotype, ethnicity, and SNP validation attributes. The output is a list of oligonucleotide primers recommended for Pyrosequencing-based typing of genetic variations. SOP3 is available at the Division of Immunogenetics computational server found at http://imgen.ccbb.pitt.edu.

Animals↗

PubMed2004

Decreased precision for BMD measurements in the prosthetic knee using a non-knee-specific software.

Non-knee-specific software has been widely used for bone mineral density (BMD) measurement at the knee, which coincide with a higher measurement error. This study was conducted to test whether software developed for BMD measurement at the hip could be used in the knee by using dual-energy X-ray absorptiometry (DXA) and whether knee rotational alignment or differences in soft tissue substitutes would influence the precision of the BMD measurement. Twelve knees operated with total knee arthroplasty were included. The knees were scanned four to six times each in four rotational positions using DXA with either a Plexiglas rod or rice bags as a soft tissue substitute. The BMD was measured in one manually defined region at the proximal tibia by using the software of Orthopedic. The precision (coefficient of variation) at the knee was 5.1-9.0% when using the Plexiglas rod and 7.3% when using rice bags. The poor precision was mainly explained by inconsistency in tissue baseline establishment and/or by low baseline bone density (Adj R2 = 0.78-0.90, p < 0.000). Neither intentional rotation of the knee nor using different soft tissue substitutes significantly altered the precision. The results suggest that the use of a non-knee-specific software in the prosthetic knee is not appropriate.

Absorptiometry, Photon↗

PubMed2004

Comparative evaluation of microarray analysis software.

A wide variety of software tools are available to analyze microarray data. To identify the optimum software for any project, it is essential to define specific and essential criteria on which to evaluate the advantages of the key features. In this review we describe the results of our comparison of several software tools. We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the "ideal microarray analysis software suite."

Data Interpretation, Statistical↗

PubMed1990

[Mental health in software engineers. I. Frequency of mental complaints, physical complaints and psychiatric disorders].

This study examined the physical complaints, mental complaints and psychiatric disorders in software engineers. Subjects were 101 male software engineers. They were evaluated by a semistructured interview. Psychiatric diagnosis was based on DSM-III (Diagnostic and Statistical Manual of Mental Disorders, third edition). The results are summarized as follows: 1) Physical complaints were observed in 68% of the subjects with 25% of the subjects complaining of physical ill-health. This study showed that 12% of the subjects had hypertension, 12%, gastritis or gastro-duodenal ulcer, 14%, allergic disease, and 19% miscellaneous diseases. 2) Of the subjects 62% had mental complaints and 31% mental ill-health. Depressive symptom was the most frequent mental complaint with 32% of the subjects diagnosed as DSM-III. The common diagnoses were adjustment disorders (19%), major affective disorders (6%), psychological factors affecting physical condition (5%) and dysthymic disorder (3%). Only one subject sought professional help from a psychiatrist for relief of mental complaints. The data suggest the severity of mental ill health in software engineers, but methodological limitations preclude a firm conclusion at this time. Further studies should be made on the mental health state in software engineers.

Adult↗

PubMed2004

Use of voice recognition software in an outpatient pediatric specialty practice.

BACKGROUND: Voice recognition software (VRS), with specialized medical vocabulary, is being promoted to enhance physician efficiency, decrease costs, and improve patient safety. This study reports the experience of a pediatric subspecialist (pediatric gastroenterology) physician with the use of Dragon Naturally Speaking (version 6; ScanSoft Inc, Peabody, MA), incorporated for use with a proprietary electronic medical record, in a large university medical center ambulatory care service. METHODS: After 2 hours of group orientation and 2 hours of individual VRS instruction, the physician trained the software for 1 month (30 letters) during a hospital slowdown. Set-up, dictation, and correction times for the physician and medical transcriptionist were recorded for these training sessions, as well as for 42 subsequently dictated letters. Figures were extrapolated to the yearly clinic volume for the physician, to estimate costs (physician: 110 dollars per hour; transcriptionist: 11 dollars per hour, US dollars). RESULTS: The use of VRS required an additional 200% of physician dictation and correction time (9 minutes vs 3 minutes), compared with the use of electronic signatures for letters typed by an experienced transcriptionist and imported into the electronic medical record. When the cost of the license agreement and the costs of physician and transcriptionist time were included, the use of the software cost 100% more, for the amount of dictation performed annually by the physician. CONCLUSIONS: VRS is an intriguing technology. It holds the possibility of streamlining medical practice. However, the learning curve and accuracy of the tested version of the software limit broad physician acceptance at this time.

Attitude of Health Personnel↗

PubMed2000

[Comparison of software programs for data analysis of complex surveys].

OBJECTIVE: To compare specific software programs for data analysis of complex surveys regarding the following characteristics: ease of application, computer efficiency and accuracy of the results. METHODS: Secondary data from the Pesquisa Nacional sobre Demografia e Saúde (National survey on demography and health) (1996) with a target population of women aged 15 to 49 years old were used. This was a probabilistic subsampling drawn in two stages, then stratified, with the probability proportional to size in the first stage. The northern and mid-western regions of the country were selected for the study. The parameters of interest were mean for the age variable, and the proportion for five other qualitative variables. The software programs used were Epi Info, Stata and WesVarPC. RESULTS: The programs have two common options for the files import: the dBASE and text type files. The number of steps previous to the execution of the analyses were twenty- one for Epi Info, eleven for Stata and nine for WesVarPC. Efficiency was high for all them, that is, less that three seconds. The standard errors estimated using Epi Info and Stata were the same, with approximation up to the third decimal; those for WesVarPC were generally higher. CONCLUSIONS: Epi Info is the most limited software program regarding the analyses currently performed; however it is easy to use and free. Stata and WesVarPC are far more complete, however the disadvantage is their cost. The choice of the software program will depend mainly on the user's specific needs.

Adolescent↗

PubMed2004

[Evaluation of students and teachers concerning the "Vital Signs" software].

This article had for objective to get students' and teacher's opinions about "Vital Signals" software. The investigation was developed in the Nursing Department of the Federal University of Ceará. The sample population was a total of 6 students and 3 teachers, who were submitted to an interview after using the software. The interviews generated 10 categories, which were separated in two themes: Features which stimulated the use of the "Vital Signals" software; and software educationally correct. The results showed that the teachers valued the correction of the content, while the students focused more on the dynamics of the program.

Education, Nursing↗

PubMed2000

Software for quantitation and visualization of expression array data.

Software is described that facilitates the analysis of phosphoimages from large array hybridizations. The Macintosh PowerPC-compatible application and its manual are available at no charge from http:¿people.bu.edu/strehlow. The software is compatible with both custom formats and array filters from three commercial manufacturers. It allows the rapid quantitation of every spot on images of hybridizations to large arrays. The user drags grids of squares over the spots on the image to define the coordinates of each spot, then aligns and edits the position of the grid. The software then corrects the positions as necessary and quantitates up to 27,000 spots per image. It stores the numerical values for each signal in a format called the fingerprint file. Fingerprint files can be directly averaged or compared, allowing the user to find mean values or differences in data from independent hybridization experiments. Data can be recalled from the fingerprint file and can be output in a variety of spreadsheet formats with several options for background correction. Finally, the software offers an output format that allows the convenient visualization of data points using animated, three-dimensional graphs.

Base Sequence↗

PubMed2006

Computer-assisted reader software versus expert reviewers for polyp detection on CT colonography.

OBJECTIVE: The purpose of our study was to assess the sensitivity of computer-assisted reader (CAR) software for polyp detection compared with the performance of expert reviewers. MATERIALS AND METHODS: A library of colonoscopically validated CT colonography cases were collated and separated into training and test sets according to the time of accrual. Training data sets were annotated in consensus by three expert radiologists who were aware of the colonoscopy report. A subset of 45 training cases containing 100 polyps underwent batch analysis using ColonCAR version 1.2 software to determine the optimum polyp enhancement filter settings for polyp detection. Twenty-five consecutive positive test data sets were subsequently interpreted individually by each expert, who was unaware of the endoscopy report, and before generation of the annotated reference via an unblinded consensus interpretation. ColonCAR version 1.2 software was applied to the test cases, at optimized polyp enhancement filter settings, to determine diagnostic performance. False-positive findings were classified according to importance. RESULTS: The 25 test cases contained 32 nondiminutive polyps ranging from 6 to 35 mm in diameter. The ColonCAR version 1.2 software identified 26 (81%) of 32 polyps compared with an average sensitivity of 70% for the expert reviewers. Eleven (92%) of 12 polyps > or = 10 mm were detected by ColonCAR version 1.2. All polyps missed by experts 1 (n = 4) and 2 (n = 3) and 12 (86%) of 14 polyps missed by expert 3 were detected by ColonCAR version 1.2. The median number of false-positive highlights per case was 13, of which 91% were easily dismissed. CONCLUSION: ColonCAR version 1.2 is sensitive for polyp detection, with a clinically acceptable false-positive rate. ColonCAR version 1.2 has a synergistic effect to the reviewer alone, and its standalone performance may exceed even that of experts.

Adult↗

PubMed2006

A new automated software system to evaluate breast MR examinations: improved specificity without decreased sensitivity.

OBJECTIVE: We sought to compare the accuracy of breast MRI interpretations with and without a new software application (CADstream) that provides automated evaluations of breast MR examinations. MATERIALS AND METHODS: Thirty-three consecutive lesions seen only on MRI (nine malignant, 24 benign) were evaluated with and without the automated software system. Automated analyses of kinetic enhancement for each lesion were recorded at 50%, 80%, and 100% enhancement thresholds. Computer-assisted analyses included presence or absence of "significant" enhancement and classification of enhancement patterns into percent volumes of washout, plateau, and persistent enhancement. Fisher's exact tests were performed to compare the likelihood of malignancy based on the presence of software-defined significant enhancement at the three thresholds. Enhancement profiles of malignant versus benign lesions were compared using the Student's t test. RESULTS: All malignant lesions showed significant enhancement at all thresholds. Compared with the unassisted interpretations, the computer-assisted analyses yielded false-positive rates that were reduced by 25% at a 50% threshold (not significant [NS]), 33% at an 80% threshold (p = 0.05), and 50% at a 100% threshold for enhancement (p < 0.01). There were no significant differences between enhancement profiles of benign and malignant lesions, with all lesions showing a wide range of washout, plateau, and persistent patterns of enhancement. CONCLUSION: New automated software applied to interpret breast MR examinations accurately showed significant enhancement in all the malignant lesions while depicting 12 of 24 benign lesions as showing insignificant enhancement. If these results are validated by a larger study, the number of unnecessary biopsies of MR lesions could be reduced without a concomitant decrease in cancer detection.

Breast Neoplasms↗

PubMed2000

Software-triggered contrast-enhanced three-dimensional MR angiography of the intracranial arteries.

OBJECTIVE: We investigated the effectiveness of software-triggered contrast-enhanced three-dimensional (3D) MR angiography in evaluating intracranial arteries. SUBJECTS AND METHODS: We studied 38 patients with suspected brain lesions. Imaging was performed using a 1.5-T superconducting MR system with a commercially available head coil. To monitor signal intensity changes we used software to place a tracker volume at the basilar artery or the internal carotid artery. A 20-ml bolus of gadodiamide hydrate was administered through the antecubital vein at a rate of 2-4 ml/sec, followed by a saline flush. Three-dimensional MR angiography using a spoiled gradient-echo sequence with centric K-space ordering was triggered by the arrival of the contrast bolus in the tracker volume. Imaging times ranged from 12 to 20 sec. We used MR images to assess the effectiveness of contrast-enhanced 3D MR angiography in revealing intracranial arteries with minimal venous overlap. RESULTS: The software triggered imaging on the arrival of the contrast bolus in 81.6% of examinations. In 77.6% of examinations, the resulting MR angiograms revealed intracranial arteries with minimal venous overlap. CONCLUSION: Software-triggered contrast-enhanced 3D MR angiography with centric K-space ordering is a promising technique for viewing intracranial arteries.

Basilar Artery↗

PubMed2002

Evaluation of software for registration of contrast-enhanced brain MR images in patients with glioblastoma multiforme.

OBJECTIVE: We evaluated commercially available software that rapidly and automatically registers brain MR images on a clinical workstation, and we studied the accuracy of these registrations. SUBJECTS AND METHODS: Ten patients with a diagnosis of glioblastoma multiforme underwent contrast-enhanced inversion recovery prepared three-dimensional (3D) volumetric spoiled gradient-recalled acquisition in the steady state (SPGR) MR imaging (contiguous 1.5-mm slice thickness, 96-104 slices). After this imaging sequence, each patient was brought out of the head coil into a sitting position and then repositioned in the coil. The inversion recovery prepared 3D SPGR sequence was then repeated. A commercially available software program operating on a clinical workstation was used to automatically register the second inversion recovery prepared SPGR series to the first. The speed of registration was recorded. The accuracy of each registration was estimated by recording the coordinates of eight anatomic landmarks on the registered and reference series and by calculating the mean error among matching landmarks. RESULTS: In nine of 10 patients, the registration software produced a visually satisfactory registration. In one patient, a second registration was necessary to produce a satisfactory registration. The processing time for each iteration was 48.3 +/- 3.8 sec (mean +/- SD). The mean error in aligning matching anatomic landmarks ranged from 0.67 to 1.41 mm, with an overall mean of 1.18 mm. The largest error among matching landmarks was 2.3 mm. CONCLUSION: Commercially available registration software can automatically register 3D imaging volumes in less than 1 min. The mean error in registration was approximately equivalent to the dimensions of a single voxel.

Adult↗

PubMedDate not supplied

The development of the software environment and data base concept in the Medical System Hannover. Decisions, plans and the gap between ideal and reality.

A long range development- and research-project like the MSH undergoes many changes and conversions. The experience with the last ten years of software development and application in the MSH showed the following trends: The emphasis shifted from optimal usage of the hardware resources towards saving of manpower. Efforts have therefore been made to standardize and generalize software as far as possible. The question of integrated versus dedicated systems remains an important and interesting area of research. New developments in software and hardware make it necessary to rethink yesterday's solutions and to adopt the application-concepts to the changing environment. This is a reactive process, but it offers the chance to develop, implement and evaluate new ideas and concepts. New decisions might become necessary in the near future in our (hospital) environment depending on software developments.

Computers↗