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PubMedDate not supplied

Developing an evaluation tool for instructional software programs.

The use of instructional software is predominant in many nursing programs. The need for cost-effective, quality programs requires faculty to evaluate instructional software before its purchase and use. The purpose of this work was to develop a tool for evaluating instructional software programs. The tool was based on data from the literature, as well as input and feedback from nurse educators and multimedia specialists. The evaluation tool assists faculty to ensure proper evaluation and selection of instructional software.

Choice Behavior↗
PubMed2002

The efficacy of a computerized caries detector in intraoral digital radiography.

BACKGROUND: A unique software tool has been developed to assist dentists in the difficult task of diagnosing radiographs for proximal caries. The software, called Logicon Caries Detector (Northrop Grumman Information Technology, Herndon, Va.), extracts image features and correlates them with a database of known caries problems. The Logicon software was combined with the digital radiography system Trophy RadioVisioGraphy (Trophy Radiologie, Croissy-Beaubourg, France) and its effectiveness was measured in a clinical study, the results of which are reported here. METHODS: The manufacturer trained 18 dentists in private practices and one university clinic across the United States to use the Logicon Caries Detector software. The dentists diagnosed 175 surfaces with potential caries and adjacent teeth expected to be clean but included as control surfaces. The dentists first did a visual diagnosis only and then repeated the diagnosis using the software. If their final diagnosis called for it, a restoration was performed and the depth of caries was recorded. RESULTS: Effectiveness was gauged by calculating three measures of performance-sensitivity, specificity and accuracy-for dentin caries diagnosis by each dentist both before and after using Logicon Caries Detector. Sensitivity among all dentists before using the Logicon software was 70.3 percent and afterward was 90.5 percent, an improvement of 20.2 percent. Dentists' specificity was 88.6 percent before using the software and 88.3 percent afterward, with a difference of-0.3 percent. Dentists' accuracy was 75.6 percent before using the software and 88.3 percent afterward, with an improvement of 12.7 percent. CONCLUSIONS: Logicon Caries Detector enabled dentists to find 20 percent more cases of caries penetrating into dentin than they were able to find without it, while not causing them to mistreat any additional healthy teeth. CLINICAL IMPLICATIONS: Digital radiography and smart software like Logicon Caries Detector will improve dentists' diagnostic abilities and lead to better patient care.

Adolescent↗
PubMed2004

Exploring genome architecture through GOV: a WWW-based gene order visualizer.

MOTIVATION: The past decade has seen extension in the methods of sequence analysis from single gene based to analyzing multiple genes and proteins simultaneously. Consequently, there is a need for software tools that will allow mining of these enormous datasets at genome level effectively. A key challenge is to make them user-friendly, available to a larger community and integrate with public domain software without much hassle. RESULTS: A web-based interactive computational tool is described for visualization and comparison of gene order from prokaryotic and selected viral genome data. Many intriguing similarities and differences in gene order of multiple genomes can be compared and revealed. The interface facilitates easy extraction of the nucleotide sequence of the gene of interest and BLAST analysis against GenBank at NCBI to provide insights into gene functions and orthologs of the gene in other species.

Algorithms↗
PubMed2004

[Fully automatic detection and quantification of emphysema on thin section MD-CT of the chest by a new and dedicated software].

PURPOSE: Introduction of a novel software tool (YACTA -- yet another CT analyzer) for detection and quantification of pulmonary emphysema in thin-slice chest MDCT data sets. MATERIALS AND METHODS: Consisting of grey-level threshold-based algorithms (e. g., region-growing), expert rules and morphological image postprocessing YACTA segments the tracheobronchial tree prior to the detection and quantification of pulmonary emphysema. In addition to general parameters, such as the mean lung density (MLD) and the emphysema index (EI -- also described as pixel index PI), the previously described bullae index (BI) is transformed into a three-dimensional parameter for a morphological description of emphysema. A first evaluation of chest MDCT data sets of 11 patients was performed as well as a comparison of MLD, lung volume (LV), emphysema volume (EV) and PI calculated with two established commercial tools of Siemens Medical Solutions (Volume and Pulmo). Furthermore, the BI was calculated with YACTA. RESULTS: YACTA processed the image data without manual interaction and demonstrated more user-comfort than Volume and Pulmo software, which require manual correction especially for lung segmentation at the hilar regions to separate central airways from lung parenchyma. MLD, LV, and EV values calculated with YACTA were systematically higher (Pulmo: + 50 HU/+ 597 ml/+ 159 ml; Volume: + 32 HU/+ 110 ml/+ 155 ml). Different segmentation algorithms are responsible for this: YACTA includes areas not assessed by mere threshold-based techniques. Constantly lowered LV values of Pulmo are caused by a missing dilatation algorithm. The error correction as a special feature of YACTA results in increased emphysema volumes and indices. The segmentation of the tracheobronchial tree lowers the part of airways falsely classified as emphysema. CONCLUSION: The new developed software shows higher user comfort as established by semi-automated tools. RESULTS: of LV, EV, MLD and PI are comparable or moderately different. Automatic calculation of a BI is possible, providing information about bullous morphology of pulmonary emphysema. Further studies are necessary to correlate data with clinical or pathological parameters.

Adult↗
PubMed2006

Gene Designer: a synthetic biology tool for constructing artificial DNA segments.

BACKGROUND: Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes. RESULTS: Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference. CONCLUSION: Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.

Base Sequence↗
PubMed2000

The first object oriented monitor for intravenous anesthesia.

OBJECTIVE: To describe the design and implementation of "INFUSION TOOLBOX," a software tool to control and monitor multiple intravenous drug infusions simultaneously using pharmacokinetic and pharmacodynamic principles. METHODS: INFUSION TOOLBOX has been designed to present a graphical interface. Object Oriented design was used and the software was implemented using Smalltalk, to run on a PC. Basic tools are available to manage patient, drugs, pumps and reports. These tools are the PatientPanel, the DrugPanel, the PumpPanel and the HistoryPanel. The screen is built dynamically. The panels may be collapsed or closed to avoid a crowded display. We also built control panels such as the Target ControlPanel which calculates the best infusion sequence to bring the drug concentration in the plasma compartment to a preset value. Before drug delivery, the user enters the patient's data, selects a drug, enters its dilution factor and chooses a pharmacokinetic model. The calculated plasma concentration is continually displayed and updated. The anesthetist may ask for the history of the delivery to obtain a graphic report or to add events to the logbook. A panel targeting the effect is used when a pharmacodynamic model is known. Data files for drugs, pumps and surgery are upgradable. DISCUSSION: By creating a resizeable ControlPanel we enable the anesthetist to display the information he wishes, when he wishes it. The available panels are diverse enough to meet the anesthetist needs; they may be adapted to the drug used, pumps used and surgery. It is the anesthetist who builds dynamically its different control screens. CONCLUSION: By adopting an evolutionary solution model we have achieved considerable success in building our drug delivery monitor. In addition we have gained valuable insight into the anesthesia information domain that will allow us to further enhance and expand the system.

Anesthesia, Intravenous↗
PubMed2006

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.

The great majority of terrestrial plants enters a beneficial arbuscular mycorrhiza (AM) or ectomycorrhiza (ECM) symbiosis with soil fungi. In the SPP 1084 "MolMyk: Molecular Basics of Mycorrhizal Symbioses", high-throughput EST-sequencing was performed to obtain snapshots of the plant and fungal transcriptome in mycorrhizal roots and in extraradical hyphae. To focus activities, the interactions between Medicago truncatula and Glomus intraradices as well as Populus tremula and Amanita muscaria were selected as models for AM and ECM symbioses, respectively. Together, almost, 20.000 expressed sequence tags (ESTs) were generated from different random and suppressive subtractive hybridization (SSH) cDNA libraries, providing a comprehensive overview of the mycorrhizal transcriptome. To automatically cluster and annotate EST-sequences, the BioMake and SAMS software tools were developed. In connection with the eNorthern software SteN, plant genes with a predicted mycorrhiza-induced expression were identified. To support experimental transcriptome profiling, macro- and microarray tools have been constructed for the two model mycorrhizae, based either on PCR-amplified cDNAs or 70mer oligonucleotides. These arrays were used to profile the transcriptome of AM and ECM roots under different conditions, and the data obtained were uploaded to the ArrayLIMS and EMMA databases that are designed to store and evaluate expression profiles from DNA arrays. Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies.

Computational Biology↗
PubMed2001

GeneOrder: comparing the order of genes in small genomes.

MOTIVATION: The recent rapid rise in the availability of whole genome DNA sequence data has led to bottlenecks in their complete analysis. Specifically, there is a need for software tools that will allow mining of gene and putative gene data at a whole genome level. These new tools will complement the current set already in use for studying specific aspects of individual genes and putative genes in detail. A key software challenge is to make them user-friendly, without losing their flexibility and capability for use in research. RESULTS: The creation of GeneOrder-a web-based interactive, computational tool-allows researchers to compare the order of genes in two genomes. It has been tested on full genome sequence data for viruses, mitochondria and chloroplasts that were obtained from the NCBI GenBank database. It is accessible at http://www.bif.atcc.org/GENEOrder/index.html. GeneOrder prepares the comparison in table form, listing the order of similar genes. Hyperlinks are provided from this output; these lead to the 'Protein Coding Regions' in the NCBI database.

Animals↗
PubMed2026

map3C: a computational tool for processing multiomic single-cell Hi-C data.

SUMMARY: The emergence of multiomic single-cell Hi-C (scHi-C) methods, which simultaneously profile chromatin conformation and other modalities such as gene expression or DNA methylation, creates tremendous opportunities for studying the genome's structure-function relationships. Existing tools for processing multiomic scHi-C datasets lack certain key functions for downstream bioinformatics analysis. We present map3C, a software tool that incorporates additional key functions. Specifically, we demonstrate that map3C facilitates multiomic scHi-C processing, quality control, and identification of structural variant locations in the genome. AVAILABILITY AND IMPLEMENTATION: map3C is available at https://github.com/luogenomics/map3C and is archived at https://doi.org/10.5281/zenodo.20724719.

Software↗
PubMed2000

Graphical tools for comparative genome analysis.

Visualization of data is important for many data-rich disciplines. In biology, where data sets are becoming larger and more complex, graphical analysis is felt to be ever more pertinent. Although some patterns and trends in data sets may only be determined by sophisticated computational analysis, viewing data by eye can provide us with an extraordinary amount of information in an instant. Recent advances in bioinformatic technologies allow us to link graphical tools to data sources with ease, so we can visualize our data sets dynamically. Here, an overview of graphical software tools for comparative genome analysis is given, showing that a range of simple tools can provide us with a powerful view of the differences and similarities between genomes.

Animals↗
PubMed2005

Bioinformatics in drug development and assessment.

Bioinformatics is playing an increasingly important role in nearly all aspects of drug discovery, drug assessment, and drug development. This growing importance lies not only in the role that bioinformatics plays in handling large volumes of data, but also in the utility of bioinformatics tools to predict, analyze, or help interpret clinical and preclinical findings. This review focuses on describing and evaluating some of the newer or more important bioinformatics resources (i.e., databases and software) that are of growing importance to understanding or predicting drug metabolism, especially with respect to the absorption, distribution, metabolism, excretion, (ADME), and toxicity (T) of both existing drugs and potential drug leads. Detailed descriptions and critical assessments of a number of potentially useful bioinformatics/cheminformatics databases and predictive ADMET software tools are provided. Additionally, several pharmaceutically important applications of both the databases and software are highlighted. Given the rapid growth in this area and the rapid changes that are taking place, a special emphasis is placed on freely available or Web-accessible resources.

Animals↗
PubMed2004

Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers.

Publicly available single nucleotide polymorphism (SNP) allele frequencies are an important resource for the selection of genetic markers that may be most useful for gene mapping and association studies. Data mining these allele frequencies through disparate public databases and Websites is time consuming and can result in inconsistent findings. We have developed a web-based software tool, Frequency Finder, to acquire SNP allele frequencies from multiple public data sources and return a summarized result to the user. Our software optimizes and automates the search of candidate markers, decreasing the amount of time it would take to extract pertinent data manually. We have included several methods to output the data, including on-screen and as a compressed text file. We show that Frequency Finder accurately retrieves available frequency data from the available sources. Using this tool, we detect significant differences between Asian, African and Caucasian populations in the allele frequency spectra of 246 097 SNPs. While limited to public databases that provide web-based access to allele frequencies, Frequency Finder provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources.

Algorithms↗
PubMed2000

Plant genome databases: from references to inference tools.

Plant genome databases play an important role in the archiving and dissemination of data arising from the international genome projects. Recent developments in bioinformatics, such as new software tools, programming languages and standards, have produced better access across the Internet to the data held within them. An increasing emphasis is placed on data analysis and indeed many resources now provide tools allied to the databases, to aid in the analysis and interpretation of the data. However, a considerable wealth of information lies untapped by considering the databases as single entities and will only be exploited by linking them with a wide range of data sources. Data from research programs such as comparative mapping and germplasm studies may be used as tools, to gain additional knowledge but without additional experimentation. To date, the current plant genome databases are not yet linked comprehensively with each other or with these additional resources, although they are clearly moving toward this. Here, the current wealth of public plant genome databases is reviewed, together with an overview of initiatives underway to bind them to form a single plant genome infrastructure.

Computational Biology↗
PubMed2006

PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats.

Identification of dispersed or interspersed repeats, most of which are derived from transposons, retrotransposons or retrovirus-like elements, is an important step in genome annotation. Software tools that compare genomic sequences with precompiled repeat reference libraries using sensitive similarity-based methods provide reliable means of finding the positions of fragments homologous to known repeats. However, their output is often incomplete and fragmented owing to the mutations (nucleotide substitutions, deletions or insertions) that can result in considerable divergence from the reference sequence. Merging these fragments to identify the whole region that represents an ancient copy of a mobile element is challenging, particularly if the element is large and suffered multiple deletions or insertions. Here we report PLOTREP, a tool designed to post-process results obtained by sequence similarity search and merge fragments belonging to the same copy of a repeat. The software allows rapid visual inspection of the results using a dot-plot like graphical output. The web implementation of PLOTREP is available at http://bioinformatics.abc.hu/PLOTREP/.

Computer Graphics↗
PubMed1991

The portable virtual simulator.

The Virtual Simulator is a software tool for support and management of the geometric component of 3-dimensional radiotherapy treatment design. The Virtual Simulator is a software implementation of a physical simulator with additional functionality not currently available on physical simulators. Treatment of a virtual patient, derived from CT or other source, is simulated using the Virtual Simulator in the same way a physical simulator would be used. The intent of this approach is to provide the user with a familiar working environment for radiotherapy treatment design. Key features include an effective and efficient user interface, and the use of computing techniques and software standards which enhance portability to a variety of computer workstations. The Virtual Simulator is implemented in the C programming language using the X Window System, and has been written with the generic UNIX workstation in mind. It has been demonstrated that it can be installed and run without modification on workstations from a number of vendors.

Computer Simulation↗
PubMed2002

Building an asynchronous web-based tool for machine learning classification.

Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.

Algorithms↗
PubMed2026

Clinical Variant Interpretation with the Integrative Genomics Viewer (IGV) for Molecular Pathologists.

The integrative genomics viewer (IGV) is a pivotal tool in clinical genomics, enabling the visualization and interpretation of complex sequencing data. Bringing clinical knowledge to bear with visual evaluation of sequencing results is the primary means by which molecular pathologists and other professionals assess and finalize cases. A variety of software tools can assist, but their relationship to the underlying data must be understood and applied systematically. This study includes essential background on next-generation sequencing (NGS) data file types (e.g., FASTQ, BAM, VCF) with a discussion of their format and purpose. We then describe features of IGV that derive nuances from these files. We utilize a series of curated practical cases based on clinical vignettes through which the reader will interact with clinical NGS sequencing data using the IGV software to review various types of clinically relevant variants relative to the human reference genome. These clinical vignettes have been curated to describe examples of some of the complexities of interpretation of genomic data, and how utilizing IGV as part of a routine workflow can provide additional interpretive information for variants beyond routine bioinformatic software algorithm variant calls. The visual inspection of genomic variants utilizing the tools within IGV can unmask subtle contextual cues (i.e., variant allele frequency, strand bias, tissue-specific context) that can influence the interpretation of genomic variants. Although this study focuses on using IGV for the detection and interpretation of somatic variants, the provided applications can be extrapolated for use in the germline setting, including analysis of complex variants and detection of mosaicism.

Humans↗
PubMed1997

In vitro 2-D networks of neurons characterized by processing the signals recorded with a planar microtransducer array.

The purpose of this paper is to extensively analyze and utilize the key features that characterize the recently available electrophysiological technique of growing selected populations of neurons on planar substrate microelectrode arrays. This experimental configuration is first simulated by modeling the signal transduction operated by an array of microtransducers coupled to a network of Hodgkin-Huxley-like neurons, connected to each other with given levels of synaptic strength. Signal processing tools are then described and validated by identifying the various degrees of connectivity previously introduced into the simulated network. Finally, these software tools are utilized to characterize the activity and identify the synaptic connectivity of networks of cultured neurons extracted from dorsal root ganglia (DRG) of chick embryos and exposed to synapse inhibiting/reinforcing ions. As a result, correlations between various regimens of electrophysiological activity and synaptic strength are obtained.

Algorithms↗