Parallel programming modelIn computing, a parallel programming model is an abstraction of parallel computer architecture, with which it is convenient to express algorithms and their composition in programs. The value of a programming model can be judged on its generality: how well a range of different problems can be expressed for a variety of different architectures, and its performance: how efficiently the compiled programs can execute. The implementation of a parallel programming model can take the form of a library invoked from a sequential language, as an extension to an existing language, or as an entirely new language.
Sequence homologySequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs). Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity.
Data parallelismData parallelism is parallelization across multiple processors in parallel computing environments. It focuses on distributing the data across different nodes, which operate on the data in parallel. It can be applied on regular data structures like arrays and matrices by working on each element in parallel. It contrasts to task parallelism as another form of parallelism. A data parallel job on an array of n elements can be divided equally among all the processors.
Multiple sequence alignmentMultiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.
Structural alignmentStructural 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.
Logic synthesisIn computer engineering, logic synthesis is a process by which an abstract specification of desired circuit behavior, typically at register transfer level (RTL), is turned into a design implementation in terms of logic gates, typically by a computer program called a synthesis tool. Common examples of this process include synthesis of designs specified in hardware description languages, including VHDL and Verilog. Some synthesis tools generate bitstreams for programmable logic devices such as PALs or FPGAs, while others target the creation of ASICs.
Single-molecule real-time sequencingSingle-molecule real-time (SMRT) sequencing is a parallelized single molecule DNA sequencing method. Single-molecule real-time sequencing utilizes a zero-mode waveguide (ZMW). A single DNA polymerase enzyme is affixed at the bottom of a ZMW with a single molecule of DNA as a template. The ZMW is a structure that creates an illuminated observation volume that is small enough to observe only a single nucleotide of DNA being incorporated by DNA polymerase. Each of the four DNA bases is attached to one of four different fluorescent dyes.
BioinformaticsBioinformatics (ˌbaɪ.oʊˌɪnfɚˈmætɪks) is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
GenomicsGenomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism.
Computational scienceComputational science, also known as scientific computing, technical computing or scientific computation (SC), is a division of science that uses advanced computing capabilities to understand and solve complex physical problems. This includes Algorithms (numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve sciences (e.
Energy auditAn energy audit is an inspection survey and an analysis of energy flows for energy conservation in a building. It may include a process or system to reduce the amount of energy input into the system without negatively affecting the output. In commercial and industrial real estate, an energy audit is the first step in identifying opportunities to reduce energy expense and carbon footprint. When the object of study is an occupied building then reducing energy consumption while maintaining or improving human comfort, health and safety are of primary concern.
OpenCLOpenCL (Open Computing Language) is a framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-programmable gate arrays (FPGAs) and other processors or hardware accelerators. OpenCL specifies programming languages (based on C99, C++14 and C++17) for programming these devices and application programming interfaces (APIs) to control the platform and execute programs on the compute devices.
