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New software tools ease move to electronic medical records.

Converting a hospital to electronic medical records can save big bucks, but it's easier said than done. Huge savings await hospitals that eliminate the cost of storing, filing and retrieving charts. But making that move is more complex than simply converting written notes to an automated format. Learn how one California hospital is embarking on its journey to a paperless environment with the help of some innovative information systems technology that will take some of the pain out of the transformation.

Abstracting and Indexing↗

Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm.

Two programs, MOTIF and PATTERN, that scan sequences for matches to user-defined motifs and patterns of motifs based on identity and set membership are described. The programs use a simple and logical notation to define motifs, and may be used either interactively or by using command line parameters (suitable for batch processing). The two programs described also incorporate a simple, yet reliable, algorithm that automatically detects in which of six possible formats the sequence entry is written.

Algorithms↗

Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using new software tools for multiple alignment and visualization.

With the tremendous expansion of molecular sequence data in recent years, multiple alignment is arguably one of the two most important analytic techniques (the other being fast database searching). A number of useful approaches to this problem have previously been developed, but often they are limited to only a subset of multiple-alignment applications and cannot easily deal with the complex structural organization seen in an increasing number of sequences. For example, a single sequence may contain several domains of different evolutionary origins, and the multiplicities and relative ordering of these domains may be quite different among related sequences. Here we describe an integrated set of interactive Unix tools that combines several multiple-alignment techniques with traditional "dot-plot" visualization to provide a flexible environment for approaching complex sequence analysis problems. We apply these tools to the identification and characterization of "catalytic" domains in ras and rho/rac GTPase-activating proteins, to "Src homology" (SH2, SH3) domains in cytoplasmic signaling proteins, to repetitive sequence motifs in the alpha and beta subunits of protein prenyltransferases, and to regulatory DNA sequences in the locus control region of the beta-globin gene cluster.

Alkyl and Aryl Transferases↗

Dynamic arrays for fast, efficient, data manipulation during image analysis: a new software tool for exploratory data analysis.

Memory reallocation is used to construct a run-time data structure for fast/efficient storage of information during collection and analysis. The data structure presented uses dynamic memory but does not require the use of pointers to link nodes of information together. It allows for simple and efficient access to data via array indexing rather than through the use of lists or tree structures and it provides flexibility for competing storage requirements that are determined dynamically. The data structure is developed in the C programming language and a suite of ANSI standard C subroutines that make up a run-time data structure management system is provided.

Abstracting and Indexing↗

A software tool for auditory and speech perception experimentation.

A computer program capable of supporting auditory and speech perception experimentation is described. Given a continuum of acoustic stimuli, the program (Paradigm) allows the user to present those stimuli under different, well-known psychophysical paradigms (simple identification, identification with a rating scale, 2IAX, ABX, AXB, and oddity task). For discrimination tests, both high uncertainty (roving designs) and minimal psychophysical uncertainty (fixed designs) procedures are available. All the relevant time intervals can be precisely specified, and feedback is also available. Response times can be measured as well. Furthermore, the program stores subjects' responses and provides summaries of experimental results for both individual subjects and groups. The program runs on Microsoft Windows (3.1 or 95) on personal computers equipped with any soundboard.

Auditory Perception↗

Modelling acquired dyslexia: a software tool for developing grapheme-phoneme correspondences.

In extending a computer model of acquired dyslexia, it has become necessary to develop a way to group printed characters in a word so that the character groups essentially have a one-to-one correspondence with the word's phonemes (speech sounds). This requires deriving a set of correspondences (legal character groupings, legal associations of character groups with phonemes, etc.) that yield a single grouping or "segmentation" of characters when applied to any English word. To facilitate and partially automate this task, a segmentation program has been developed that uses an interchangeable set of correspondences. The program segments words according to these correspondences and tabulates their success over large sets of words. The program has been used successfully to segment a 20,000 word corpus, demonstrating that this approach can be used effectively and efficiently.

Algorithms↗

Software tools for using a personal computer as a timer device to assess human kinematic performance: a case study.

Frequently, the assessment of the physical condition of a sportsman depends on the evaluation of different tests, based on biomechanical performance. The data acquisition in these tests is usually hand made, because its automatization is difficult. But when movements are constrained by means of their specific nature, simple tools can be used to achieve that data acquisition. In this paper, a simple and inexpensive system is described to make use of the timing capabilities of a personal computer (PC) to use it as a timer, with applications in biomechanics and sport training. The data acquisition method is based on a PC that, using a specific programming dealing with event timing, gets signals through the printer port, from a receptor device that detects cuts in an infrared cell beam. Low level procedures are provided that can be used in higher level algorithmic designs, problem dependent, to build specific systems. The case of the evaluation of the Wingate Anaerobic Test is discussed.

Algorithms↗

FAST (Flexible Analysis by Software Tool) and CHAMP (CHemico-physical AMinoacidic Parameter data bank): a new tool to investigate protein structure.

A flexible package designed to study protein structure is described. The package is devoted to the analysis of protein sequences by drawing structural profiles of specific structure-related amino acid parameters. An Aminoacidic Parameters Data Bank (CHAMP) containing 32 different series of physico-chemical parameters of amino acids is available. Sequences can be loaded from any ASCII format data bank or from keyboard. The program possesses a routine which enables easy updating of the protein data bank and CHAMP Data Bank. FAST reads statistical correlations between two plots in order to identify structural similarities. Plots can be printed, saved or used for correlation, comparison or graph overlap by using common spreadsheets (e.g. Lotus 123). Plots can be smoothed by a running mean or a running median. The program also has a special feature--a global flexibility analysis of proteins. The package runs on IBM or compatibles and requires DOS 3.0 or later.

Amino Acids↗

A software tool to acquire, synchronise and playback multimedia data: an application in kinesiology.

Assessing the physical condition of the human body frequently requires evaluating different tests performed by different devices. This information has to be analysed simultaneously to derive conclusions, and so a temporal relationship must be established between the data sources. In this paper, synchronisation of the sources of information is achieved by synchronising the clocks of computers connected in a Local Area Network. A clock synchronisation protocol is used and a global time is stamped in each information data flow. During analysis, the time-stamp is used to playback the data in a synchronised way. The proposed system is valid for any medical application in which data synchronisation is needed. However, it has initially been used in a distributed medical environment for analysing electrical muscular activity and lumbar movement. The dual aim is to detect injuries and plan training sessions for athletes. It was specifically used to analyse data generated by: electromyographs; lumbar equipment; and images generated by video cameras. The simple operation of the application and the precision of the synchronisation protocol enabled several interesting medical conclusions to be made.

Electromyography↗

A tool for software and hardware evaluation.

The proliferation of information technology has enormously eased the burden of computing for medical users. However, it has also created a confusing, difficult problem in evaluation and selection of appropriate software and hardware components. This paper presents an easy to use software tool based on Anderson's Ranking Methodology implemented in Excel 5 that enables one an objective evaluation and selection.

Computers↗

BCE: a tool for software integration.

The integration of software into special-purpose systems (e.g. for gene sequence analysis) can be a difficult task. We describe a general-purpose software integration tool, the BCE program, that facilitates assembly of VAX-based software into application systems and provides an easy-to-use, intuitive user interface. We describe the use of BCE to integrate a heterogeneous collection of sequence analysis tools. Many BCE design features are generally applicable and can be implemented in other language or hardware environments.

Algorithms↗

A new approach to computer guidance in orthopedic surgery using real time volume rendering.

The purpose of this paper was to evaluate the ability of a new real time volume rendering system using raw unprocessed CT data on a four processor Pentium PC. A CT data set of the pelvic area was used to demonstrate the systems ability to integrate and visualize both data from a CT scan and a tracking system. The computer system consisted of a four processor Pentium PC and the software tool VGInsight (Volume Graphics GmbH). For study purposes in a laboratory setting a magnetic tracking system (Polemus Inc.) was used to simulate tracked surgical tools. With this new software tool and the tracking system the exact relative location of a tracked instrument within all structures of the pelvic area, soft tissue as well as bone, could be displayed in 3D and real time without preprocessing of the data set. Until recently real time volume rendering required expensive workstations. With a new software tool on a four processor Pentium PC the authors were able to introduce a 3D real time processed data supply to the surgeon.

Fractures, Bone↗

RadNotes: a novel software development tool for radiology education.

RadNotes is a novel software development tool that enables physicians to develop teaching materials incorporating text and images in an intelligent, highly usable format. Projects undertaken in the RadNotes environment require neither programming expertise nor the assistance of a software engineer. The first of these projects, Thoracic Imaging, integrates image teaching files, concise disease and topic summaries, references, and flash card quizzes into a single program designed to provide an overview of chest radiology. RadNotes is intended to support the academic goals of teaching radiologists by enabling authors to create, edit, and electronically distribute image-oriented presentations. RadNotes also supports the educational goals of physicians who wish to quickly review selected imaging topics, as well as to develop a visual vocabulary of corresponding radiologic anatomy and pathologic conditions. Although Thoracic Imaging was developed with the aim of introducing chest radiology to residents, RadNotes can be used to develop tutorials and image-based tests for all levels; create corresponding World Wide Web sites; and organize notes, images, and references for individual use.

Computer-Assisted Instruction↗

Automated planning target volume generation: an evaluation pitting a computer-based tool against human experts.

PURPOSE: Software tools are seeing increased use in three-dimensional treatment planning. However, the development of these tools frequently omits careful evaluation before placing them in clinical use. This study demonstrates the application of a rigorous evaluation methodology using blinded peer review to an automated software tool that produces ICRU-50 planning target volumes (PTVs). METHODS AND MATERIALS: Seven physicians from three different institutions involved in three-dimensional treatment planning participated in the evaluation. Four physicians drew partial PTVs on nine test cases, consisting of four nasopharynx and five lung primaries. Using the same information provided to the human experts, the computer tool generated PTVs for comparison. The remaining three physicians, designated evaluators, individually reviewed the PTVs for acceptability. To exclude bias, the evaluators were blinded to the source (human or computer) of the PTVs they reviewed. Their scorings of the PTVs were statistically examined to determine if the computer tool performed as well as the human experts. RESULTS: The computer tool was as successful as the human experts in generating PTVs. Failures were primarily attributable to insufficient margins around the clinical target volume and to encroachment upon critical structures. In a qualitative analysis, the human and computer experts displayed similar types and distributions of errors. CONCLUSIONS: Rigorous evaluation of computer-based radiotherapy tools requires comparison to current practice and can reveal areas for improvement before the tool enters clinical practice.

Expert Systems↗

Software engineering tools.

We have looked at general descriptions and illustrations of several software development tools, such as tools for prototyping, developing DFDs, testing, and maintenance. Many others are available, and new ones are being developed. However, you have at least seen some examples of powerful CASE tools for systems development.

Data Display↗

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.

Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://@www.sdsc.edu/CompSci/Biomed/ MEME.

Algorithms↗

Visualization of multiple influences on ocellar flight control in giant honeybees with the data-mining tool Viscovery SOMine.

Viscovery SOMine is a software tool for advanced analysis and monitoring of numerical data sets. It was developed for professional use in business, industry, and science and to support dependency analysis, deviation detection, unsupervised clustering, nonlinear regression, data association, pattern recognition, and animated monitoring. Based on the concept of self-organizing maps (SOMs), it employs a robust variant of unsupervised neural networks--namely, Kohonen's Batch-SOM, which is further enhanced with a new scaling technique for speeding up the learning process. This tool provides a powerful means by which to analyze complex data sets without prior statistical knowledge. The data representation contained in the trained SOM is systematically converted to be used in a spectrum of visualization techniques, such as evaluating dependencies between components, investigating geometric properties of the data distribution, searching for clusters, or monitoring new data. We have used this software tool to analyze and visualize multiple influences of the ocellar system on free-flight behavior in giant honeybees. Occlusion of ocelli will affect orienting reactivities in relation to flight target, level of disturbance, and position of the bee in the flight chamber; it will induce phototaxis and make orienting imprecise and dependent on motivational settings. Ocelli permit the adjustment of orienting strategies to environmental demands by enforcing abilities such as centering or flight kinetics and by providing independent control of posture and flight course.

Animals↗

Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package.

The peptide sequential assignment algorithm presented here was implemented as a macro within the CONnectivity TRacing ASsignment Tools (CONTRAST) computer software package. The algorithm provides a semi- or fully automated global means of sequentially assigning the NMR backbone resonances of proteins. The program's performance is demonstrated here by its analysis of realistic computer-generated data for IIIGlc, a 168-residue signal-transducing protein of Escherichia coli [Pelton et al. (1991) Biochemistry, 30, 10043-10057]. Missing experimental data (19 resonances) were generated so that a complete assignment set could be tested. The algorithm produces sequential assignments from appropriate peak lists of nD NMR data. It quantifies the ambiguity of each assignment and provides ranked alternatives. A 'best first' approach, in which high-scoring local assignments are made before and in preference to lower scoring assignments, is shown to be superior (in terms of the current set of CONTRAST scoring routines) to approaches such as simulated annealing that seek to maximize the combined scores of the individual assignments. The robustness of the algorithm was tested by evaluating the effects of imposed frequency imprecision (scatter), added false signals (noise), missing peaks (incomplete data), and variation in user-defined tolerances on the performance of the algorithm.

Algorithms↗