Threading

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Threading may refer to:

Thread (computing) smallest sequence of programmed instructions that can be managed independently by a scheduler

In computer science, a thread of execution is the smallest sequence of programmed instructions that can be managed independently by a scheduler, which is typically a part of the operating system. The implementation of threads and processes differs between operating systems, but in most cases a thread is a component of a process. Multiple threads can exist within one process, executing concurrently and sharing resources such as memory, while different processes do not share these resources. In particular, the threads of a process share its executable code and the values of its dynamically allocated variables and non-thread-local global variables at any given time.

Threading (epilation) method of hair removal

Threading is a method of hair removal originating in Iran, India and Central Asia. In more recent times it has gained popularity in Western countries, especially with a cosmetic application.

Threading is the process of creating a screw thread for screwing the nut and bolt. More screw threads are produced each year than any other machine element. There are many methods of generating threads, including subtractive methods ; deformative or transformative methods ; additive methods ; or combinations thereof.

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In computer science, the term threaded code refers to a programming technique where the code has a form that essentially consists entirely of calls to subroutines. It is often, but not only, found in compiler implementations that generate code in that form and/or are implemented in that form themselves. The code may be processed by an interpreter, or may simply be a sequence of machine code call instructions.

Sequence alignment

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the edit distance cost between strings in a natural language or in financial data.

Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles. It is also a product and services market, with an estimated value of $168 billion by 2017.

Tap, Taps, TAP or tapped may refer to:

Structural alignment

Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.

Thread pool

In computer programming, a thread pool is a software design pattern for achieving concurrency of execution in a computer program. Often also called a replicated workers or worker-crew model, a thread pool maintains multiple threads waiting for tasks to be allocated for concurrent execution by the supervising program. By maintaining a pool of threads, the model increases performance and avoids latency in execution due to frequent creation and destruction of threads for short-lived tasks. The number of available threads is tuned to the computing resources available to the program, such as parallel processors, cores, memory, and network sockets.

Biological small-angle scattering

Biological small-angle scattering is a small-angle scattering method for structure analysis of biological materials. Small-angle scattering is used to study the structure of a variety of objects such as solutions of biological macromolecules, nanocomposites, alloys, and synthetic polymers. Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are the two complementary techniques known jointly as small-angle scattering (SAS). SAS is an analogous method to X-ray and neutron diffraction, wide angle X-ray scattering, as well as to static light scattering. In contrast to other X-ray and neutron scattering methods, SAS yields information on the sizes and shapes of both crystalline and non-crystalline particles. When used to study biological materials, which are very often in aqueous solution, the scattering pattern is orientation averaged.

Protein methods are the techniques used to study proteins. There are experimental methods for studying proteins. Computational methods typically use computer programs to analyze proteins. However, many experimental methods require computational analysis of the raw data.

Protein threading, also known as fold recognition, is a method of protein modeling which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure. It differs from the homology modeling method of structure prediction as it is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do. Threading works by using statistical knowledge of the relationship between the structures deposited in the PDB and the sequence of the protein which one wishes to model.

Homology modeling method of protein structure prediction

Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein. Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.

Thread Level Speculation (TLS) is a technique to speculatively execute a section of computer code that is anticipated to be executed later in parallel with the normal execution on a separate independent thread. Such a speculative thread may need to make assumptions about the values of input variables. If these prove to be invalid the speculative thread will need to be discarded and squashed. If the assumptions are correct the program can complete in a shorter time provided the thread was able to be scheduled efficiently.

In computational biology, de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its amino acid primary sequence. The problem itself has occupied leading scientists for decades while still remaining unsolved. According to Science, the problem remains one of the top 125 outstanding issues in modern science. At present, some of the most successful methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure.

Multithreading (computer architecture) ability of a central processing unit (CPU) or a single core in a multi-core processor to execute multiple processes or threads concurrently

In computer architecture, multithreading is the ability of a central processing unit (CPU) to execute multiple processes or threads concurrently, supported by the operating system. This approach differs from multiprocessing. In a multithreaded application, the processes and threads share the resources of a single or multiple cores, which include the computing units, the CPU caches, and the translation lookaside buffer (TLB).

RAPTOR (software) protein threading software

RAPTOR is protein threading software used for protein structure prediction. It has been replaced by RaptorX, which is much more accurate than RAPTOR.

David Tudor Jones British bioinformatician

David Tudor Jones is a Professor of Bioinformatics, and Head of Bioinformatics Group in the University College London. He is also the director in Bloomsbury Center for Bioinformatics, which is a joint Research Centre between UCL and Birkbeck, University of London and which also provides bioinformatics training and support services to biomedical researchers. In 2013, he is a member of editorial boards for PLoS ONE, BioData Mining, Advanced Bioinformatics, Chemical Biology & Drug Design, and Protein: Structure, Function and Bioinformatics.

CS23D web server to generate 3D structural models from NMR chemical shifts

CS23D is a web server to generate 3D structural models from NMR chemical shifts. CS23D combines maximal fragment assembly with chemical shift threading, de novo structure generation, chemical shift-based torsion angle prediction, and chemical shift refinement. CS23D makes use of RefDB and ShiftX.

I-TASSER software for for protein structure prediction and refinement, and structure-based protein function annotations

I-TASSER is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences. It detects structure templates from the Protein Data Bank by a technique called fold recognition. The full-length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations. I-TASSER is one of the most successful protein structure prediction methods in the community-wide CASP experiments.

Asynchrony, in computer programming, refers to the occurrence of events independent of the main program flow and ways to deal with such events. These may be "outside" events such as the arrival of signals, or actions instigated by a program that take place concurrently with program execution, without the program blocking to wait for results. Asynchronous input/output is an example of the latter cause of asynchrony, and lets programs issue commands to storage or network devices that service these requests while the processor continues executing the program. Doing so provides a degree of parallelism.