|
GenoCAD Workflow
GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene networks and other genetic constructs for genetic engineering and is based on the theory of formal languages. History GenoCAD originated as an offshoot of an attempt to formalize functional constraints of genetic constructs using the theory of formal languages. In 2007, the website genocad.org (now retired) was set up as a proof of concept by researchers at Virginia Bioinformatics Institute, Virginia Tech. Using the website, users could design genes by repeatedly replacing high-level genetic constructs with lower level genetic constructs, and eventually with actual DNA sequences. On August 31, 2009, the National Science Foundation granted a three-year $1,421,725 grant to Dr. Jean Peccoud, an associate professor at the Virginia Bioinformatics ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GenoCAD Logo
GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene networks and other genetic constructs for genetic engineering and is based on the theory of formal languages. History GenoCAD originated as an offshoot of an attempt to formalize functional constraints of genetic constructs using the theory of formal languages. In 2007, the website genocad.org (now retired) was set up as a proof of concept by researchers at Virginia Bioinformatics Institute, Virginia Tech. Using the website, users could design genes by repeatedly replacing high-level genetic constructs with lower level genetic constructs, and eventually with actual DNA sequences. On August 31, 2009, the National Science Foundation granted a three-year $1,421,725 grant to Dr. Jean Peccoud, an associate professor at the Virginia Bioinformat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mice
A mouse (: mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus''). Mice are also popular as pets. In some places, certain kinds of field mice are locally common. They are known to invade homes for food and shelter. Mice are typically distinguished from rats by their size. Generally, when a muroid rodent is discovered, its common name includes the term ''mouse'' if it is smaller, or ''rat'' if it is larger. The common terms ''rat'' and ''mouse'' are not taxonomically specific. Typical mice are classified in the genus '' Mus'', but the term ''mouse'' is not confined to members of ''Mus'' and can also apply to species from other genera such as the deer mouse (''Peromyscus''). Domestic mice sold as pets often differ substantially in size from the common house mouse. This is attributable to breedin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wizard (software)
A software wizard or setup assistant or multi-step form is a user interface that leads a user through a sequence of small steps, such as a dialog box to configure a program for the first time. They are used to make complex, unfamiliar tasks easier by breaking them into smaller pieces. History Before the 1990s, "wizard" was a common term for a technical expert, comparable to "hacker." The 1985 textbook Structure and Interpretation of Computer Programs was nicknamed the "Wizard Book" for the illustration on its cover; its first chapter says, "A computational process is indeed much like a sorcerer's idea of a spirit." When developing the first version of its desktop publishing software, Microsoft Publisher, around 1991, Microsoft wanted to help users create well-presented documents in spite of their lack of graphic design skills. Microsoft reasoned that, no matter the tools a program offered, users would not know how best to use them. Publisher's "Page Wizards" instead provided a s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SBML
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. History Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST), Hiroaki Kitano and John C. Doyle assembled a small team of researchers to work on developing better software infrastructure for computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka. Bolouri identified the need ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases. FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance. There are several programs in this package that allow the alignment of protein sequences and DNA sequences. Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm. FASTA is pronounced "f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tab Delimited
Tab-separated values (TSV) is a simple, text-based file format for storing tabular data. Records are separated by newlines, and values within a record are separated by tab characters. The TSV format is thus a delimiter-separated values format, similar to comma-separated values. TSV is a simple file format that is widely supported, so it is often used in data exchange to move tabular data between different computer programs that support the format. For example, a TSV file might be used to transfer information from a database to a spreadsheet. Example The head of the Iris flower data set can be stored as a TSV using the following plain text (note that the HTML rendering may convert tabs to spaces): The TSV plain text above corresponds to the following tabular data: Character escaping The IANA media type standard for TSV achieves simplicity by simply disallowing tabs within fields. Since the values in the TSV format cannot contain literal tabs or newline characters, a co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC). In October 2024, GenBank contained 34 trillion base pairs from over 4.7 billion nucleotide sequences and more than 580,000 formally described species. The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. Submissions Only original sequences can be submitted to GenBank. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lucene
Apache Lucene is a free and open-source search engine software library, originally written in Java by Doug Cutting. It is supported by the Apache Software Foundation and is released under the Apache Software License. Lucene is widely used as a standard foundation for production search applications. Lucene has been ported to other programming languages including Object Pascal, Perl, C#, C++, Python, Ruby and PHP. History Doug Cutting originally wrote Lucene in 1999. Lucene was his fifth search engine. He had previously written two while at Xerox PARC, one at Apple, and a fourth at Excite. It was initially available for download from its home at the SourceForge web site. It joined the Apache Software Foundation's Jakarta family of open-source Java products in September 2001 and became its own top-level Apache project in February 2005. The name Lucene is Doug Cutting's wife's middle name and her maternal grandmother's first name. Lucene formerly included a number of sub-p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Database
In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("Digital data, digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable. Search Searching in a sequence database involves looking for similarities between a genomic/protein sequence and a query string and, finding the sequence in the database that "best" matches the target sequence (based on criteria which vary depending on the search method). The number of matches/hits is used to formulate a score that determines the similarity between the sequence query and the sequences in the sequence database. The main goal is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression (the synthesis of Gene product, RNA or protein from a gene), DNA is first transcription (biology), copied into RNA. RNA can be non-coding RNA, directly functional or be the intermediate protein biosynthesis, template for the synthesis of a protein. The transmission of genes to an organism's offspring, is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype, that is specific to every given individual, within the gene pool of the population (biology), population of a given species. The genotype, along with environmental and developmental factors, ultimately determines the phenotype ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Promoter (biology)
In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription (genetics), transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, Upstream and downstream (DNA), upstream on the DNA (towards the Directionality (molecular biology)#5′-end, 5' region of the sense strand). Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism. Overview For transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Formal Grammar
A formal grammar is a set of Terminal and nonterminal symbols, symbols and the Production (computer science), production rules for rewriting some of them into every possible string of a formal language over an Alphabet (formal languages), alphabet. A grammar does not describe the semantics, meaning of the strings — only their form. In applied mathematics, formal language theory is the discipline that studies formal grammars and languages. Its applications are found in theoretical computer science, theoretical linguistics, Formal semantics (logic), formal semantics, mathematical logic, and other areas. A formal grammar is a Set_(mathematics), set of rules for rewriting strings, along with a "start symbol" from which rewriting starts. Therefore, a grammar is usually thought of as a language generator. However, it can also sometimes be used as the basis for a "recognizer"—a function in computing that determines whether a given string belongs to the language or is grammatical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
