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PubMed2006

Enabling computer models of the heart for high-performance computers and the grid.

Although it is now feasible to compute multi-cellular models of the heart on a personal desktop or laptop computer, it is not feasible to undertake the detailed sweeps of high-dimensional parameter spaces required if we are to undertake in silico experimentation of the complex processes that constitute heart disease. For this research, modelling requirements move rapidly beyond the limit of commodity computers' resource both in terms of their memory footprint and the speed of calculation, so that multi-processor architectures must be considered. In addition, as such models have become more mature and have been validated against experimental data, there is increasing pressure for experimentalists to be able to make use of these models themselves as a key tool for hypothesis formulation and in planning future experimental studies to test those hypotheses. This paper discusses our initial experiences in a large-scale project (the Integrative Biology (IB) e-Science project) aimed at meeting these dual aims. We begin by putting the research in context by describing in outline the overall aims of the IB project, in particular focusing on the challenge of enabling novice users to make full use of high-performance resources without the need to gain detailed technical expertise in computing. We then discuss our experience of adapting one particular heart modelling package, Cellular Open Resource, and show how the solving engine of this code was dissected from the rest of the package, ported to C++ and parallelized using the Message-Passing Interface. We show that good parallel efficiency and realistic memory reduction can be achieved on simple geometries. We conclude by discussing lessons learnt in this process.

Action Potentials↗
PubMed2001

An Internet-based simulation model for nitrogen management in agricultural settings.

Complex chemical, physical, and biological processes mediate nitrogen (N) transformations and movement during agricultural production, making the optimization of fertilizer use and environmental protection exceedingly difficult. Various computer models have been developed to simulate the site-specific fate and transport of N resulting from different crop production scenarios, but these models are very complex and difficult to use for most farmers, consultants, and conservationists. In an effort to facilitate access and simplify the use of sophisticated models, the U.S. Department of Agriculture (USDA) has developed an Internet-based nitrogen analysis tool. Based on the Nitrate Leaching and Economic Analysis Package (NLEAP), the Web site allows a user to conduct multiyear N simulation modeling specific to a crop field. Servers handle much of the required data assembly and formatting, thus sparing the user"s resources. Model runs are executed on the servers and the results are transmitted to the user. This new tool is presented along with early implementation results.

Agriculture↗
PubMed2004

The Ensembl analysis pipeline.

The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules ("Runnables" and "RunnableDBs") which are 'wrappers' for a variety of commonly used analysis tools. These retrieve sequence data from a relational database, run the analysis, and write the results back to the database. They inherit from a common interface, which simplifies the writing of new wrapper modules. On top of this sits a job submission system (the "RuleManager") which allows efficient and reliable submission of large numbers of jobs to a compute farm. Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis.

Base Sequence↗
PubMed2006

Solving structures of protein complexes by molecular replacement with Phaser.

Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ;tree search with pruning' approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ;automated MR' mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

Algorithms↗
PubMed2003

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.

A control system for high-throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

Crystallography↗
PubMed1989

OVERSEER: a prototype expert system for monitoring drug treatment in the psychiatric clinic.

This paper describes the development of OVERSEER: a prototype knowledge-based system that monitors the drug treatment of psychiatric patients in real time. Using treatment protocols developed by the expert clinician, OVERSEER monitors the drug treatment process and issues alerts when standard clinical practices are not followed or when laboratory results are abnormal. Written in Prolog, OVERSEER is designed to interface directly with the hospital's database, and, thereby, utilizes all available pharmacy and laboratory data. Moreover, unlike the interactive expert systems developed for the psychiatric clinic, OVERSEER does not require extensive data entry by the clinician. Consequently, the chief benefit of OVERSEER's monitoring approach is the unobtrusive manner in which it evaluates psychopharmacological treatment and provides information regarding patient management to the hospital.

Drug Therapy, Computer-Assisted↗
PubMed1990

A logical state model of reentrant ventricular activation.

The ventricular surface of the heart was modeled as two-dimensional, 4096 element, network of cells connected logically to each other. An ischemic area was represented by a central core of prolonged refractoriness, distributed into eccentrically-layered elliptical contours such that refractoriness declined along varying gradients to the surrounding normal area. Propagation of cardiac action potentials was stimulated by five sequential states ranging from activation to inactivation. Reentrant activation was induced by premature stimulation of the network and resembled a "figure 8" type reentry seen experimentally. Activation patterns of reentry appeared as two propagation wavefronts which traveled around the ends of a continuous line of functional conduction block, merged into a single wavefront, then conducted slowly along a retrograde path to reactivate a region proximal to the block. Reentry could be prevented by modifying the distribution of recovery of excitability through stimulation at two strategically located sites during basic rhythm. Prevention occurred when the second site was situated in an area of prolonged refractoriness, just distal to the line of block. These simulations indicate that reentrant activation is characterized by the formation of long lines of conduction block which occur along a border of steeply graded refractoriness, and retrograde slow conduction which occurs along a more shallow refractory gradient. The occurrence of reentry is dependent on: 1) the coupling interval of the premature stimulus, 2) the location of the stimulus relative to the maximum refractory gradient, and 3) the activation sequence of the basic paced beats. Thus, this paper presents an efficient logical state model of cardiac activation which simulates experimentally observed activation patterns of reentry and its prevention.

Action Potentials↗
PubMed1997

Calcium ion current from an extracellular electrolyte toward a channel opening in an insulating membrane: quantitative model with rotational symmetry.

A mathematical model of three-dimensional (3-D) ion transport is formulated in an approximation assuming rotational symmetry. The model consists of three particle-conservation equations for sodium, calcium, and chlorine ions complemented with the Poisson equation. The numerical method of solution is based on the Gummel-Scharfetter semianalytical approach, the program is written in FORTRAN and the system of discrete equations is solved explicitly in the axial direction and by iterations in the radial direction. The present report deals with calcium flux toward a channel opening in an insulating impermeable membrane, assuming depolarization to zero potential. The initial homogeneous concentrations of sodium, calcium, and chlorine ions are 8.729 x 10(19), 6.02 x 10(17), and 8.849 x 10(19) (cm-3), respectively, corresponding to molar concentrations of 145-mM NaCl and 1-mM of CaCl2; the calcium concentration in the circle representing the channel entry is set at 0.1 microM, corresponding approximately to the concentration of free calcium ions in the cytoplasm. The calculations were carried out up to 3 microseconds. The calcium flux caused a perturbation of quasi-neutrality and the formation of a space charge, which reached the maximum value (i.e., maximum in absolute value) of -0.2 Ccm-3 at the channel entry; the corresponding maximum of the axial component of the electric field was about 1 kV/cm. The maximum value of the calcium current was 0.362 pA, decreasing to 0.283 pA at 3 microseconds. A review of several experimental studies of calcium currents yielded the average current values for higher and lower conductance channels (mainly L- and T-type) 0.76 and 0.42 pA, respectively. This implies that, at Ca++ concentrations of 1 mM or lower the calcium ion current may be limited by the ion influx from an extracellular medium.

Animals↗
PubMed1991

Parametric classification of segments in ocular nystagmus.

A new method for nystagmus classification, using system identification techniques, is presented. We formulate a system whose input is head position and whose output is eye position. We approximate this system with an autoregressive with exogenous input (ARX) model which relates the input and output (transfer function) regardless of the temporal profile for the sensory stimulation. The system is then identified using a least squares criteria and three indicators are produced. From these a flag is produced that marks slow and fast phases as well as blinks and bad data segments. Tests with simulated and real data are presented and indicate that the segment classification is remarkably insensitive to recording noise and that it is more robust than previous techniques. Operator intervention is minimal. We expect the method to be applicable for all types of ocular nystagmus. Here, however, we illustrate our results only in the context of the vestibuloocular reflex (VOR). A discussion explains how this method can also be applied for optokinetic (OKN) or pursuit nystagmus.

Algorithms↗
PubMed1998

Design and development of an interactive medical teleconsultation system over the World Wide Web.

The objective of the medical teleconsultation system presented in this paper is to demonstrate the use of the World Wide Web (WWW) for telemedicine and interactive medical information exchange. The system, which is developed based on Java, could provide several basic Java tools to fulfill the requirements of medical applications, including a file manager, data tool, bulletin board, and digital audio tool. The digital audio tool uses point-to-point structure to enable two physicians to communicate directly through voice. The others use multipoint structure. The file manager manages the medical images stored in the WWW information server, which come from a hospital database. The data tool supports cooperative operations on the medical data between the participating physicians. The bulletin board enables the users to discuss special cases by writing text on the board, send their personal or group diagnostic reports on the cases, and reorganize the reports and store them in its report file for later use. The system provides a hardware-independent platform for physicians to interact with one another as well as to access medical information over the WWW.

Internet↗
PubMed2000

The thought translation device (TTD) for completely paralyzed patients.

The thought translation device trains locked-in patients to self-regulate slow cortical potentials (SCP's) of their electroencephalogram (EEG). After operant learning of SCP self-control, patients select letters, words or pictograms in a computerized language support program. Results of five respirated, locked-in-patients are described, demonstrating the usefulness of the thought translation device as an alternative communication channel in motivated totally paralyzed patients with amyotrophic lateral sclerosis.

Biofeedback, Psychology↗