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). This is then reported as a text string, called a read. Some DNA sequencers can be also considered optical instruments as they analyze light signals originating from fluorochromes attached to nucleotides.
Eclipse is an integrated development environment (IDE) used in computer programming. It contains a base workspace and an extensible plug-in system for customizing the environment. It is the second-most-popular IDE for Java development, and, until 2016, was the most popular. Eclipse is written mostly in Java and its primary use is for developing Java applications, but it may also be used to develop applications in other programming languages via plug-ins, including Ada, ABAP, C, C++, C#, Clojure, COBOL, D, Erlang, Fortran, Groovy, Haskell, JavaScript, Julia, Lasso, Lua, NATURAL, Perl, PHP, Prolog, Python, R, Ruby, Rust, Scala, and Scheme. It can also be used to develop documents with LaTeX and packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java and Scala, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others.
BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence alignment, biological database parsing, structural biology and other bioinformatics tasks. BioRuby is released under the GNU GPL version 2 or Ruby licence and is one of a number of Bio* projects, designed to reduce code duplication.
This article provides basic comparisons for notable text editors. More feature details for text editors are available from the Category of text editor features and from the individual products' articles. This article may not be up-to-date or necessarily all-inclusive.
Heinrich Magnus Manske is a senior staff scientist at the Wellcome Trust Sanger Institute in Cambridge, UK and a software developer of one of the first versions of the MediaWiki software, which powers Wikipedia.
Gramps is a free and open source genealogy software. Gramps is programmed in Python using PyGObject. It uses Graphviz to create relationship graphs.
The nested sampling algorithm is a computational approach to the Bayesian statistics problems of comparing models and generating samples from posterior distributions. It was developed in 2004 by physicist John Skilling.
16S ribosomal RNA is the RNA component of the 30S subunit of a prokaryotic ribosome. It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
RNA-Seq is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome.
GeneNetwork is a combined database and open-source bioinformatics data analysis software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence differences to corresponding differences in gene and protein expression and to variation in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes and phenotypes from groups of individuals, including humans, strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes makes it practical to carry out web-based gene mapping to discover those regions of genomes that contribute to differences among individuals in mRNA, protein, and metabolite levels, as well as differences in cell function, anatomy, physiology, and behavior.
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections, an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These "barcodes" are sometimes used in an effort to identify unknown species or parts of an organism, simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries.
Leafpad is a free and open-source graphical text editor for Linux, BSD, and Maemo that is similar to the Microsoft Windows program Notepad. Created with the focus of being a lightweight text editor with minimal dependencies, it is designed to be simple-to-use and easy-to-compile.
The phenotype microarray approach is a technology for high-throughput phenotyping of cells. A phenotype microarray system enables one to monitor simultaneously the phenotypic reaction of cells to environmental challenges or exogenous compounds in a high-throughput manner. The phenotypic reactions are recorded as either end-point measurements or respiration kinetics similar to growth curves.
Julia is a high-level, dynamic programming language. Its features are well suited for numerical analysis and computational science.
Phabricator is a suite of web-based development collaboration tools, which includes Differential code review tool, Diffusion repository browser, Herald change monitoring tool, Maniphest bug tracker, Phriction wiki.
DNF or Dandified YUM is the next-generation version of the Yellowdog Updater, Modified (yum), a package manager for .rpm-based Linux distributions. DNF was introduced in Fedora 18 in 2013, it has been the default package manager since Fedora 22 in 2015, Red Hat Enterprise Linux 8., and OpenMandriva; and also an alternative package manager for Mageia.
Zstandard, commonly known by the name of its reference implementation zstd, is a lossless data compression algorithm developed by Yann Collet at Facebook. Zstd is the reference implementation in C. Version 1 of this implementation was released as open-source software on 31 August 2016.
Microsoft, a technology company historically known for its opposition to the open source software paradigm, turned to embrace the approach in the 2010s. From the 1970s through 2000s under CEOs Bill Gates and Steve Ballmer, Microsoft viewed the community creation and sharing of communal code, later to be known as free and open source software, as a threat to its business, and both executives spoke negatively against it. In the 2010s, as the industry turned towards cloud, embedded, and mobile computing—technologies powered by open source advances—CEO Satya Nadella led Microsoft towards open source adoption although Microsoft's traditional Windows business continued to grow throughout this period generating revenues of 26.8 billion in the third quarter of 2018, while Microsoft's Azure cloud revenues nearly doubled.
GDevelop is a 2D cross-platform, free and open-source game engine, which mainly focuses on creating simple PC and Mobile games, as well as HTML5 games playable in the browser. Created by Florian Rival; a software engineer at Google, GDevelop is mainly aimed at non-programmers and game developers of all skillsets, employing event based visual programming similar to engines like Construct, Stencyl, and Tynker.
