DNA计算机的研究和展望

DNA计算机是计算机科学和分子生物学互相结合、互相渗透而产生的新兴交叉研究领域.目前已取得较大进展.DNA计算机是以编码的DNA序列为运算对象,通过分子生物学的运算操作以解决复杂的数学难题.DNA计算机的重要特点是信息容量的巨量性和密集性,和处理操作的高度并行性,通过强力搜索策略迅速得出正确的答案,从而使其运算速度大大超过常规计算机的计算速度.介绍了DNA计算机的近期进展和工作原理及其分子生物学的运算操作过程.并对DNA计算机的未来发展前景及在生物信息学中的意义,进行了分析和讨论.     

Demonstration of a universal surface DNA computer

A fundamental concept in computer science is that of the universal Turing machine, which is an abstract definition of a general purpose computer. A general purpose (universal) computer is defined as one which can compute anything that is computable. It has been shown that any computer which is able to simulate Boolean logic circuits of any complexity is such a general purpose computer. The field of DNA computing was founded in 1994 by Adleman's solution of a 7-bit instance of the Hamiltonian path problem. This work, as well as most of the subsequent experimental and theoretical investigations in the area, focused primarily upon the solution of NP-complete problems, which are a subset of the larger universal class of problems. In the present work a surface DNA computer capable of simulating Boolean logic circuits is demonstrated. This was done by constructing NOR and OR gates and combining them into a simple logic circuit. The NOR gate is one of the universal gates in Boolean logic, meaning that any other logic gate can be built from it alone. The circuit was solved using DNA-based operations, demonstrating the universal nature of this surface DNA computing model.     

An introduction to hybrid computers and their application to optimization problems

The author, who is Secretary of the Analog Section of the British Computer Society, describes the way in which some of the logic components of a parallel logic analog computer function, and goes on to discuss the use of such a computer in optimization problems, as for instance in finding the best estimates of the parameters on compartmentation analysis of isotopic tracer experiments. The increased power which is gained when an analog computer is coupled to (hybridized with) a general purpose digital computer is then discussed, as shown for example in the increased speed of random-search optimization techniques when an analog computer is used to integrate the differential equations, or the improvement in steepest ascent methods when the parallel logic can be used to keep the hill-climb path continuously on the line of steepest ascent. Finally, the use of a hybrid computer in solving partial differential equations is briefly outlined.     

Does the computer act like the braine, or like any biological cell?

A new conception of computer functioning is proposed, which suggests that a computer is a reactor in which a unique enzymic reaction at a single operation mode occurs. The analogy between informatics and enzymology is considered. In the context of the parallelism proposed, the work of the brain is analogous to the work of a global computer network. Not the brain as a network of neuron processors but a network of computers as the brain!     

Efficient interaction for automated chromosome analysis using asynchronous parallel processes.

It is likely that any practical automated chromosome analysis system will be interactive. To prevent long pauses in the stream of operator interactions, it is necessary, if using standard computer hardware, to configure for asynchronous and parallel operation. A system is presented which uses several computer processors, which can support one or more operators, and which divides processing into interactive and noninteractive sections, smoothes the rate of presentation of interactions, and keeps both the operator and the computer fully employed.     

Image processing software for enhanced visualization of faint or noisy autoradiographic images

A computer program for digital image processing is described which can be implemented using scanning densitometer hardware pre-existing in most biology departments plus computer video hardware which may either pre-exist in the biology department or would represent a moderate upgrade over an already planned computer purchase. The primary purpose of this computer program is to provide contrast enhancement of faint or low contrast autoradiograph images and to implement background subtraction and digital smoothing methods which permit visualization of blurry electrophoresis bands against noisy backgrounds. However, the program also has modest editing capabilities that allow its use in the routine preparation of images for publication. Finally, the program has facilities for deblurring, edge enhancement and multiple image averaging, which give it usefulness in other forms of photographic analysis.     

DNA计算机原理、现状及发展

DNA计算机是一种基于DNA生化反应 ,与传统计算机完全不同的新型生物计算机。本文概述了DNA计算机的原理、特点与现状。并对其发展进行展望     

On the interpretation of biochemical data by molecular dynamics computer simulation.

The application of computer simulation to molecular systems of biochemical interest is reviewed. It is shown that computer simulation is a tool complementary to experimental methods, which can be used to access atomic details inaccessible to experimental probes. Examples are given in which computer simulation augments the experimental information by providing an atomic picture of high resolution with respect to space, energy or time. The usefulness of a computer simulation largely depends on its quality. The most important factors that limit the accuracy of simulated results are discussed. The accuracy of different simulation studies can differ by orders of magnitude. The accuracy will depend on the type of biomolecular system and process studied. It will also depend on the choice of force field, the simulation set-up and the protocol that is used. A list of quality-determining factors is given, which may be useful when interpreting simulation studies appearing in the literature.     

Interfacing a flow cytometer computer with a PC-based patient information system

We have established an interface between our flow cytometer's computer and the personal computer (PC) which supports our patient database system. The PC has been equipped with a commercially available IEEE-488 bus interface board which is connected to the interface bus of the cytometer's Hewlett-Packard 9000/300 computer (HP). The PC is set as a bus device with the same address as that of the HP's printer. It is programmed to examine the stream of data sent to the printer and extract from it and store in an MS-DOS text file selected information which subsequently may be transferred to the database system.     

Simulating complex intracellular processes using object-oriented computational modelling

The aim of this paper is to give an overview of computer modelling and simulation in cellular biology, in particular as applied to complex biochemical processes within the cell. This is illustrated by the use of the techniques of object-oriented modelling, where the computer is used to construct abstractions of objects in the domain being modelled, and these objects then interact within the computer to simulate the system and allow emergent properties to be observed. The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation.     

A computer program for displaying two-dimensional gel electrophoresis data

A computer program is described which facilitates comparison between the pattern of spots seen on different two-dimensional polyacrylamide electrophoresis gels. Essentially, the position of each spot is replotted on a graph by the computer using its molecular weight and isoelectric point as coordinates. An intensity factor is also assigned to each point by the operator which will determine the size and shape of the final plotted spot on the computer drawn figure. The resulting plot makes it more feasible to compare patterns of spots between independently run two-dimensional electrophoresis gels.     

A semi-automated method for the reading of nucleic acid sequencing gels.

A collection of computer programs is described which permit automatic entering of nucleotide sequence data directly from an autoradiograph into a computer. This collection, called DIGITPAD, makes use of a digitizing tablet for the data entry and allows the rapid and accurate transfer of the sequence into the computer.     

Knowledge-based design of artificial worlds

We review the concepts of knowledge representation and modelling and simulation methodology which facilitate computer exploration of alternative artificial worlds, such as self-sufficient human habitats. An object-oriented computer environment which supports such simulation studies is briefly described. A simplified example of an artificial world model is given to demonstrate the power of the approach.     

医院计算机网络信息资源管理的优化策略探析

计算机网络技术在医院信息资源管理中的普遍应用在很大程度上优化医院的工作方式,加强医疗信息的整合能力,提升医院的工作效率,在应用中计算机网络技术发挥重要作用。我们从医院计算机网络信息资源的内涵及特点入手,分析当前医院信息资源管理现状,最后针对医院信息管理现状中出现的具体问题,提出相应的优化策略,以期对以后计算机网络技术在医院信息资源管理中的进一步研究有所裨益。     

PC-based system for an objective quantification of manual movement disability for clinical and scientific purposes

In clinical management and research of movement disorders exact knowledge about the extent of motor impairment is essential. This paper presents a computer program which allows for an objective measurement of manual movement disability. The program was developed for standard hardware and can easily be used in a variety of clinical and research environments. The program runs on MS-DOS computers and uses a Microsoft computer mouse as the only input device. The temporal resolution is 100 Hz, the spatial resolution 400 dots per inch. The user may choose between standard test sets or he may design sets according to his individual needs from a pool of available protocols which includes tracking tasks, ballistic tasks, complex sequential tasks, and finger tapping. All tasks are implemented in a similar way in order to keep the test environment as consistent as possible for the patient. The patient must usually carry out movements which correspond to the movements of a target symbol on the computer screen. This entails the manipulation of a follower symbol, also visible on the computer screen, via the computer mouse. The program itself and the theoretical background of the protocols are described in the paper. Additionally, preliminary results from pilot experiments are presented.     

A mobile agent model for fault-tolerant manipulation on distributed objects

In this paper, we discuss how to realize fault-tolerant applications on distributed objects. Servers supporting objects can be fault-tolerant by taking advantage of replication and checkpointing technologies. However, there is no discussion on how application programs being performed on clients are tolerant of clients faults. For example, servers might block in the two-phase commitment protocol due to the client fault. We newly discuss how to make application programs fault-tolerant by taking advantage of mobile agent technologies where a program can move from a computer to another computer in networks. An application program to be performed on a faulty computer can be performed on another operational computer by moving the program in the mobile agent model. In this paper, we discuss a transactional agent model where a reliable and efficient application for manipulating objects in multiple computers is realized in the mobile agent model. In the transactional agent model, only a small part of the application program named routing subagent moves around computers. A routing subagent autonomously finds a computer which to visit next. We discuss a hierarchical navigation map which computer should be visited price to another computer in a transactional agent. A routing subagent makes a decision on which computer visit for the hierarchical navigation map. Programs manipulating objects in a computer are loaded to the computer on arrival of the routing subagent in order to reduce the communication overhead. This part of the transactional agent is a manipulating subagent. The manipulation subagent still exists on the computer even after the routing subagent leaves the computer in order to hold objects until the commitment. We assume every computer may stop by fault while networks are reliable. There are kinds of faulty computers for a transactional agent; current, destination, and sibling computers where a transactional agent now exists, will move, and has visited, respectively. The types of faults are detected by neighbouring manipulation subagents by communicating with each other. If some of the manipulation subagents are faulty, the routing subagent has to be aborted. However, the routing subagent is still moving. We discuss how to efficiently deliver the abort message to the moving routing subagent. We evaluate the transactional agent model in terms of how long it takes to abort the routing subagent if some computer is faulty.

Effect of computer use in the consultation on the delivery of care.

The effects of the use of a computer on the delivery of care in consultations in general practice were examined. In this trial a computer system provided for the review and update of patients'' medical histories, notes on doctor-patient contacts, and information on repeat prescribing. Thirty consultations in which the computer system was used and 30 consultations in which no computer was used were matched individually for the doctor consulted, the sex and age of the patient, and the presenting problem(s). Six independent general practitioners blind rated each consultation for the standard of care attained. A minor negative effect of computer use on the doctors'' clinical performance was found. We suggest, however, that this small effect would disappear if a computer system was used routinely.     

Computer assisted screening: effect on the patient and his consultation.

The initial impact of computer assisted preventive screening in general practice consultations has been monitored. The technology has not been found stressful by patients, and the power of the consultation to alleviate low arousal has been increased by computer use. No appreciable increase in the durations of consultation was detected, despite an average computer initiated input of two minutes eight seconds. The computer has successfully prompted preventive screening and health education with a sixfold increase in the number of potentially relevant procedures being mentioned. The actual information presented by the computer has been shown to be crucial, with the terminal''s mere presence an ineffective reminder. The computer terminal was used in 65% of the consultations for which it was available, which, if sustained, represents an effective screening programme for attending patients.     

Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time

The problem of determining a phylogeny of maximum parsimony from a given set of protein sequences is defined. It is shown that this problem is what is called, in computer science, NP-complete. The implication of this result is that it is equivalent in difficulty to a host of other problems in combinatorial optimization which are notorious for their intractability. This implies that it is more fruitful to attempt to develop heuristic techniques (which do not guarantee maximum parsimony but which do run in reasonable computer time) than to try to develop exact algorithms for phylogeny construction