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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↗

PubMed2002

Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR.

Real-time reverse transcription followed by polymerase chain reaction (RT-PCR) is the most suitable method for the detection and quantification of mRNA. It offers high sensitivity, good reproducibility and a wide quantification range. Today, relative expression is increasingly used, where the expression of a target gene is standardised by a non-regulated reference gene. Several mathematical algorithms have been developed to compute an expression ratio, based on real-time PCR efficiency and the crossing point deviation of an unknown sample versus a control. But all published equations and available models for the calculation of relative expression ratio allow only for the determination of a single transcription difference between one control and one sample. Therefore a new software tool was established, named REST (relative expression software tool), which compares two groups, with up to 16 data points in a sample and 16 in a control group, for reference and up to four target genes. The mathematical model used is based on the PCR efficiencies and the mean crossing point deviation between the sample and control group. Subsequently, the expression ratio results of the four investigated transcripts are tested for significance by a randomisation test. Herein, development and application of REST is explained and the usefulness of relative expression in real-time PCR using REST is discussed. The latest software version of REST and examples for the correct use can be downloaded at http://www.wzw.tum.de/gene-quantification/.

Animals↗

PubMed2005

dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.

Off-target effects are one of the most serious problems in RNA interference (RNAi). Here, we present dsCheck (http://dsCheck.RNAi.jp/), web-based online software for estimating off-target effects caused by the long double-stranded RNA (dsRNA) used in RNAi studies. In the biochemical process of RNAi, the long dsRNA is cleaved by Dicer into short-interfering RNA (siRNA) cocktails. The software simulates this process and investigates individual 19 nt substrings of the long dsRNA. Subsequently, the software promptly enumerates a list of potential off-target gene candidates based on the order of off-target effects using its novel algorithm, which significantly improves both the efficiency and the sensitivity of the homology search. The website not only provides a rigorous off-target search to verify previously designed dsRNA sequences but also presents 'off-target minimized' dsRNA design, which is essential for reliable experiments in RNAi-based functional genomics.

Algorithms↗

PubMed2005

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed and tuned for gene prediction in prokaryotic, eukaryotic and viral genomic sequences. Currently, the server allows the analysis of nearly 200 prokaryotic and >10 eukaryotic genomes using species-specific versions of the software and pre-computed gene models. In addition, genes in prokaryotic sequences from novel genomes can be identified using models derived on the spot upon sequence submission, either by a relatively simple heuristic approach or by the full-fledged self-training program GeneMarkS. A database of reannotations of >1000 viral genomes by the GeneMarkS program is also available from the web site. The GeneMark website is frequently updated to provide the latest versions of the software and gene models.

Algorithms↗

PubMed2005

GeMS: an advanced software package for designing synthetic genes.

A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.

Base Sequence↗

PubMed2006

New softwares for automated microsatellite marker development.

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.

Arachis↗

PubMed1994

Revision of dietary analysis software for the Health Habits and History Questionnaire.

The software for analysis of the Health Habits and History Questionnaire (HHHQ) has been revised and is available to researchers. As in earlier versions of the software, questionnaires other than the standard National Cancer Institute versions can be analyzed. Foods can be added or dropped, nutrients can be added or changed, and many other revisions and options are facilitated. Estimates of 33 nutrients and up to 20 user-defined food groups are produced. The validity is unchanged from the previous software. Other features include a data entry key-and-verify system, standardized editing, a computer-assisted interview, and the calculation of health indices including pack-years of smoking and social network index.

Data Collection↗

PubMed1995

Density adjustment of software settings minimizes bias in automated sperm motility estimation.

To minimize overestimation of motility, it is recommended that fresh semen be diluted with seminal plasma prior to automated analysis. However, for glycerolated or cryopreserved semen this is impractical, and alternative methods are needed to minimize automated motility bias. In the present study, the proportion of motile spermatozoa was determined in fresh, diluted and cryopreserved semen (n = 25 ejaculates) using visual and automated methods. The effect of software settings on motility was investigated by assessing samples at a range of modified settings. At standard settings, automated motility was biased in fresh semen (+7.2%) after dilution with cryopreservative (-2.9%) and after cryopreservation (-7.8%) (P < 0.0001 versus visual). Automated motility was inversely related to the minimum number of frames for motility sampling (P < 0.0001), with mean estimates of 41.0, 46.1, 52.0 and 58.2% generated at settings of 8, 4, 2 and 1 frame(s) respectively (n = 15 fresh, diluted and cryopreserved samples). Based on an arbitrary ordinal scale, a method was developed whereby motility sampling was adjusted prior to analysis according to sperm density. Analysis of an independent set of semen samples with density-adjusted software settings reduced bias in automated estimates (n = 30) before and after freezing (P < 0.0001). In addition, bias was no longer related to sperm density. In conclusion, modification of software settings is an effective alternative to dilution to minimize bias in automated motility estimates in fresh, diluted and cryopreserved human semen.

Autoanalysis↗

PubMed2004

Development of software for internal dose calculation from bioassay measurements.

Recently developed biokinetic models of ICRP permit increasingly realistic descriptions of the behaviour of radionuclides in the human body. This, however, has made the interpretation of bioassay data extremely difficult. Thus computer programs for implementing these models are in need, but very few are available. The present work describes personal-computer-based software, MONDAL2 (monitoring to dose calculation ver. 2), that enables users to estimate intake activity and the resulting effective doses from bioassay measurements for both workers and members of the public. This software runs on Microsoft Windows 95, 98, Millennium edition, 2000 or XP. If the system is to be fully copied to a hard disk, hard disk space of 23 MB is required. This software is distributed by the National Institute of Radiological Sciences free of charge.

Age Factors↗

PubMed2006

Quality assurance (QA) procedures for software: evaluation of an ADC quality system.

Image viewing and processing software in computed radiography manipulates image contrast in such a way that all relevant image features are rendered to an appropriate degree of visibility, and improves image quality using enhancement algorithms. The purpose of this study was to investigate procedures for the quality assessment of image processing software for computed radiography with the use of existing test objects and to assess the influence that processing introduces on physical image quality characteristics. Measurements of high-contrast resolution, low-contrast resolution, spatial resolution, greyscale (characteristic curve) and geometric distortion were performed 'subjectively' by three independent observers and 'objectively' by the use of criteria based on pixel intensity values. Results show quality assessment is possible without the need for human evaluators, using digital images. It was discovered that the processing software evaluated in this study was able to improve some aspects of image quality, without introducing geometric distortion.

Algorithms↗

PubMed2004

Validity of scores generated by a web-based multimedia simulated patient case software: a pilot study.

PURPOSE: The value of multimedia simulated patient cases (MSPCs) in medical education remains unclear. The authors conducted a pilot study to assess the validity of automated scores of diagnostic reasoning ability provided by DxR Clinician, a widely available Web-based MSPC software. METHOD: In 2002-03, all 89 students enrolled in a required third-year primary care clerkship at the University of California, Davis, School of Medicine were assigned to complete four MSPCs. The authors determined the degree of correlation between the Clinical Reasoning Score (CRS) and Level of Diagnostic Performance (LDP) generated by the MSPC software and subscale scores from a validated measure of diagnostic reasoning sophistication, the Diagnostic Thinking Inventory (DTI). RESULTS: Of 356 completed case events, instructor override of automated scoring was required in 206 (58%) to obtain an accurate LDP and CRS. Mean DTI subscale scores improved significantly from the beginning to the end of the year (p <.0001, Wilcoxon signed rank test). However, there were no significant correlations between CRS or LDP scores on any of the four cases and either of the two DTI subscale scores. CONCLUSION: Automated diagnostic reasoning scores generated by one widely available MSPC software appear to lack criterion validity. The validity of automated diagnostic reasoning scores generated by MSPCs should be established before such cases can be confidently employed as educational tools.

Clinical Clerkship↗

PubMed1996

A software application to estimate exposure around 131I cancer and hyperthyroid patients.

A Windows-based software application (IDOSE) has been developed to estimate time-dependent radiation exposure around patients who receive 131I-sodium iodide (NaI) for hyperthyroidism or thyroid cancer therapy. This application is based on radiation exposure associations which relate pharmacokinetically such factors as administered dose, distance from patient, directional projection and time. The software was tested by comparing its predictability with that obtained with a survey meter in-house as well as at neighbouring hospitals for a total of 74 patients who were administered 131I(NaI). The latter surveys were performed at the patient's surface, at 30 cm and at 100 cm, from 0.25 to 56 h post-administration for a total of 133 data points. Statistical testing showed r-coefficients of > 0.9 and paired t-test values of > 0.39 between the predicted and measured survey values for all distances surveyed. The versatility of IDOSE lies in its ability to predict radiation exposure to others who come into contact with the patient relative to projection, time and distance. The latter is based on patient- and literature-generated default values at administration for three distances: surface, 30 cm and 100 cm. Thereafter, IDOSE predicts exposures at the default distances as a function of time. User-generated survey values at administration are an input option. IDOSE will never take the place of an actual survey. Its potential lies with estimating such information at times when surveys are not possible. Hypothetical 131I(NaI) patients are followed to illustrate the multifaceted nature of IDOSE. This paper describes the development, implementation and efficacy of a user-friendly Windows-based software application for predicting radiation exposure around 131I(NaI) patients.

Humans↗

PubMed1997

Clinical evaluation of a topographically based contact lens fitting software.

BACKGROUND: Second generation corneal topography-based contact lens software programs attempt to fit the cornea based on topographical information rather than simulated keratometry and nomogram-based fits. The EyeSys System 2000 Pro-Fit software (Version 3.1) was clinically evaluated for efficiency in fitting rigid gas permeable (RGP) lenses on 22 normal subjects. METHODS: Balanced manifest refractions, slitlamp examinations, keratometry, computerized topographic analysis and lens fitting, and manual diagnostic RGP fitting were performed on all patients. The topographically fit eyes were compared to corresponding eyes which were manually fit with diagnostic trial lenses. Lens parameters for the topographically fit eye were chosen after an optimal fluorescein pattern was achieved by either accepting the initially recommended Pro-Fit lens or a modification. Final lens parameters were based on clinical performance. Lenses were reordered when there was a need for base curve changes of 0.1 mm or more, power alterations of +/- 0.50 D or more, or for any alteration in diameter, optic zone, or edge lift. RESULTS: Both manual and topographically fit groups achieved 17/22 (77%) eyes successfully fit without any subsequent lens modifications. Time records for the manually fit group averaged 16.5 min, whereas the topographically fit group averaged 8.0 min. CONCLUSIONS: This study reports a 51.4% reduction in chair time when using a topographically based contact lens software program while achieving the same clinical results as in traditional diagnostic RGP fitting, suggesting increased efficiency in fitting RGPs to normal eyes.

Astigmatism↗

PubMedDate not supplied

Use of MindMapper software for research domain mapping.

The application of concept mapping software to facilitate the first steps of the research review process is discussed in relation to other software programs currently used for research synthesis. MindMapper software was used to develop a strategy for organizing the results of a comprehensive literature search into discrete categories with relationships among concepts graphically displayed to reveal the structure of the research domain. A Mind Map was developed for the scholarly literature on Web-based consumer health information. A second Mind Map examined the subconcept of barriers to consumer use of the Internet for health information. MindMapper has many features that facilitate description of the breadth and depth of literature in a domain of inquiry. It also facilitates identification of the number and nature of studies underpinning mapped relationships among concepts, thus laying the groundwork for systematic research reviews and meta-analyses.

Computer Graphics↗

PubMed2004

Can improved software facilitate the wider use of ambulatory blood pressure measurement in clinical practice?

BACKGROUND: 24-h ambulatory blood pressure measurement (ABPM) is now recognized as being indispensable in the diagnosis and management of hypertension. The technique must, therefore, be made available in primary care, but in doing so it must be recognized that unfamiliarity with the technique may lead to misinterpretation of data. OBJECTIVE: To facilitate the wider application of ABPM, especially in primary care, we examined the features that would facilitate the development of a standardized user-friendly software program for the presentation, analysis and interpretation of data. METHODS AND RESULTS: The following features were considered essential to any software program for ABPM: standardized plots of 24-h profiles; computer interpretation of ABPM data and patterns; a user-friendly one-page report, flexible statistical analysis, and the facility to group data and to export data for audit and research analysis. The dabl ABPM program incorporating these features was introduced into the Blood Pressure Unit, Beaumont Hospital in 2000 and has been used in over 15 000 ABPM recordings. The program is now being used widely in general practice and specialized centres. CONCLUSIONS: It is feasible to design a software program to provide a standardized plotting format for ABPM, a basic analysis of data for day-to-day clinical work, or elaborate analyses for research, and an interpretative report to assist diagnosis and to provide an educational process for doctors and nurses not familiar with the technique.

Blood Pressure Monitoring, Ambulatory↗

PubMedDate not supplied

Visualization of spinal cord motion associated with the cardiac pulse by tagged magnetic resonance imaging with particle image velocimetry software.

OBJECTIVE: The purpose of this study was to evaluate whether or not tagged magnetic resonance (MR) imaging with particle image velocimetry (PIV) software could reveal spinal cord motion clearly. METHODS: Six volunteers were enrolled in this study. Tagged MR imaging using fast spoiled gradient-recalled acquisition in the steady state with spatial modulation of the magnetization technique was performed using a 1.5-T MR system. RESULTS: Sagittal vector maps analyzed by PIV software revealed entire spinal cord motion sequentially during the cardiac cycle. The cervical spinal cord initially moved in a caudal direction and then continually oscillated from a cephalic-to-caudal direction. Each volunteer had a different cycle. In the thoracic spinal area, similar findings were observed, although they were slightly less clear than in the cervical area. CONCLUSION: Tagged MR imaging combined with PIV software, referred to as tagged MR image velocimetry, revealed spinal cord motion associated with the cardiac pulse, especially in the cervical spine.

Adult↗

PubMed2005

Color-coded automated signal intensity curves for detection and characterization of breast lesions: preliminary evaluation of a new software package for integrated magnetic resonance-based breast imaging.

OBJECTIVES: The objective of this study was to evaluate the value of a color-coded automated signal intensity curve software package for contrast-enhanced magnetic resonance mammography (CE-MRM) in patients with suspected breast cancer. MATERIALS AND METHODS: Thirty-six women with suspected breast cancer based on mammographic and sonographic examinations were preoperatively evaluated on CE-MRM. CE-MRM was performed on a 1.5-T magnet using a 2D Flash dynamic T1-weighted sequence. A dosage of 0.1 mmol/kg of Gd-BOPTA was administered at a flow rate of 2 mL/s followed by 10 mL of saline. Images were analyzed with the new software package and separately with a standard display method. Statistical comparison was performed of the confidence for lesion detection and characterization with the 2 methods and of the diagnostic accuracy for characterization compared with histopathologic findings. RESULTS: At pathology, 54 malignant lesions and 14 benign lesions were evaluated. All 68 (100%) lesions were detected with both methods and good correlation with histopathologic specimens was obtained. Confidence for both detection and characterization was significantly (P < or = 0.025) better with the color-coded method, although no difference (P > 0.05) between the methods was noted in terms of the sensitivity, specificity, and overall accuracy for lesion characterization. Excellent agreement between the 2 methods was noted for both the determination of lesion size (kappa = 0.77) and determination of SI/T curves (kappa = 0.85). CONCLUSIONS: The novel color-coded signal intensity curve software allows lesions to be visualized as false color maps that correspond to conventional signal intensity time curves. Detection and characterization of breast lesions with this method is quick and easily interpretable.

Adult↗

PubMed2005

TaxI: a software tool for DNA barcoding using distance methods.

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.

Animals↗