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PubMed2003

A survey of current software for linkage analysis.

There is now a wide choice of software available for linkage analysis. The most well known packages are briefly reviewed here. The package with the most extensive range of analyses is GENEHUNTER, but for many of its functions there are other programs with better performance. These include FASTLINK and VITESSE for parametric analysis ALLEGRO and MERLIN for non-parametric analysis and SOLAR for variance components analysis. The computational limits of current approaches can be improved with SIMWALK2 and the promising new SUPERLINK program. Directions for future work include improved user interfaces and consensus formats for data input and exchange.

Algorithms↗

PubMed2005

PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies.

The PBAT software package (v2.5) provides a unique set of tools for complex family-based association analysis at a genome-wide level. PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes. The data analysis can be adjusted for covariates and gene/environment interactions. Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands. PBAT's screening tools allow the user successfully to handle the multiple comparisons problem at a genome-wide level, even for 100,000 SNPs and more. Moreover, PBAT is computationally fast. A genome scan of 300,000 SNPs in 2,000 trios takes 4 central processing unit (CPU)-days. PBAT is available for Linux, Sun Solaris and Windows XP.

Family↗

PubMed2005

Software for tag single nucleotide polymorphism selection.

This paper reviews the theoretical basis for single nucleotide polymorphism (SNP) tagging and considers the use of current software made freely available for this task. A distinction between haplotype block-based and non-block-based approaches yields two classes of procedures. Analysis of two different sets of SNP genotype data from the HapMap is used to judge the practical aspects of using each of the programs considered, as well as to make some general observations about the performance of the programs in finding optimal sets of tagging SNPs. Pairwise R2 methods, while the simplest of those considered, do tend to pick more tagging SNPs than are strictly needed to predict unmeasured (non-tagging) SNPs, since a combination of two or more tagging SNPs can form a prediction of SNPs that have no direct (pairwise) surrogate. Block-based methods that exploit the linkage disequilibrium structure within haplotype blocks exploit this sort of redundancy, but run a risk of over-fitting if used without some care. A compromise approach which eliminates the need first to analyse block structure, but which still exploits simple relationships between SNPs, appears promising.

Chromosome Mapping↗

PubMed2004

Versatile and open software for comparing large genomes.

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer.

Animals↗

PubMed2006

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts.

Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these large datasets requires effective computational methods. We present a new approach that includes data pre-processing, visualization, quality assessment, and statistical inference. The software is freely available in the Bioconductor package prada. The method permits analysis of large screens to detect the effects of molecular interventions in cellular systems.

Databases, Factual↗

PubMed2003

Evaluation of the estimation of midazolam concentrations and pharmacokinetic parameters in intensive care patients using a bayesian pharmacokinetic software (PKS) according to sparse sampling approach.

The aim of the study was to assess the performance of a bayesian program (PKS System, Abbott) for predicting midazolam concentrations and pharmacokinetic parameters in intensive care patients by comparing the pharmacokinetic parameters estimated by PKS to those calculated according to rich data. The study involved 42 patients receiving midazolam infusion for two hours or for several days. The program was used to predict plasma midazolam concentrations after feedback of 1, 2 or 3 concentrations. High correlation between observed and estimated concentrations was shown (r(2) > 0.992). Mean prediction error, mean absolute prediction error and root mean squared error were low for the patients of the reference and validation groups. From two or three feedback concentrations, midazolam pharmacokinetic parameters estimated by PKS were statistically comparable with those obtained using a rich pharmacokinetic analysis (P > 0.05 paired Wilcoxon test). Thus, PKS is useful for predicting midazolam concentrations and pharmacokinetic parameters when at least two feedback concentrations are known. This software seems to be appropriate for providing significant help to the clinician for midazolam dosage adjustment, according to midazolam concentrations and clinical sedation.

Area Under Curve↗

PubMed1987

Interstitial brachytherapy of malignant brain tumors using computed tomography-guided stereotaxis and available imaging software: technical report.

The implantation of radioactive sources into malignant intraaxial brain tumors, interstitial brachytherapy, is a theoretically attractive treatment for these nearly uniformly fatal lesions. Optimal application of this treatment modality requires careful preoperative planning, computer-assisted dosimetry, and computed tomography-guided stereotactic implantation of the isotope-bearing catheters. A method is presented by which available computed tomographic imaging software can be used with a standard radiotherapy treatment planning computer and the Brown-Roberts-Wells stereotactic system for preoperative imaging, dosimetry planning, and brachytherapy catheter insertion. Dedicated computer facilities are not required, making this method available to any neurosurgeon with access to a current generation computed tomographic scanner.

Brachytherapy↗

PubMed2005

Measurements of the periocular facial area with Web-based software.

We developed a simple Web-based program to make measurements on displayed photographs between several ocular and periocular landmarks. The measurements were: (1) vertical distance between the margin of the upper and lower eyelids (palpebral aperture), (2) distance between the lower eyelid margin and the inferior corneal margin (palpebro-limbar distance); (3) interpupillary distance; (4) ocular proptosis. We measured the distances using the Web program and compared them with manual measurements on the subject's face. The measurements involved 102 eyes of 51 patients with a variety of ophthalmic conditions. There was good agreement between manual and computer measurements. For example, for manual measurements in 49 patients, we obtained interpupillary distances ranging from 45 to 69 mm (mean 61, SD 6), whereas for computer measurements we found values ranging from 42 to 49 mm (mean 59, SD 6). The mean of the differences between manual and computer measurements was -2.0 mm (SD 4.3) and the 95% limits of agreement were -6.5 to 10.5 mm. Thus, computer measurements tended to give a higher reading by between 0.8 and 3.2 mm (95% confidence interval for the difference). Web-based software may be used to perform measurements on two-dimensional pictures and the technique appears to be suitable for telemedical purposes.

Adolescent↗

PubMed1991

Automatic analysis of radiographic images: II. Software implementation and testing on bitewing radiographs.

A prototype, completely automatic image-analysis system for dental bitewing radiographs was implemented in 'C' on a Unix workstation. A multiple layer hierarchical image model was created in software for each radiograph using production rule-based knowledge. The highest model layer formed an English-like description of anatomical structures including tooth type, interdental alveolar bone crest margins and spaces. A representation of spatial relationships between anatomical structures was formed, providing a method for comparing similar regions of a patient in serial, but not absolutely standardized, images. In 31 clinical radiographs, the system automatically identified 93% (193) of all available interdental spaces which are the key image regions for model creation. Each image required 2 minutes of processing time. The reproducibility of finding 34 interdental spaces in five films revealed one error. Further work is required to improve the recognition rate of the interdental regions towards 100% and to develop automatic comparisons between areas of change (disease?) in serial films.

Humans↗

PubMed2004

Analysis of antimicrobial drug resistance of Staphylococcus aureus strains by WHONET 5: microbiology laboratory database software.

OBJECTIVES: To analyze our hospital laboratory microbiological data by using WHONET 5-Microbiology laboratory database software-, and to acquire information about antimicrobial resistance of Staphylococcus aureus strains among every ward. MATERIALS AND METHODS: The database of Staphylococcus aureus strains had been brought to our hospital microbiology laboratory from every ward in our hospital from September 2001 till December 2002. Analysis was performed under the condition as one isolate per one patient. Starting of "resistance profile" analysis in WHONET 5 and analyzing the microbiological laboratory testing reports for every ward. We chose Oxacillin, Levofloxacin, Erythromycin and Gentamicin as the antimicrobials that need to be investigated for resistance. We evaluated the monthly transition of resistance ratios with regard to the specific wards that have the moving lines of inpatients in order to verify the hypothesis that resistant strains may be carried from ward to ward along the moving lines of inpatients. RESULTS: The data of 2,113 Staphylococcus aureus strains were accumulated and analyzed. Overall Oxacillin resistance ratio in our hospital was 65.7%. The ward of the smallest Oxacillin resistance ratio was Pediatrics/Ophthalmology ward. The ratios of Oxacillin resistant were varied as from 67.9% to 96.7% regardless the categories of wards such as internal medicine or surgery. Multi-resistant MRSA strains were overwhelmingly dominant in the wards of surgery. The ratios of the Gentamicin sensitive strains that were resistant to Oxacillin were high over the every ward. The moving lines of inpatients existed between ICU/CCU ward and three rear wards. Two rear wards whose Oxacillin resistance changes were reflected to those of ICU/CCU, but one rear ward was not. CONCLUSION: Variation of resistant degree among wards were very obvious and large. We could survey the wards where patient-to-patient transmission of resistant organisms might occur along the moving lines of inpatients. WHONET 5 will be recognized as an analysis and surveillance tool for every infection control team to survey the suspicious wards.

Anti-Bacterial Agents↗

PubMed1990

Managing clinical research data: software tools for hypothesis exploration.

Data representation, data file specification, and the communication of data between software systems are playing increasingly important roles in clinical data management. This paper describes the concept of a self-documenting file that contains annotations or comments that aid visual inspection of the data file. We describe access of data from annotated files and illustrate data analysis with a few examples derived from the UNIX operating environment. Use of annotated files provides the investigator with both a useful representation of the primary data and a repository of comments that describe some of the context surrounding data capture.

Data Interpretation, Statistical↗

PubMed2001

Speech recognition software.

This article discusses the use of speech recognition software by means of reviewing two leading packages. Both programs require considerable training before they can be used effectively, but are then able to convert continuous speech into text with varying degrees of success.

CD-ROM↗

PubMed1989

The librarian as consultant and educator for personal file management software.

Librarians are encouraged to extend their information managing skills to include familiarity with personal file management software. Knowledge of automated solutions to overgrown manual reprint files can be valuable to the institution that a librarian serves. The capabilities of REFERENCE MANAGER, PRO-CITE, ASKSAM, and SCI-MATE are compared in a series of classes given for faculty and staff by the Medical College of Wisconsin Libraries reference staff.

Consultants↗

PubMed1991

Cost recovery and usage tracking of CD-ROM databases with menuing software.

CD-ROM database products are in widespread use and offer potential cost savings over online products. Many libraries would find a cost-benefit analysis useful. Libraries often do not have sufficient funding simply to underwrite all costs related to CD-ROM workstations. Inexpensive menuing software permits usage tracking for data analysis and cost recovery of CD-ROM subscription, start-up, and operating costs. This article will explore the approach taken at the Fox Chase Cancer Center in Philadelphia to recover CD-ROM related expenses through user fees.

CD-ROM↗

PubMed2004

Evaluation of drug interaction software to identify alerts for transplant medications.

BACKGROUND: The ability of computerized physician order entry (CPOE) systems to identify clinically significant drug interactions is dependent upon the integrity of the drug information populating the software. A CPOE system with incomplete or inaccurate drug information will fail to identify clinically important drug interactions and, therefore, fail to reduce preventable adverse drug events (pADEs). OBJECTIVE: To evaluate, from the prescribers' perspective, the ability of a common drug interaction database to identify clinically important drug interactions involving drugs used in transplantation. METHODS: The clinical significance of drug interactions involving 5 transplant drugs was evaluated by an expert panel to determine whether alerts should be generated for physicians not involved in the transplant at the time of order entry. Drug interactions included in the analysis were generated from the expert panel, a common drug interaction database, and 2 standard drug interaction references. Responses on the clinical significance were used to calculate the sensitivity, specificity, and positive and negative predictive values for each severity setting of a common electronic drug interaction database. RESULTS: Overall, the database failed to identify approximately 70% of interactions considered significant by the expert panel. Of the alerts that were generated, >85% were considered clinically significant. The database was most deficient in identifying interactions resulting from additive toxicity. CONCLUSIONS: To expect a decrease in pADEs caused by drug interactions, the information used to populate CPOE systems must be validated. Establishing consistency and integrity of this information may be a future role for pharmacists.

Databases as Topic↗

PubMed2003

Measurement of body size and shape perception in eating-disordered and control observers using body-shape software.

A disturbance in the perception of personal body size and shape is a key feature of both anorexia and bulimia nervosa, but it has proved difficult to quantify. Previous attempts have used methods like the distorting video technique (DVT), which alters an image by stretching the figure in either the X- or Y-axis. This is a poor representation of the way fat is added to or lost from the body, and the pattern of distortion provides a host of cues to the degree to which the image has been altered. To overcome these problems we have used a specially designed software system that uses biometric data based on real body shapes, instead of simply stretching or compressing images of bodies. This technique also allows individual body parts to be altered separately, so we can determine whether a specific body part is overestimated relative to others. We can also calculate the apparent body mass index (BMI) of our modified pictures, using the perimeter-area ratio (PAR). This allows us to compare an observer's actual BMI with that calculated for their estimated and ideal bodies. We tested 30 anorexic, 30 bulimic and 137 control observers. Our results show that all three observer groups tend to overestimate their body size, but not significantly so. Both the control and bulimic observers prefer an ideal body with a BMI of 20, which is at the lower end of the 'normal' BMI range. However, the anorexics ideal BMI is 15, which is on the border between the emaciated and underweight BMI categories.

Adult↗

PubMed2005

SNPdetector: a software tool for sensitive and accurate SNP detection.

Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool), and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozygosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency) in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov).

Algorithms↗

PubMed2002

Comparative evaluation of the DPX and DPX-IQ lunar densitometer systems following software upgrade.

Bone densitometry research departments perform system and software upgrades infrequently in order to maintain high precision. This study compares the results obtained on a Lunar densitometer with DPX, and DPX-IQ installed to achieve year 2000 compliance. The DPX-IQ provides an improved femur edge detection algorithm with an expanded reference database. Two hundred data files for each measurement site acquired on DPX were reanalyzed on DPX-IQ. There was no change to the bone mineral density (BMD), bone mineral content (BMC), T-scores or Z-scores for the L2-L4 spine, radius (ultradistal and 33%), and total body. There was a significant high correlation for the femoral neck BMD (r = 0.98; p < 0.05). The mean differences in BMD, BMC, T-scores, and Z-scores at the femoral neck and Ward's and trochanteric regions were not significant (p > 0.05). The limits of agreement within the 95% confidence interval for the femoral neck BMD using the Bland and Altman method was between -0.057 and 0.063 g/cm(2). This order of magnitude magnifies the long-term precision error and alters the usual confidence limits for interpretation of true change in densitometry practice. Therefore, it is important for reanalysis of DPX data files with the DPX-IQ to be performed so that longitudinal changes in BMD can be accurately assessed.

Absorptiometry, Photon↗