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GenoCAD
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 Bioinformati ... [...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 Bioinformatics ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 Bioinformati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms ( SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virginia Bioinformatics Institute
The Biocomplexity Institute of Virginia Tech (formerly the Virginia Bioinformatics Institute) is a research organization specializing in bioinformatics, computational biology, and systems biology. The institute has more than 250 personnel, including over 50 tenured and research faculty. Research at the institute involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology and medicine. The institute develops -omic and bioinformatic tools and databases that can be applied to the study of human, animal and plant diseases as well as the discovery of new vaccine, drug and diagnostic targets. The institute's programs are supported by a variety of government and private agencies including the National Institutes of Health, National Science Foundation, U.S. Department of Defense, U.S. Department of Agriculture, and U.S. Department of Energy. Since inception, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Arabidopsis Thaliana
''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter annual with a relatively short lifecycle, ''A. thaliana'' is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, ''A. thaliana'' has a relatively small genome around 135 megabase pairs. It was the first plant to have its genome sequenced, and is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing. Description ''Arabidopsis thaliana'' is an annual (rarely biennial) plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, with a few leaves also on the flowering stem. The basal leaves are green to slightly purplish in color, 1.5–5 cm long, and 2–10 mm broad, with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wizard (software)
A software wizard or setup assistant is a user interface that presents a dialog box to lead the user through a sequence of small steps. It's often used to configure a program or service for the first time. Complex, rare, or unfamiliar tasks may be easier with a wizard that breaks the task down into simpler pieces. However, a wizard may be a barrier to deeper understanding, and a substitute for clearer design. History Before the 1990s, "wizard" was a common term for a technical expert, like "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 let users with no graphic design skill make documents that still looked good. Publisher was targeted at non-professionals, and ... [...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
A tab-separated values (TSV) file is a simple text format for storing data in a tabular structure, e.g., a database table or spreadsheet data, and a way of exchanging information between databases. Each record in the table is one line of the text file. Each field value of a record is separated from the next by a tab character. The TSV format is thus a variation of the comma-separated values format. 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 program to a spreadsheet. The IANA standard for TSV achieves simplicity by simply disallowing tabs within fields. 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): Sepal length Sepal width Petal length Petal width&Ta ... [...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). GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 500,000 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. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submis ... [...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 non-research 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, having 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 s ... [...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") 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 to have a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
