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PubMed2003

The development of a theoretical framework and design tool for process usability assessment.

The purpose of usability engineering is to facilitate the deployment of new products by decreasing development costs and improving the quality of systems. This paper will discuss the development and delivery of a unique, theoretically based software tool that provides engineers and designers with easy access to the most recent advances in human-machine interface design. This research combines several theoretical views of the interaction process into a hybrid model. Based on this model, a software tool was produced that allows engineers to model the human interaction process within their design. The system then provides feedback on the interaction process through items such as: the amount of mental effort required by a user, the degree to which the system conforms to human capabilities, the expected time to complete the interaction, where potential human error may occur, as well as potential misunderstandings or points of confusion to the users. The designer may then use this information to improve the design of the system. Validation of this technique indicates that the hybrid model produces accurate predictions of usability attributes and that the technique transfers from the laboratory to the real world.

Adult↗
PubMed1998

The integration of a novice user interface into a professional modeling tool.

This paper describes a software tool, the Oncology Thinking Cap (OncoTCAP) and reports on our efforts to develop a novice user interface to simplify the task of describing biological models of cancer and its treatment. Oncology Thinking Cap includes a modeling tool for making relationships explicit and provide dynamic feedback about the interaction between cancer cell kinetics, treatments, and patient outcomes. OncoTCAP supports student learning by making normally invisible processes visible and providing a representational tool that can be used to conduct thought experiments. We also describe our novice interface and report the results of initial usability testing.

Cell Cycle↗
PubMed2001

Molecular Biocomputing Suite: a word processor add-in for the analysis and manipulation of nucleic acid and protein sequence data.

In all fields of molecular biology, researchers are increasingly challenged by experiments planned and evaluated on the basis of nucleic acid and protein sequence data generally retrieved from public databases. Despite the wide spectrum of available Web-based software tools for sequence analysis, the routine use of these tools has disadvantages, particularly because of the elaborate and heterogeneous ways of data input, output, and storage. Here we present a Visual Basic-encoded Microsoft Word Add-In, the Molecular BioComputing Suite (MBCS), available at the BioTechniques Software Library (www.BioTechniques.com). The MBCS software aims to manage and expedite a wide range of sequence analyses and manipulations using an integrated text editor environment including menu-guided commands. Its independence of sequence formats enables MBCS to be used as a pivotal application between other software tools for sequence analysis, manipulation, annotation, and editing.

Amino Acid Sequence↗
PubMed1999

The development cycle of a pharmaceutical discovery chemi-informatics system.

The rate at which we now produce, test, and warehouse new compound structures in the Discovery process strains our ability to evaluate and comprehend the information that results [Fayyad U. Database Programming and Design 1998;11(3):24]. With the advent of robotic systems and specialized software tools, the profusion of data yielded by the pharmaceutical discovery process is testing the manageability and usefulness of the information resource. Clearly, the challenge faced by Discovery today lies not in the generation of data, but in the generation of software tools that provide the means to store, extract, analyze, and display the data contained within the this expanding resource, and thereby meet the needs of the disciplines participating in the Discovery process. In this review a schematic of a chemi-informatics system, that aids our adaptation to the evolving Discovery process and the expanded flow of pharmaceutical data, is discussed.

Database Management Systems↗
PubMed1995

Assessment of mass properties of human head using various three-dimensional imaging modalities.

Better methods are needed to analyse personal protective devices, such as helmets or facemasks, before they are used in practice. Software tools to quantify three-dimensional craniofacial mass properties are developed to improve our understanding of craniofacial impact biomechanics, supplement existing knowledge of osseous structure and provide a comprehensive description of human head morphology. The application of state-of-the-art imaging systems, solid modelling and other software tools are studied to determine the associated errors in mass property estimation by spiral computed tomography, three-dimensional magnetic resonance and optical surface scanning using phantoms and cadaver head studies. Volume, centre of gravity and principal moments of inertia are determined from solid mathematical models for each scanning modality. Landmark-based registration is used to register scans of the same object obtained from the three imaging modalities to a common reference co-ordinate system. Physically and analytically determined mass properties are used as the standard for truth. Although this comparative study does not lend itself to statistical analysis owing to the small sample size, results indicate that any of the three imaging modalities can be used to predict mass properties within the uncertainty of existing methods. Applying these techniques in vivo is practical and feasible.

Cephalometry↗
PubMed2003

A software tool-box for analysis of regulatory RNA elements.

We describe an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5' UTR, CDS, 3' UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3' UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops. In addition, consensus templates are used to determine whether there are any functional structures present for translational control (template: IRE), structured RNA (template: tRNA consensus) or catalytic RNA (template: trans-splicing RNA), giving indications as to how well the structures found match to these templates. The tool box has been implemented as a WWW server at http://wb2x01.biozentrum.uni-wuerzburg.de/.

Internet↗
PubMed1994

Bioinformatics.

Computer databases, networks and software tools are essential materials and methods for biomedical research and are involved in almost every aspect of disease gene mapping and positional cloning. Public databases of DNA and protein sequences and genetic and physical map information are increasing rapidly in size and complexity and are also improving in quality, comprehensiveness, interoperability and access. A new generation of software tools for navigating through the biomedical literature has become available. Programs for sequence homology searching and genetic map construction have become more sophisticated, yet easier to use. Global computer networks are bringing state-of-the-art capabilities to all.

Chromosome Mapping↗
PubMed2002

Combining fuzzy querying of imprecise data and predictive microbiology using category-based reasoning for prediction of the possible microbial spoilage in foods: application to Listeria monocytogenes.

Various predictive models of microbial behavior have been created and extensive data collection has been done by numerous private or public laboratories. However, significant differences between predicted and observed values in foods have been observed and need to be stressed, understood and explained as much as possible. In this paper, we present a software tool (currently at the level of a prototype) able: (i) to store in a database all relevant information expressed on one hand as qualitative or quantitative data and on the other hand as precise or imprecise data; (ii) to retrieve the more relevant information from the database using queries where criteria may be expressed as fuzzy values in order to enhance the flexibility of the search: (iii) to compute, in addition to the nearest data, an estimation of searched values using statistical models. The architecture of this software tool is structured as a category-based reasoning system. Example queries about Listeria monocytogenes (L. monocytogenes) illustrate the functionalities of this tool.

Computer Simulation↗
PubMed2025

Generating multiple alignments on a pangenomic scale.

MOTIVATION: Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data. RESULTS: We show that the combination of a well-known anchor-based method with the technique of prefix-free parsing yields an approach that is able to generate multiple alignments on a pangenomic scale, provided that large-scale structural variants are rare. Furthermore, experiments with real world data show that our software tool PANgenomic Anchor-based Multiple Alignment significantly outperforms current state-of-the art programs. AVAILABILITY AND IMPLEMENTATION: Source code is available at: https://gitlab.com/qwerzuiop/panama, archived at swh:1:dir:e90c9f664995acca9063245cabdd97549cf39694.

Software↗
PubMed2002

Interpretation and reporting of myocardial perfusion SPECT: a summary for technologists.

Interpretation of cardiac perfusion SPECT images, and the subsequent reporting of results to referring physicians, are sometimes taken to be outside the sphere of the nuclear medicine technologist. However, all personnel involved with nuclear medicine procedures contribute to the timeliness and usefulness of the final report. The goal of this article is to review the principles of scan interpretation and reporting, from the standpoint of what technologists need to understand about these processes. In addition, software tools to aid these processes will be discussed, including quantitative image analysis, telemedicine, computer-aided scan interpretation, databases, computer-aided reporting, and Internet-based reporting. Finally, the accuracy of the scan report will be related to the tasks normally performed by technologists, such as the acquisition and processing of images and the entry, transfer, and networking of data. After reading this article, the reader will be able to describe the principles of scan interpretation and reporting, the software tools for telemedicine and computer-aided interpretation, and the role of the technologist in this process.

Allied Health Personnel↗
PubMed2001

Correlation between nerve conduction studies and clinical scores in diabetic neuropathy.

Polyneuropathy, a frequent complication of diabetes, can be assessed clinically and electrophysiologically. Neurological examination can be quantified by validated scores, e.g., the neuropathy symptom score (NSS) or the neuropathy disability score (NDS). Such scores exclude electrophysiological aspects of the neuropathy. A software tool was designed to convert electrophysiological data into one single index of polyneuropathy (IPN). This index was calibrated to grade the severity of a polyneuropathy from 0.00 to 1.00. In a series of 38 diabetic patients, we have calculated NSS, NDS, and IPN. We found correlations between these variables, NDS and IPN exhibiting the more significant association. The use of IPN allowed us to demonstrate that nerve conduction values correlated with clinical scores in diabetic polyneuropathy. Such a software tool, by providing a single electrophysiological index, may facilitate clinico-electrophysiological assessment in large descriptive studies or therapeutic trials of diabetic polyneuropathy.

Adolescent↗
PubMed1998

New software provides tool for managing contact capitation.

The main drawback to contact capitation has been its administrative complexity. Now, a San Francisco managed care firm has released an Internet-based system that offers a simple process for determining contact values and payment amounts.

California↗
PubMed2002

Use of three-dimensional computer graphic animation to illustrate cleft lip and palate surgery.

OBJECTIVE: Three-dimensional (3D) computer animation is not commonly used to illustrate surgical techniques. This article describes the surgery-specific processes that were required to produce animations to teach cleft lip and palate surgery. MATERIALS AND METHODS: Three-dimensional models were created using CT scans of two Chinese children with unrepaired clefts (one unilateral and one bilateral). We programmed several custom software tools, including an incision tool, a forceps tool, and a fat tool. RESULTS: Three-dimensional animation was found to be particularly useful for illustrating surgical concepts. Positioning the virtual "camera" made it possible to view the anatomy from angles that are impossible to obtain with a real camera. Transparency allows the underlying anatomy to be seen during surgical repair while maintaining a view of the overlaying tissue relationships. Finally, the representation of motion allows modeling of anatomical mechanics that cannot be done with static illustrations. The animations presented in this article can be viewed on-line at http://www.smiletrain.org/programs/virtual_surgery2.htm. CONCLUSIONS: Sophisticated surgical procedures are clarified with the use of 3D animation software and customized software tools. The next step in the development of this technology is the creation of interactive simulators that recreate the experience of surgery in a safe, digital environment.

Child↗
PubMed1998

[A comparison of the monitor and alternator findings of digital thoracic images with the aid of a computer-supported procedure].

PURPOSE: To compare softcopy and hardcopy reading of chest radiographs a software tool was designed for creating lesions with clearly defined size, location and contrast. METHOD: An ROC study was performed using a set of chest radiographs with 300 simulated small nodules and linear details displayed on film and on a 1 K monitor. Six observers participated in the study. ROC curves were generated on the basis of 7200 decisions. RESULTS: There was no significant difference in observer performance overall (AUC = Area under curve). Monitor: 0.84 +/- 0.08 vs. AUC, Film: 0.84 +/- 0.08). Slight, but not statistical significant differences were found in the detection of low-contrast lung nodules and of linear lung details. CONCLUSION: Soft-copy reading using a high quality 1 K CRT display provides the same accuracy for the detection of subtle computer-simulated lesions as hardcopy reading. A software tool could be used for assigning optimal characteristics of CRT- and hardcopy displays using clearly defined lesions as a gold standard.

Computer Simulation↗
PubMed2003

Software for automated analysis of DNA fingerprinting gels.

Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.

Animals↗
PubMed2002

Dynamic computed tomography: a novel technique to study lung aeration and atelectasis formation during experimental CPR.

OBJECTIVE: To develop an image based technique to study the effect of different ventilatory strategies on lung ventilation and alveolar recruitment during cardiopulmonary resuscitation (CPR). DESIGN: (1) Technical development of the following components: (a) construction of an external chest compression device, which does not interfere with CT imaging, and (b) development of a software tool to detect lung parenchyma automatically and to calculate radiological density parameters. (2) Feasibility studies: three strategies of CPR ventilation were performed and imaged in one animal each (pigs, 25 kg): volume-constant ventilation (VCV), no ventilation, or continuous airway pressure (CPAP). One minute after induction of circulatory arrest inside the CT scanner, external chest compressions started at a rate of 100 cpm, and one of the ventilation modes was initiated. After 1 min, intravenous epinephrine was added as a bolus (40 microg/kg), followed by a continuous infusion (13 microg/kg per min). Six minutes later, dynamic CT acquisitions (temporal resolution: 100 ms) commenced. Simultaneously, arterial blood gases, acid base status and haemodynamics were sampled. RESULTS: Using a modified chest compression device, dynamic CT acquisitions are feasible during closed-chest CPR. In three pilot experiments with different ventilation strategies, the dedicated software tool allowed to quantify ventilated, atelectatic and over-distended fractions of total lung area. VCV showed a large amount of atelectasis, which was recruited during every respiratory cycle. No ventilation led to atelectasis to govern over 50% of the total lung area. CPAP caused less atelectasis as VCV, and no cyclic recruitment and de-recruitment phenomena were observed. CONCLUSIONS: We demonstrate a novel experimental set up, which allows quantification of different lung compartments during ongoing CPR and may become useful in comparing the direct pulmonary effects of different ventilatory strategies in the settings of Basic and Advanced Cardiac Life Support.

Animals↗
PubMed2002

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.

DNA, Plant↗