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JavaScope is a Web-based java applet that implements an "exploration/browser" tool for operating a Philips CM200 transmission electron microscope and viewing digital images remotely. The primary use of the application is as a collaborative tool for remote consultations.
Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed.
By taking advantage of network-based computing and the recent developments in Web interfaces, centralized research facilities housing specialized and unique imaging instruments along with associated high-performance computing can be made available to researchers for use from their own laboratories. In addition to increasing access and utilization of these facilities, operation over the Internet is expected to enhance research by facilitating collaboration between researchers. We describe the implementation of a platform-independent Web-based system written in Java that supplements automated functions with video-guided interactive, collaborative remote control and data acquisition from an intermediate-high-voltage electron microscope.
We present EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs. The goal of this project is to provide software capable of performing single-particle reconstructions beyond 10 A as such high-resolution data become available. A complete single-particle reconstruction algorithm is implemented. Options are available to generate an initial model for particles with no symmetry, a single axis of rotational symmetry, or icosahedral symmetry. Model refinement is an iterative process, which utilizes classification by model-based projection matching. CTF (contrast transfer function) parameters are determined using a new paradigm in which data from multiple micrographs are fit simultaneously. Amplitude and phase CTF correction is then performed automatically as part of the refinement loop. A graphical user interface is provided, so even those with little image processing experience will be able to begin performing reconstructions. Advanced users can directly use the lower level shell commands and even expand the package utilizing EMAN's extensive image-processing library. The package was written from scratch in C++ and is provided free of charge on our Web site. We present an overview of the package as well as several conformance tests with simulated data.
The dramatic development of new electronic devices within the last 25 years has had a substantial influence on the control and automation of industrial bioprocesses. Within this short period of time the method of controlling industrial bioprocesses has changed completely. In this paper, the authors will use a practical approach focusing on the industrial applications of automation systems. From the early attempts to use computers for the automation of biotechnological processes up to the modern process automation systems some milestones are highlighted. Special attention is given to the influence of Standards and Guidelines on the development of automation systems.
Computer graphics offers an unprecedented opportunity to probe new and old ideas in vision testing, without going to the expense of building dedicated equipment. However, the large variety of computer hardware is bewildering and only occasionally can commercial software tools be used. This mini review of the basic principles of computer graphics on personal computers is intended to help the newcomer to the field.
The differentiation of T Lymphocytes within the thymus is an important biological phenomenon during which these cell acquire their functions to further control the immune system. Numerous experiments under various conditions have been devised to understand the different mechanisms involved in this complex process. Nevertheless, interpretation of these experiments lead to still contradictory debatable hypotheses. Modelisation of this process through classical simulation methods cannot be envisaged because they are not adapted to modifications of the model structure, which is the point of interest. For these reasons, we proposed a new approach of automatic search for model. The program consists of four independent connected modules: The generator produces model, based on the rationale of formal grammars. Protocol and experimental data are stored in a set of experiments. The simulator using a protocol and a model provides simulated results. Finally, the supervisor by comparing simulated results and experimental data, adapts the model parameters to increase their fit and either chooses a new experiment to explore, or modifies the model structure. Change of the model structure is performed among still unexplored models according to their "promise" level, which is iteratively evaluated relatively to previously explored models through a proposed model distance. The generator is written in Prolog and the other modules in C++. The architecture of the program allows us to modify or complete a module without changing anything in the other modules. As a consequence, the proposed modeling approach conceived to study T lymphocyte differentiation within the thymus remains independent of this biological phenomenon and can be applied to other biological problems.
The Johns Hopkins Hospital has initiated an ambitious program to apply modern technologies to the development of a new, comprehensive clinical information system. One component of this system is a networking technology for supporting the integration of diverse and functionally distinct information systems. This paper discusses the selection of the networking technology implemented at JHH, issues and problems, networking concepts, protocols, and reliability.
Microcomputers are perfectly suited for the input, storage, display, and printing of medical information. The most efficient method of data input and verification is by health professionals themselves, at the bedside or in the exam room. Battery-powered microcomputers are now available with all the power and function of desktops. One patient-care software package [Smart-Chart(tm)] allows entry of clinical data into battery-powered computers such as the Epson Geneva or Data General One, and two-way communication of such data with IBM-PC compatibles. This system inexpensively places a complete computer system in the hands of health professionals in all locations of practice (even at home for use during telephone calls). A dozen or so floppy disks can allow primary physicians to have immediate access to current information on all patients in their practice. Medical notation by computer may now achieve its full potential for clarifying medical records, improving patient care, and diminishing the frustration of medical practice.
Object-oriented programming techniques were used to develop computer based data display and storage systems. These have been operating in the 8 anaesthetising areas of the Adelaide Children's Hospital for 3 years. The analogue and serial outputs from an array of patient monitors are connected to IBM compatible PC-XT computers. The information is displayed on a colour screen as wave-form and trend graphs and digital format in 'real time'. The trend data is printed simultaneously on a dot matrix printer. This data is also stored for 24 hours on 'hard' disk. The major benefit has been the provision of a single visual focus for all monitored variables. The automatic logging of data has been invaluable in the analysis of critical incidents. The systems were made possible by recent, rapid improvements in computer hardware and software. This paper traces the development of the program and demonstrates the advantages of object-oriented programming techniques.
PURPOSE: Our purpose was to develop a data processing system for a large in Vitro Fertilization/Gamete Intrafallopian Transfer (IVF/GIFT) practice which would (1) require minimal data entry time, (2) be easy to operate, (3) be simple to construct (no knowledge of procedural language or programming necessary), and (4) quickly collate and reduce data. RESULTS: A database management system was successfully constructed on an Apple MacIntosh computer which met the above criteria. The key elements of this database were its user-friendly features (MacIntosh-based system), adaptability (user was constantly able to update and revise the program as informational needs changed), and ability to perform complex searches and data analyses imposed by the individual operators. CONCLUSIONS: The software and hardware described in this report were found to be highly effective in meeting the ever-changing administrative and clinical needs of our IVF/GIFT program.
A method is described for recording a child's performance with a computer-controlled audio-visual device designed to stimulate language behavior in nonspeaking children. From the recorded data a child's position can be estimated on a curve derived from normal children. This position could be of value in planning treatment for a nonspeaking child and assessing his progress.
An IBM AT monitoring system is the current version of a series of monitoring system developments at Vanderbilt University. This system and its predecessors have been used in over 800 cases to date. Within the past year, this system has been upgraded with a new serial communications board and with touchscreen input. The new communications board has allowed improved communication with serial devices in the operating room, and will allow for additional devices to be added. The most dramatic improvement in the system has come from the addition of touchscreen input. Our present use of this feature has dramatically improved a casual users ability to input data into the computer system, extensions are possible to entirely get rid of the necessity of any keyboard input of data to the system under normal operations.
In developing a large-scale Hospital Information System (HIS), a client-server architecture has been gaining in popularity. It is important to introduce a standard message protocol that is independent both on the database structure and on the vender's proprietary platform. We introduced Health Level Seven (HL7) to our hospital information system. From our experiences, although we had to modify the original HL7 specifications in order to introduce the protocol to a client-server HIS especially in the area of order entry and record-oriented query, it was found that HL7 can be adopted in a client-server HIS.
A model of the cardiovascular system is presented. The model includes representations of the left and right ventricles, a nonlinear multielement model of the aorta and its main branches, and lumped models of the systemic veins and the pulmonary circulation. A simulation of the intra-aortic balloon pump and representations of physiological compensatory mechanisms are also incorporated in the model. Parameters of the left ventricular model were set to simulate either the normal or failing canine circulation. Pressure and flow waveforms throughout the circulation as well as ventricular pressure and volume were calculated for the normal, failing, and assisted failing circulation. Cardiac oxygen supply and consumption were calculated from the model. They were used as direct indices of cardiac energy supply and utilization to assess the effects of cardiac assistance.
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Use of hospital information systems (HIS) are no longer limited to administrative functions. The addition to these systems of decision support capability is now a necessity. Development of the decision support modules requires a different software architecture than that employed by most HIS systems today. This paper describes the generic uses of decision support throughout the many hospital applications. Several levels of decision support are outlined with examples to illustrate the many areas where decision support is useful. At LDS Hospital in Salt Lake City, Utah we have developed an HIS using a new software architecture which supports the creation of decision support applications. This system uses a frame structure to represent knowledge. Examples of the frames and their syntax is presented. Using the frame tools which are provided, an application developer can easily develop and test decision support modules which interact directly with the clinical user and the patient database.
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