Transcription factorIn molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism.
Sequence motifIn biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue. When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
Cross-platform softwareIn computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software requires a separate build for each platform, but some can be directly run on any platform without special preparation, being written in an interpreted language or compiled to portable bytecode for which the interpreters or run-time packages are common or standard components of all supported platforms.
Zinc fingerA zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells.
Sequence alignmentIn 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.
Consensus sequenceIn molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Such information is important when considering sequence-dependent enzymes such as RNA polymerase.
Nucleic acid sequenceA nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used.
Cross-platform playIn video games with online gaming functionality, also called cross-compatible play, cross-platform play, crossplay, or cross-play describes the ability of players using different video game hardware to play with each other simultaneously. It is commonly applied to the ability for players using a game on a specific video game console to play alongside a player on a different hardware platform such as another console or a computer.
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 motifIn a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have to be associated with a sequence motif; it can be represented by different and completely unrelated sequences in different proteins or RNA. Non-B database Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is thought to have biological significance.
Digital curationDigital curation is the selection, preservation, maintenance, collection, and archiving of digital assets. Digital curation establishes, maintains, and adds value to repositories of digital data for present and future use. This is often accomplished by archivists, librarians, scientists, historians, and scholars. Enterprises are starting to use digital curation to improve the quality of information and data within their operational and strategic processes.
Point mutationA point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. Point mutations have a variety of effects on the downstream protein product—consequences that are moderately predictable based upon the specifics of the mutation. These consequences can range from no effect (e.g. synonymous mutations) to deleterious effects (e.g. frameshift mutations), with regard to protein production, composition, and function.
Content managementContent management (CM) is a set of processes and technologies that supports the collection, managing, and publishing of information in any form or medium. When stored and accessed via computers, this information may be more specifically referred to as digital content, or simply as content. Digital content may take the form of text (such as electronic documents), images, multimedia files (such as audio or video files), or any other file type that follows a content lifecycle requiring management.
Java (software platform)Java is a set of computer software and specifications developed by James Gosling at Sun Microsystems that provides a system for developing application software and deploying it in a cross-platform computing environment. Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. Java applets, which are less common than standalone Java applications, were commonly run in secure, sandboxed environments to provide many features of native applications through being embedded in HTML pages.
Transformer (machine learning model)A transformer is a deep learning architecture that relies on the parallel multi-head attention mechanism. The modern transformer was proposed in the 2017 paper titled 'Attention Is All You Need' by Ashish Vaswani et al., Google Brain team. It is notable for requiring less training time than previous recurrent neural architectures, such as long short-term memory (LSTM), and its later variation has been prevalently adopted for training large language models on large (language) datasets, such as the Wikipedia corpus and Common Crawl, by virtue of the parallelized processing of input sequence.
Enterprise content managementEnterprise content management (ECM) extends the concept of content management by adding a timeline for each content item and, possibly, enforcing processes for its creation, approval, and distribution. Systems using ECM generally provide a secure repository for managed items, analog or digital. They also include one (or more) methods for importing content to bring manage new items, and several presentation methods to make items available for use. Although ECM content may be protected by digital rights management (DRM), it is not required.
Large language modelA large language model (LLM) is a language model characterized by its large size. Their size is enabled by AI accelerators, which are able to process vast amounts of text data, mostly scraped from the Internet. The artificial neural networks which are built can contain from tens of millions and up to billions of weights and are (pre-)trained using self-supervised learning and semi-supervised learning. Transformer architecture contributed to faster training.
Attention (machine learning)Machine learning-based attention is a mechanism mimicking cognitive attention. It calculates "soft" weights for each word, more precisely for its embedding, in the context window. It can do it either in parallel (such as in transformers) or sequentially (such as recursive neural networks). "Soft" weights can change during each runtime, in contrast to "hard" weights, which are (pre-)trained and fine-tuned and remain frozen afterwards. Multiple attention heads are used in transformer-based large language models.
Open dataOpen data is data that is openly accessible, exploitable, editable and shared by anyone for any purpose. Open data is licensed under an open license. The goals of the open data movement are similar to those of other "open(-source)" movements such as open-source software, open-source hardware, open content, open specifications, open education, open educational resources, open government, open knowledge, open access, open science, and the open web. The growth of the open data movement is paralleled by a rise in intellectual property rights.
Free contentFree content, libre content, libre information, or free information, is any kind of functional work, work of art, or other creative content that meets the definition of a free cultural work, meaning "works or expressions which can be freely studied, applied, copied and/or modified, by anyone, for any purpose." A free cultural work is, according to the definition of Free Cultural Works, one that has no significant legal restriction on people's freedom to: use the content and benefit from using it, study the content and apply what is learned, make and distribute copies of the content, change and improve the content and distribute these derivative works.
