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Emboss Example
EMBOSS is a free open source software analysis package developed for the needs of the molecular biology and bioinformatics user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. ''EMBOSS'' is an acronym for European Molecular Biology Open Software Suite. The ''European'' part of the name hints at the wider scope. The core EMBOSS groups are collaborating with many other groups to develop the new applications that the users need. This was done from the beginning with EMBnet, the European Molecular Biology Network. EMBnet has many nodes worldwide most of which are national bioinformatics services. EMBnet has the p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physical structure of biological macromolecules is known as molecular biology. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena - uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology. In 1945 the term molecular biology was used by physicist William Astbury. In 1953 Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by Ro ... [...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 (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
EMBnet
The European Molecular Biology network (EMBnet) is an international scientific network and interest group that aims to enhance bioinformatics services by bringing together bioinformatics expertises and capacities. On 2011 EMBnet has 37 nodes spread over 32 countries. The nodes include bioinformatics related university departments, research institutes and national service providers. Operations The main task of most EMBnet nodes is to provide their national scientific community with access to bioinformatics databanks, specialised software and sufficient computing resources and expertise. EMBnet is also working in the fields of bioinformatics training and software development. Examples of software created by EMBnet members are: EMBOSS, wEMBOSS, UTOPIA. EMBnet represents a wide user group and works closely together with the database producers such as EMBL's European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics ( Swiss-Prot), the Munich Information Center for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hinxton
Hinxton is a village in South Cambridgeshire, England. The River Cam runs through the village, as does the Cambridge to Liverpool Street railway, though the village has no station. Hinxton parish's southern boundaries form the border between Cambridgeshire and Essex. The village is five miles (8 km) north-west of Saffron Walden and nine miles (14 km) south of Cambridge. The 2001 population was 315. Hinxton is the home of the Wellcome Genome Campus, which includes the Wellcome Sanger Institute and the European Bioinformatics Institute. History The name Hinxton is a contraction of ''Hengestestun'', "the town of Hengest". The village of Hinxton is listed in the Domesday Book of 1086 as ''Hestitona'', as ''Hyngeston'' in the Ely Registers of 1341 and ''Hengestone'' in the Ramsey Chartulary. Its parish church is the medieval St Mary and St John Church. Hinxton Hall Hinxton Hall, set on an estate of on the banks of the River Cam, is a Grade II* red-brick building built ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In 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. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a parti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU Library General Public Licence
The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate a software component released under the LGPL into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own components. However, any developer who modifies an LGPL-covered component is required to make their modified version available under the same LGPL license. For proprietary software, code under the LGPL is usually used in the form of a shared library, so that there is a clear separation between the proprietary and LGPL components. The LGPL is primarily used for software libraries, although it is also used by some stand-alone applications. The LGPL was developed as a compromise between the strong copyleft of the GNU General Public License (GPL) and more permissive licenses such as the BSD licenses and the MIT L ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU General Public Licence
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general use and was originally written by the founder of the Free Software Foundation (FSF), Richard Stallman, for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. These GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. It is more restrictive than the Lesser General Public License and even further distinct from the more widely used permissive software licenses BSD, MIT, and Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open-source software domain. Prominent free software programs licensed under the GPL include the Linux kernel a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple 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. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non-profit, volunteer-run organization focused on supporting open source programming in bioinformatics. The mission of the foundation is to support the development of open source toolkits for bioinformatics, organise developer-centric hackathon events and generally assist in the development and promotion of open source software development in the life sciences. The foundation also organises and runs the annual Bioinformatics Open Source Conference, a satellite meeting of the Intelligent Systems for Molecular Biology conference. The foundation participates in the Google Summer of Code, acting as an umbrella organisation for individual bioinformatics-related projects. The Open Bioinformatics Foundation was started in 2001, arising from the BioJava, BioPerl and BioPython projects. A formal membership for the foundation was created in 2005. In October 2012, the foundation began an association with Software in the Public Interest (SPI), a US-base ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SOAP (protocol)
Soap is a salt of a fatty acid used in a variety of cleansing and lubricating products. In a domestic setting, soaps are surfactants usually used for washing, bathing, and other types of housekeeping. In industrial settings, soaps are used as thickeners, components of some lubricants, and precursors to catalysts. When used for cleaning, soap solubilizes particles and grime, which can then be separated from the article being cleaned. In hand washing, as a surfactant, when lathered with a little water, soap kills microorganisms by disorganizing their membrane lipid bilayer and denaturing their proteins. It also emulsifies oils, enabling them to be carried away by running water. Soap is created by mixing fats and oils with a base. A similar process is used for making detergent which is also created by combining chemical compounds in a mixer. Humans have used soap for millennia. Evidence exists for the production of soap-like materials in ancient Babylon around 2800 BC. Typ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genostar
Genostar is a bioinformatics provider based in Grenoble, France. The company was founded in 2004 following the "Genostar consortium" that was created in 1999 as a public-private consortium by Genome Express, Hybrigenics, INRIA (Institut National de Recherche en Informatique et Automatique / French National Institute for Research in Computer Science and Control) and The Pasteur Institute. Software Metabolic Pathway Builder is a bioinformatics environment dedicated to microbial research. This covers sequence assembly, mapping, annotation transfer and identification of protein domains, comparative genomics, structural searches, metabolic pathway analysis, modeling and simulation of biological networks. Genostar's software is platform independent and can thus be used for both Mac OS X, Windows, and Linux. Sequence assembly *Mapping an ensemble of sequences on a reference sequence *between a reference sequence and contigs, between two sequences or between two sets of sequences *findin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
