Software: Sequential operating programs and data which instruct the functioning of a digital computer.Software Design: Specifications and instructions applied to the software.Software Validation: The act of testing the software for compliance with a standard.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Programming Languages: Specific languages used to prepare computer programs.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Image Processing, Computer-Assisted: A technique of inputting two-dimensional images into a computer and then enhancing or analyzing the imagery into a form that is more useful to the human observer.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Microcomputers: Small computers using LSI (large-scale integration) microprocessor chips as the CPU (central processing unit) and semiconductor memories for compact, inexpensive storage of program instructions and data. They are smaller and less expensive than minicomputers and are usually built into a dedicated system where they are optimized for a particular application. "Microprocessor" may refer to just the CPU or the entire microcomputer.Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.Imaging, Three-Dimensional: The process of generating three-dimensional images by electronic, photographic, or other methods. For example, three-dimensional images can be generated by assembling multiple tomographic images with the aid of a computer, while photographic 3-D images (HOLOGRAPHY) can be made by exposing film to the interference pattern created when two laser light sources shine on an object.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Systems Integration: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Computer Systems: Systems composed of a computer or computers, peripheral equipment, such as disks, printers, and terminals, and telecommunications capabilities.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Automatic Data Processing: Data processing largely performed by automatic means.Automation: Controlled operation of an apparatus, process, or system by mechanical or electronic devices that take the place of human organs of observation, effort, and decision. (From Webster's Collegiate Dictionary, 1993)ComputersComputer Communication Networks: A system containing any combination of computers, computer terminals, printers, audio or visual display devices, or telephones interconnected by telecommunications equipment or cables: used to transmit or receive information. (Random House Unabridged Dictionary, 2d ed)Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Radiology Information Systems: Information systems, usually computer-assisted, designed to store, manipulate, and retrieve information for planning, organizing, directing, and controlling administrative activities associated with the provision and utilization of radiology services and facilities.Workflow: Description of pattern of recurrent functions or procedures frequently found in organizational processes, such as notification, decision, and action.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Data Display: The visual display of data in a man-machine system. An example is when data is called from the computer and transmitted to a CATHODE RAY TUBE DISPLAY or LIQUID CRYSTAL display.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Image Interpretation, Computer-Assisted: Methods developed to aid in the interpretation of ultrasound, radiographic images, etc., for diagnosis of disease.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.Computer-Assisted Instruction: A self-learning technique, usually online, involving interaction of the student with programmed instructional materials.Automation, Laboratory: Controlled operations of analytic or diagnostic processes, or systems by mechanical or electronic devices.Hypermedia: Computerized compilations of information units (text, sound, graphics, and/or video) interconnected by logical nonlinear linkages that enable users to follow optimal paths through the material and also the systems used to create and display this information. (From Thesaurus of ERIC Descriptors, 1994)Radiographic Image Interpretation, Computer-Assisted: Computer systems or networks designed to provide radiographic interpretive information.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Artificial Intelligence: Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.Computing Methodologies: Computer-assisted analysis and processing of problems in a particular area.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Diagnosis, Computer-Assisted: Application of computer programs designed to assist the physician in solving a diagnostic problem.Observer Variation: The failure by the observer to measure or identify a phenomenon accurately, which results in an error. Sources for this may be due to the observer's missing an abnormality, or to faulty technique resulting in incorrect test measurement, or to misinterpretation of the data. Two varieties are inter-observer variation (the amount observers vary from one another when reporting on the same material) and intra-observer variation (the amount one observer varies between observations when reporting more than once on the same material).Computer-Aided Design: The use of computers for designing and/or manufacturing of anything, including drugs, surgical procedures, orthotics, and prosthetics.Documentation: Systematic organization, storage, retrieval, and dissemination of specialized information, especially of a scientific or technical nature (From ALA Glossary of Library and Information Science, 1983). It often involves authenticating or validating information.Equipment Design: Methods of creating machines and devices.Speech Recognition Software: Software capable of recognizing dictation and transcribing the spoken words into written text.Medical Records Systems, Computerized: Computer-based systems for input, storage, display, retrieval, and printing of information contained in a patient's medical record.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Online Systems: Systems where the input data enter the computer directly from the point of origin (usually a terminal or workstation) and/or in which output data are transmitted directly to that terminal point of origin. (Sippl, Computer Dictionary, 4th ed)Bayes Theorem: A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Information Systems: Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Proteome: The protein complement of an organism coded for by its genome.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Quality Control: A system for verifying and maintaining a desired level of quality in a product or process by careful planning, use of proper equipment, continued inspection, and corrective action as required. (Random House Unabridged Dictionary, 2d ed)Systems Biology: Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.Data Mining: Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.Phantoms, Imaging: Devices or objects in various imaging techniques used to visualize or enhance visualization by simulating conditions encountered in the procedure. Phantoms are used very often in procedures employing or measuring x-irradiation or radioactive material to evaluate performance. Phantoms often have properties similar to human tissue. Water demonstrates absorbing properties similar to normal tissue, hence water-filled phantoms are used to map radiation levels. Phantoms are used also as teaching aids to simulate real conditions with x-ray or ultrasonic machines. (From Iturralde, Dictionary and Handbook of Nuclear Medicine and Clinical Imaging, 1990)Hospital Information Systems: Integrated, computer-assisted systems designed to store, manipulate, and retrieve information concerned with the administrative and clinical aspects of providing medical services within the hospital.Computers, Handheld: A type of MICROCOMPUTER, sometimes called a personal digital assistant, that is very small and portable and fitting in a hand. They are convenient to use in clinical and other field situations for quick data management. They usually require docking with MICROCOMPUTERS for updates.Local Area Networks: Communications networks connecting various hardware devices together within or between buildings by means of a continuous cable or voice data telephone system.Databases as Topic: Organized collections of computer records, standardized in format and content, that are stored in any of a variety of computer-readable modes. They are the basic sets of data from which computer-readable files are created. (from ALA Glossary of Library and Information Science, 1983)Markov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.Tomography, X-Ray Computed: Tomography using x-ray transmission and a computer algorithm to reconstruct the image.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Diagnostic Imaging: Any visual display of structural or functional patterns of organs or tissues for diagnostic evaluation. It includes measuring physiologic and metabolic responses to physical and chemical stimuli, as well as ultramicroscopy.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Cone-Beam Computed Tomography: Computed tomography modalities which use a cone or pyramid-shaped beam of radiation.Signal Processing, Computer-Assisted: Computer-assisted processing of electric, ultrasonic, or electronic signals to interpret function and activity.Photography: Method of making images on a sensitized surface by exposure to light or other radiant energy.Word Processing: Text editing and storage functions using computer software.Computer Security: Protective measures against unauthorized access to or interference with computer operating systems, telecommunications, or data structures, especially the modification, deletion, destruction, or release of data in computers. It includes methods of forestalling interference by computer viruses or so-called computer hackers aiming to compromise stored data.Models, Theoretical: Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Medical Informatics: The field of information science concerned with the analysis and dissemination of medical data through the application of computers to various aspects of health care and medicine.Surgery, Computer-Assisted: Surgical procedures conducted with the aid of computers. This is most frequently used in orthopedic and laparoscopic surgery for implant placement and instrument guidance. Image-guided surgery interactively combines prior CT scans or MRI images with real-time video.Image Enhancement: Improvement of the quality of a picture by various techniques, including computer processing, digital filtering, echocardiographic techniques, light and ultrastructural MICROSCOPY, fluorescence spectrometry and microscopy, scintigraphy, and in vitro image processing at the molecular level.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Likelihood Functions: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Data Compression: Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.Search Engine: Software used to locate data or information stored in machine-readable form locally or at a distance such as an INTERNET site.Models, Anatomic: Three-dimensional representation to show anatomic structures. Models may be used in place of intact animals or organisms for teaching, practice, and study.Tandem Mass Spectrometry: A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection.Radiographic Image Enhancement: Improvement in the quality of an x-ray image by use of an intensifying screen, tube, or filter and by optimum exposure techniques. Digital processing methods are often employed.Artifacts: Any visible result of a procedure which is caused by the procedure itself and not by the entity being analyzed. Common examples include histological structures introduced by tissue processing, radiographic images of structures that are not naturally present in living tissue, and products of chemical reactions that occur during analysis.Microscopy: The use of instrumentation and techniques for visualizing material and details that cannot be seen by the unaided eye. It is usually done by enlarging images, transmitted by light or electron beams, with optical or magnetic lenses that magnify the entire image field. With scanning microscopy, images are generated by collecting output from the specimen in a point-by-point fashion, on a magnified scale, as it is scanned by a narrow beam of light or electrons, a laser, a conductive probe, or a topographical probe.Magnetic Resonance Imaging: Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques.Computer Storage Devices: Devices capable of receiving data, retaining data for an indefinite or finite period of time, and supplying data upon demand.Decision Making, Computer-Assisted: Use of an interactive computer system designed to assist the physician or other health professional in choosing between certain relationships or variables for the purpose of making a diagnostic or therapeutic decision.CD-ROM: An optical disk storage system for computers on which data can be read or from which data can be retrieved but not entered or modified. A CD-ROM unit is almost identical to the compact disk playback device for home use.Teleradiology: The electronic transmission of radiological images from one location to another for the purposes of interpretation and/or consultation. Users in different locations may simultaneously view images with greater access to secondary consultations and improved continuing education. (From American College of Radiology, ACR Standard for Teleradiology, 1994, p3)Monte Carlo Method: In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)Radiology: A specialty concerned with the use of x-ray and other forms of radiant energy in the diagnosis and treatment of disease.Biochemical Processes: Chemical reactions or functions, enzymatic activities, and metabolic pathways of living things.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Anatomy, Cross-Sectional: Descriptive anatomy based on three-dimensional imaging (IMAGING, THREE-DIMENSIONAL) of the body, organs, and structures using a series of computer multiplane sections, displayed by transverse, coronal, and sagittal analyses. It is essential to accurate interpretation by the radiologist of such techniques as ultrasonic diagnosis, MAGNETIC RESONANCE IMAGING, and computed tomography (TOMOGRAPHY, X-RAY COMPUTED). (From Lane & Sharfaei, Modern Sectional Anatomy, 1992, Preface)Information Management: Management of the acquisition, organization, storage, retrieval, and dissemination of information. (From Thesaurus of ERIC Descriptors, 1994)Mathematical Computing: Computer-assisted interpretation and analysis of various mathematical functions related to a particular problem.Chromatography, Liquid: Chromatographic techniques in which the mobile phase is a liquid.Feasibility Studies: Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project.Geographic Information Systems: Computer systems capable of assembling, storing, manipulating, and displaying geographically referenced information, i.e. data identified according to their locations.

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Mac OS X Server 1.0List of software development philosophies: This is a list of approaches, styles, and philosophies in software development not included in the category tree of software development philosophies. It contains also software development processes, software development methodologies and single practices, principles and laws.Jigsaw (power tool): A jigsaw power tool is a jigsaw made up of an electric motor and a reciprocating saw blade.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Immersive technologyRDF query language: An RDF query language is a computer language, specifically a query language for databases, able to retrieve and manipulate data stored in Resource Description Framework format.List of molecular graphics systems: This is a list of software systems that are used for visualizing macromolecules.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.SciDBImage fusion: In computer vision, Multisensor Image fusion is the process of combining relevant information from two or more images into a single image.Haghighat, M.Generalizability theory: Generalizability theory, or G Theory, is a statistical framework for conceptualizing, investigating, and designing reliable observations. It is used to determine the reliability (i.Conference and Labs of the Evaluation Forum: The Conference and Labs of the Evaluation Forum (formerly Cross-Language Evaluation Forum), or CLEF, is an organization promoting research in multilingual information access (currently focusing on European languages). Its specific functions are to maintain an underlying framework for testing information retrieval systems and to create repositories of data for researchers to use in developing comparable standards.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Visual 1050Volume rendering: 250px|thumb| A volume rendered cadaver head using view-aligned [[texture mapping and diffuse reflection]]Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.VisionxXAP Home Automation protocol: xAP is an open protocol used for home automation and supports integration of telemetry and control devices primarily within the home. Common communications networks include RS232, RS485, Ethernet& wireless.Calculator: An electronic calculator is a small, portable electronic device used to perform both basic operations of arithmetic and complex mathematical operations.Acknowledgement (data networks): In data networking, an acknowledgement (or acknowledgment) is a signal passed between communicating processes or computers to signify acknowledgement, or receipt of response, as part of a communications protocol. For instance, ACK packets are used in the Transmission Control Protocol (TCP) to acknowledge the receipt of SYN packets when establishing a connection, data packets while a connection is being used, and FIN packets when terminating a connection.CS-BLASTInverse probability weighting: Inverse probability weighting is a statistical technique for calculating statistics standardized to a population different from that in which the data was collected. Study designs with a disparate sampling population and population of target inference (target population) are common in application.DR Systems: DR Systems, Inc. is an independent provider of enterprise imaging and information management systems for hospitals, integrated healthcare networks and diagnostic imaging centers.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Screen buffer: In computing, a screen buffer is a part of computer memory used by a computer application for the representation of the content to be shown on the computer display.Protein subcellular localization prediction: Protein subcellular localization prediction (or just protein localization prediction) involves the computational prediction of where a protein resides in a cell.Human Proteinpedia: Human Proteinpedia is a portal for sharing and integration of human proteomic data,.Kandasamy et al.Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.List of sequenced eukaryotic genomesLattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Assay sensitivity: Assay sensitivity is a property of a clinical trial defined as the ability of a trial to distinguish an effective treatment from a less effective or ineffective intervention. Without assay sensitivity, a trial is not internally valid and is not capable of comparing the efficacy of two interventions.Proteomics Standards Initiative: The Proteomics Standards Initiative (PSI) is a working group of Human Proteome Organization. It aims to define data standards for proteomics in order to facilitate data comparison, exchange and verification.Kiten (program)Journal of Laboratory Automation: The Journal of Laboratory Automation is a bimonthly peer-reviewed scientific journal published by the Society for Laboratory Automation and Screening in partnership with SAGE Publications. The journal's editor-in-chief is Dean Ho (University of California Los Angeles).Hyperlinks in virtual worlds: Hyperlinks are, at present, a novel feature in virtual world platforms, aside from hyperlinks in the in-built chat clients between users' avatars. In the latter 2000s, however, a number of architectures were created for various decentralized virtual world platforms in order to facilitate easier travel of avatars between two or more separately-hosted grids or servers.Mexican International Conference on Artificial Intelligence: MICAI (short for Mexican International Conference on Artificial Intelligence) is the name of an annual conference covering all areas of Artificial Intelligence (AI), held in Mexico. The first MICAI conference was held in 2000.Andy HardyMatrix model: == Mathematics and physics ==Chromosome regionsComputer-aided diagnosis: In radiology, computer-aided detection (CADe), also called computer-aided diagnosis (CADx), are procedures in medicine that assist doctors in the interpretation of medical images. Imaging techniques in X-ray, MRI, and Ultrasound diagnostics yield a great deal of information, which the radiologist has to analyze and evaluate comprehensively in a short time.TebisPoint of care: Clinical point of care is when clinicians deliver healthcare products and services to patients at the time of care.Information at the Point of Care: Answering Clinical Questions.Beta encoder: A beta encoder is an analog to digital conversion (A/D) system in which a real number in the unit interval is represented by a finite representation of a sequence in base beta, with beta being a real number between 1 and 2. Beta encoders are an alternative to traditional approaches to pulse code modulation.DragonDictate: DragonDictate, Dragon Dictate, or Dragon for Mac, is proprietary speech recognition software. The older program, DragonDictate, was originally developed by Dragon Systems for Microsoft Windows.Atomic mass: right |thumb|200px|Stylized [[lithium-7 atom: 3 protons, 4 neutrons, & 3 electrons (total electrons are ~1/4300th of the mass of the nucleus). It has a mass of 7.Massive parallel sequencing: Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and became commercially available since 2005.Biological pathway: A biological pathway is a series of actions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein.Hyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Patient-Reported Outcomes Measurement Information System: The Patient Reported Outcomes Measurement Information System (PROMIS®) provides clinicians and researchers access to reliable, valid, and flexible measures of health status that assess physical, mental, and social well–being from the patient perspective. PROMIS measures are standardized, allowing for assessment of many patient-reported outcome domains—including pain, fatigue, emotional distress, physical functioning and social role participation—based on common metrics that allow for comparisons across domains, across chronic diseases, and with the general population.Plant Proteome Database: The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants.Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Analytical quality control: Analytical quality control, commonly shortened to AQC refers to all those processes and procedures designed to ensure that the results of laboratory analysis are consistent, comparable, accurate and within specified limits of precision.analytical quality control (AQC) program to ensure the highest level of confidence in reported data Constituents submitted to the analytical laboratory must be accurately described to avoid faulty interpretations, approximations, or incorrect results.List of systems biology conferences: Systems biology is a biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences.Process mining: Process mining is a process management technique that allows for the analysis of business processes based on event logs. The basic idea is to extract knowledge from event logs recorded by an information system.Imaging phantom: Phantom}}Palm (PDA): Palm handhelds were Personal Digital Assistants (PDAs) that ran the Palm OS.Heterogeneous network: A heterogeneous network is a network connecting computers and other devices with different operating systems and/or protocols. For example, local area networks (LANs) that connect Microsoft Windows and Linux based personal computers with Apple Macintosh computers are heterogeneous.Vladimir Andreevich Markov: Vladimir Andreevich Markov (; May 8, 1871 – January 18, 1897) was a Russian mathematician, known for proving the Markov brothers' inequality with his older brother Andrey Markov. He died of tuberculosis at the age of 25.Dense artery sign: In medicine, the dense artery sign or hyperdense artery sign is a radiologic sign seen on computer tomography (CT) scans suggestive of early ischemic stroke. In earlier studies of medical imaging in patients with strokes, it was the earliest sign of ischemic stroke in a significant minority of cases.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.PlanmecaDemodulation: Demodulation is the act of extracting the original information-bearing signal from a modulated carrier wave. A demodulator is an electronic circuit (or computer program in a software-defined radio) that is used to recover the information content from the modulated carrier wave.Outline of photography: The following outline is provided as an overview of and topical guide to photography:Word Juggler: Word Juggler was a word processor application by Quark, Inc. for the Apple IIe, IIc, and III computers.Salt (cryptography): In cryptography, a salt is random data that is used as an additional input to a one-way function that hashes a password or passphrase.Salts are closely related to the concept of nonce.Von Neumann regular ring: In mathematics, a von Neumann regular ring is a ring R such that for every a in R there exists an x in R such that . To avoid the possible confusion with the regular rings and regular local rings of commutative algebra (which are unrelated notions), von Neumann regular rings are also called absolutely flat rings, because these rings are characterized by the fact that every left module is flat.Translational bioinformatics: Translational Bioinformatics (TBI) is an emerging field in the study of health informatics, focused on the convergence of molecular bioinformatics, biostatistics, statistical genetics, and clinical informatics. Its focus is on applying informatics methodology to the increasing amount of biomedical and genomic data to formulate knowledge and medical tools, which can be utilized by scientists, clinicians, and patients.Image-guided surgery: Today, doctors are using computerized technologies that are familiar to people in the consumer world to help fight cancer in the operating room. An important example of that application is image guided surgery (IGS) and it helps surgeons perform safer and less invasive procedures and remove brain tumors that were once considered inoperable due to their size and/or location.Coles PhillipsDecoding methods: In coding theory, decoding is the process of translating received messages into codewords of a given code. There have been many common methods of mapping messages to codewords.Temporal analysis of products: Temporal Analysis of Products (TAP), (TAP-2), (TAP-3) is an experimental technique for studyingLempel–Ziv–Oberhumer: Lempel–Ziv–Oberhumer (LZO) is a lossless data compression algorithm that is focused on decompression speed.Ark (search engine): Ark is a personal search engine that uses filters such as hometown, current city, high school, college, gender, relationship status, employee, and interests, to search for new people, old classmates, old friends or acquaintances, and new business contacts. Features include managing users' inboxes from their mobile devices, and syncing data from their Yahoo, Aol, Gmail or Google Apps email accounts, while also finding information about whom they are communicating with.Tandem mass spectrometry: 300 px|right|thumb|A [[Quadrupole mass analyzer|quadrupole time-of-flight hybrid tandem mass spectrometer.]]Unsharpness

(1/21774) An effective approach for analyzing "prefinished" genomic sequence data.

Ongoing efforts to sequence the human genome are already generating large amounts of data, with substantial increases anticipated over the next few years. In most cases, a shotgun sequencing strategy is being used, which rapidly yields most of the primary sequence in incompletely assembled sequence contigs ("prefinished" sequence) and more slowly produces the final, completely assembled sequence ("finished" sequence). Thus, in general, prefinished sequence is produced in excess of finished sequence, and this trend is certain to continue and even accelerate over the next few years. Even at a prefinished stage, genomic sequence represents a rich source of important biological information that is of great interest to many investigators. However, analyzing such data is a challenging and daunting task, both because of its sheer volume and because it can change on a day-by-day basis. To facilitate the discovery and characterization of genes and other important elements within prefinished sequence, we have developed an analytical strategy and system that uses readily available software tools in new combinations. Implementation of this strategy for the analysis of prefinished sequence data from human chromosome 7 has demonstrated that this is a convenient, inexpensive, and extensible solution to the problem of analyzing the large amounts of preliminary data being produced by large-scale sequencing efforts. Our approach is accessible to any investigator who wishes to assimilate additional information about particular sequence data en route to developing richer annotations of a finished sequence.  (+info)

(2/21774) A computational screen for methylation guide snoRNAs in yeast.

Small nucleolar RNAs (snoRNAs) are required for ribose 2'-O-methylation of eukaryotic ribosomal RNA. Many of the genes for this snoRNA family have remained unidentified in Saccharomyces cerevisiae, despite the availability of a complete genome sequence. Probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snoRNAs, snR50 to snR71. Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs.  (+info)

(3/21774) Randomly amplified polymorphic DNA analysis of clinical and environmental isolates of Vibrio vulnificus and other vibrio species.

Vibrio vulnificus is an estuarine bacterium that is capable of causing a rapidly fatal infection in humans. A randomly amplified polymorphic DNA (RAPD) PCR protocol was developed for use in detecting V. vulnificus, as well as other members of the genus Vibrio. The resulting RAPD profiles were analyzed by using RFLPScan software. This RAPD method clearly differentiated between members of the genus Vibrio and between isolates of V. vulnificus. Each V. vulnificus strain produced a unique band pattern, indicating that the members of this species are genetically quite heterogeneous. All of the vibrios were found to have amplification products whose sizes were within four common molecular weight ranges, while the V. vulnificus strains had an additional two molecular weight range bands in common. All of the V. vulnificus strains isolated from clinical specimens produced an additional band that was only occasionally found in environmental strains; this suggests that, as is the case with the Kanagawa hemolysin of Vibrio parahaemolyticus, the presence of this band may be correlated with the ability of a strain to produce an infection in humans. In addition, band pattern differences were observed between encapsulated and nonencapsulated isogenic morphotypes of the same strain of V. vulnificus.  (+info)

(4/21774) Melanoma cells present a MAGE-3 epitope to CD4(+) cytotoxic T cells in association with histocompatibility leukocyte antigen DR11.

In this study we used TEPITOPE, a new epitope prediction software, to identify sequence segments on the MAGE-3 protein with promiscuous binding to histocompatibility leukocyte antigen (HLA)-DR molecules. Synthetic peptides corresponding to the identified sequences were synthesized and used to propagate CD4(+) T cells from the blood of a healthy donor. CD4(+) T cells strongly recognized MAGE-3281-295 and, to a lesser extent, MAGE-3141-155 and MAGE-3146-160. Moreover, CD4(+) T cells proliferated in the presence of recombinant MAGE-3 after processing and presentation by autologous antigen presenting cells, demonstrating that the MAGE-3 epitopes recognized are naturally processed. CD4(+) T cells, mostly of the T helper 1 type, showed specific lytic activity against HLA-DR11/MAGE-3-positive melanoma cells. Cold target inhibition experiments demonstrated indeed that the CD4(+) T cells recognized MAGE-3281-295 in association with HLA-DR11 on melanoma cells. This is the first evidence that a tumor-specific shared antigen forms CD4(+) T cell epitopes. Furthermore, we validated the use of algorithms for the prediction of promiscuous CD4(+) T cell epitopes, thus opening the possibility of wide application to other tumor-associated antigens. These results have direct implications for cancer immunotherapy in the design of peptide-based vaccines with tumor-specific CD4(+) T cell epitopes.  (+info)

(5/21774) Imagene: an integrated computer environment for sequence annotation and analysis.

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page:  (+info)

(6/21774) Stem Trace: an interactive visual tool for comparative RNA structure analysis.

MOTIVATION: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. RESULTS: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stem Trace elucidates preservation of structures in this region across the various strains of HIV. AVAILABILITY: The program can be made available upon request. It runs on SUN, SGI and DEC (Compaq) Unix workstations.  (+info)

(7/21774) Bayesian inference on biopolymer models.

MOTIVATION: Most existing bioinformatics methods are limited to making point estimates of one variable, e.g. the optimal alignment, with fixed input values for all other variables, e.g. gap penalties and scoring matrices. While the requirement to specify parameters remains one of the more vexing issues in bioinformatics, it is a reflection of a larger issue: the need to broaden the view on statistical inference in bioinformatics. RESULTS: The assignment of probabilities for all possible values of all unknown variables in a problem in the form of a posterior distribution is the goal of Bayesian inference. Here we show how this goal can be achieved for most bioinformatics methods that use dynamic programming. Specifically, a tutorial style description of a Bayesian inference procedure for segmentation of a sequence based on the heterogeneity in its composition is given. In addition, full Bayesian inference algorithms for sequence alignment are described. AVAILABILITY: Software and a set of transparencies for a tutorial describing these ideas are available at  (+info)

(8/21774) E-CELL: software environment for whole-cell simulation.

MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at:  (+info)

Free Software F

  • Stallman later established the Free Software Foundation in 1985 to support the movement. (
  • The Free Software Foundation also believes all software needs free documentation , in particular because conscientious programmers should be able to update manuals to reflect modification that they made to the software, but deems the freedom to modify less important for other types of written works. (
  • Free Software Foundation Latin America (FSFLA) è l'organizzazione sorella in America latina della Free Software Foundation. (
  • Free Software Foundation Free Software Foundation of India Free Software Foundation Europe Linux-libre Free Software Directory Associazione per il software libero Richard Stallman Altri progetti Wikimedia Commons Wikimedia Commons contiene immagini o altri file su Free Software Foundation Latin America Sito di FSFLA, (


  • The core work of the free software movement focused on software development. (


  • Consider the Therac-25 [], a well-known radiation therapy machine which killed at least 5 patients due to a software bug. (


  • but the majority of software developers don't work in those environments. (


  • What I mean is it's very easy to come up with the examples of where this sort of strictness of design is necessary (medical software, flight control, etc - stuff where people's lives are at stake! (


  • Creating the software with a tool like Alloy would have caught the bug (probably) but it would have also taken a hell of a lot longer to get the software written. (


  • Some supporters of the free software movement take up public speaking , or host a stall at software-related conferences to raise awareness of software freedom. (