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Software

Webpages concerning "Software"

The Department of Molecular Genetics and Biochemistry at the University of Pittsburgh School of Medicine
http://www.mgb.pitt.edu/moleculartoolbox.htm
Keywords:
Molecular, Genetics, Biochemistry, Pittsburgh, University, microbiology, pathogenesis, virology, immunology, gene therapy, gene expression, herpes, mycobacterium, tuberculosis, tumor, apoptosis, peptide, sequence, DNA, protein, angiogenesis, Trypanosoma cruzi, vaccine, Duchenne muscular dystrophy, developmental biology, zebrafish, bioinformatics, computational biology

http://www.mgb.pitt.edu/moleculartoolbox.htm

DNA-Match, die geniale Software zur Fragmentanalyse von bj diagnostik und Mellau Consulting. Automatische Genotypisierung in der large scale Microsatellitenanalyse. Statistik und Datenbankentwicklung.
http://www.linkage-analysis.com/
Keywords:
Bioinformatik, Genotypisierung, DNA-Match, microsatellite, statistik, DNA, Fragmentanalyse, Pharmaforschung, allele, calling, sizing, fragment, analysis, genotyping, pedigree, Stammbaum, Abstammung, PCR, genetischer, Fingerabdruck, mtDNA

http://www.linkage-analysis.com/

Chang Bioscience develops software for microarray data analysis, primer sequence database and design
http://www.changbioscience.com/
Keywords:
BioToolKit, microarray analysis software, PCR primer design, PCR

http://www.changbioscience.com/

Radically improve and visualize your Multiplex PCR's, Allelle-specific primers and probes, taqman probes, molecular beacons, microarrays, scorpion probes and primers, RNAi and FRET assays .
http://www.dnasoftware.com/
Keywords:
DNA Software, Visual OMP, OMP DE, primer design, probe design, primer design software, probe design software, molecular beacons, scorpion probes, multiplex PCR, multiplex PCR software

http://www.dnasoftware.com/

Koada Technology - Software development and consultancy services. Specialization in molecular biology and laboratory instrumentation. Koadarray - Unique software for fully automated analysis and quantification of microarray images. Free download of evaluation version.
http://www.koada.com
Keywords:
Koada Technology, Koada, Koadarray, Roland Howe, software, free download, microarray, microarrays, array, arrays, macroarray, macroarrays, spot, spots, find, finding, spotfinding, quality, DNA, protein, automated, automatic, multiple, unattended, quantify, quantification, background, subtraction, artefact, artifact, intensity, volume, data, output, text, tab, image, images, 16-bit, 8-bit, TIFF, ...

http://www.koada.com

Niles Scientific produces SpotReader, the next generation in microarray image analysis software. Niles Scientific is a bioinformatics software development company based in San Francisco.
http://www.nilesscientific.com/
Keywords:
Niles Scientific, SpotReader, GridMaker, bioinformatics, software, microarray, micro-array, array, automated, automatic, gridding, grid, RNA, DNA, analyze, analysis, scanners, chip, gene chip, DNA chip, genepix, scanalyze, quantarray, acuity, genomics, proteomics, DNA reader, DNA microarray, gene expression, protein expression, Niles, Rich Niles, Richard Niles, automated gridding, ...

http://www.nilesscientific.com/

strand Life Sciences - a premier in silico technologies innovation company for drug discovery and development.
http://www.strandgenomics.com/
Keywords:
strand, life sciences, in silico technologies, Decision analytics, Data Mining, Predictive Modeling, Computational Chemistry, Software Engineering, Research Biology, genomics, avadis, focus library, acuris, life science, informatics company, Software for drug discovery, data analysis, knowledge management, workflow process, microarray, microarray data analysis, gene expression, ...

http://www.strandgenomics.com/

Improved Outcomes provides GeneLinker software for gene expression (microarray) and proteomics analysis as well as software consulting services for bioinformatics, image guided surgery (IGS) and information technology (IT).
http://www.improvedoutcomes.com
Keywords:
predictive patterns, predictive, patterns, genomics, proteomics, data analysis, software, tutorial, GeneLinker, Molecular Mining, MMC, 2 color, 2 colour, 9i, acuity, Affymetrix, Agilent, Amersham, agglomerative, analysis, array, array intensity, array plot, association, associations, association rule, association mining, average linkage, axon, axon acuity, autogene, bagging, bayes, bayesian, ...

http://www.improvedoutcomes.com

Integrated Genomics, Inc., based in Chicago, Illinois, offers all levels of analysis of bacterial and fungal genomes, from high-throughput sequencing to sophisticated bioinformatics. The company is a leader in sequence-based metabolic reconstruction and pathway design. Integrated Genomics now is offering annotated structure of genomes, their encoded metabolism, comparative pathway analysis, etc.
http://www.integratedgenomics.com/
Keywords:
Integrated Genomics Inc, WIT, genomics, microbial genomics, bioinformatics, genome, microbes, microbial, genomic technology, computational genomics, DNA sequencing, DNA sequence, genetic information, bioinformatics, metabolic reconstruction, functional reconstruction, metabolic modeling, high throughput, ERGO, TIGR, The, Institute, for, Genomic, Research, Celera, LION, JGI, ...

http://www.integratedgenomics.com/

Manufacturer and distributor of Oligo Primer Analysis Software. OLIGO (©1989-2004) performs a range of functions for researchers in PCR and related technologies, priming efficiency algorithm enables to design consensus, multiplex and degenerate primers; back translation, restriction enzyme analysis and prediction, oligonucleotide database, primer secondary structure/dimers, LCR and more.
http://www.oligo.net/
Keywords:
oligo software, PCR software, Oligo program, PCR primer analysis, sequencing primers design, primer design software, probe design software, consensus primers, multiplex primers, site directed mutagenesis, back translation, reverse translation, Oligo 6, oligonucleotide analysis, Molecular Biology Insights, MBI

http://www.oligo.net/

Scientific software for the molecular biologist. Complete with oligo DB management. Analyses DNA for restriction enzymes (digest) , primer sites, finds and translates open reading frames. Backtranslates proteins or open reading frames. Aligns DNA or protein. Generates DNA/plasmid plots, virtual agarose gel plots, XY-homology plots (dotplot)- and more!
http://134.99.88.55/aio/
Keywords:
Plasmid drawing software, DNA analysis, DNA sequence, DNA cloning, restriction enzyme digestion, oligonucleotide primer analysis, biology, clone, gene, digest, download, enzyme recognition sequence, freeware, gene, mapping, molecular biology, ORF, open, reading, frame, translation, genetic codes, scientific software, plasmid, plotting, primers, programs, protein, automation, science, search, ...

http://134.99.88.55/aio/

DNAStar Website, designed by ViV!D Web Design Group, LLC.
http://www.dnastar.com/
Keywords:
DNAStar

http://www.dnastar.com/

Redasoft Corporation - makers of Visual Cloning sequence analysis and DNA plasmid mapping software, PCR primer, restriction mapping, BLAST, sequence alignment, bioinformatics
http://www.redasoft.com/

http://www.redasoft.com/

Rosetta Biosoftware is the leading provider of bioinformatics solutions to aid in drug discovery and the development of pharmaceutical and agricultural products
http://www.rosettabio.com/tech/geml/
Keywords:
rosetta bioinformatics, rosetta biosoftware, genomics, proteomics, gene expression analysis, gene expression, expression

http://www.rosettabio.com/tech/geml/

http://www.scienceandresearchdevelopmentinstitute.com/genkia.html

http://www.scienceandresearchdevelopmentinstitute.com/genkia.html

http://lola.gwu.edu/

http://lola.gwu.edu/

http://www.stud.uni-karlsruhe.de/~uzbar/

http://www.stud.uni-karlsruhe.de/~uzbar/

Developers of software: Real time PCR primer design, including TaqMan,  molecular beacons, SYBR green, FRET assays, pathogen detection, species/taxa identification; DNA whole genome, expression, SNP detection and tiling microarray design software; software for drawing plasmid maps for restriction, TA and Gateway cloning technology.
http://www.premierbiosoft.com/

http://www.premierbiosoft.com/

http://www.cs.cmu.edu/~jernst/stem/

http://www.cs.cmu.edu/~jernst/stem/

http://www.sanger.ac.uk/Software/Artemis/
Keywords:
Artemis, Genome Annotation Tool, ACT, Sanger Institute, Sequence Annotation Tool, DNA, Pathogen Sequencing Unit, Kim Rutherford

http://www.sanger.ac.uk/Software/Artemis/

http://www.psc.edu/general/software/categories/sequence_analysis.html

http://www.psc.edu/general/software/categories/sequence_analysis.html

http://www.mpiz-koeln.mpg.de/~weisshaa/Adis/DNA-software-links.html

http://www.mpiz-koeln.mpg.de/~weisshaa/Adis/DNA-software-links.html

http://bioinf.charite.de/oligodb/

http://bioinf.charite.de/oligodb/

http://oligodb.charite.de/

http://oligodb.charite.de/

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Wikipedia-Article "Software"

"Software" redirects here. For other uses, see Software (disambiguation).
A screenshot of computer software in action.
Enlarge
A screenshot of computer software in action.

Computer software (or simply software) is that part of a computer system that consists of encoded information, as opposed to the physical computer equipment (hardware) which is used to store and process this information. The term is roughly synonymous with computer program but is more generic in scope.

The term "software" was first used in this sense by John W. Tukey in 1957. In computer science and software engineering, computer software is all information processed by computer systems, programs and data. The concept of software was first proposed by Alan Turing in an essay.

Contents

Relationship to hardware

Computer software is so called in contrast to computer hardware, which is the physical substrate which is required to store and execute (or run) the software. In computers, software is loaded in RAM and executed on the central processing unit. At the lowest level, software consists of a machine language specific to an individual processor. Machine language consists of groups of binary values signifying processor instructions and data. Software is generally written in high-level languages that are easy and efficient for humans to use. High-level languages are compiled into machine language.

Relationship to data

Software has historically been considered an intermediary between electronic hardware and data, which the hardware processes according to instructions defined by the software. As computational science becomes increasingly complex, the distinction between software and data becomes less precise. Data has generally been considered as either the output or input of software. However, data is not the only possible output or input. For example, configuration information can also be considered input, although not necessarily considered data. The output of a particular piece of software may be the input for another piece of software. Therefore, software may be considered an interface between hardware, data, or software.

System, application and programming software

Practical computer systems divide software into three major classes: system software, application software and programming software, although the distinction is somewhat arbitrary, and often blurred.

System software helps run the computer hardware and computer system. It includes operating systems, device drivers, diagnostic tools, servers, windowing systems, utilities and more.
Application software allows a user to accomplish one or more specific tasks. Typical applications include office suites, business software, educational software, databases and computer games. Most application software has a graphical user interface (GUI).
Programming software usually provides some useful tools to help programmer to write computer programs and software using different programming language in a more convenient way. The tools include text editor, compiler, interpreter, linker, debugger, and so on. Integrated development environment (IDE) merges those tools in a software bundle, and programmer may not need to type a lot of commands for compiling, interpreter, debugging, tracing, and etc., because IDE mostly has a GUI.

Software program and library

Software program is usually the directly executable part of a software. Software libraries are software components that are used by stand-alone programs, but which cannot be executed on their own.

Users see three layers of software

Starting in the 1980s, application software has been sold in mass-produced packages through retailers
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Starting in the 1980s, application software has been sold in mass-produced packages through retailers

Users often see things differently than programmers. People who use modern general purpose computers (as opposed to embedded systems) usually see three layers of software performing a variety of tasks: platform, application, and user software.

Platform software 
Platform includes the basic input-output system (often described as firmware rather than software), device drivers, an operating system, and typically a graphical user interface which, in total, allow a user to interact with the computer and its peripherals (associated equipment). Platform software often comes bundled with the computer, and users may not realize that it exists or that they have a choice to use different platform software.
Application software 
Application software or Applications are what most people think of when they think of software. Typical examples include office suites and video games. Application software is often purchased separately from computer hardware. Sometimes applications are bundled with the computer, but that does not change the fact that they run as independent applications. Applications are almost always independent programs from the operating system, though they are often tailored for specific platforms. Most users think of compilers, databases, and other "system software" as applications.
User-written software 
User software tailors systems to meet the users specific needs. User software include spreadsheet templates, word processor macros, scientific simulations, graphics and animation scripts. Even email filters are a kind of user software. Users create this software themselves and often overlook how important it is.

See also: Software architecture.

Software creation

Look back to Computer software

Software operation

Computer software has to be "loaded" into the computer's storage (also known as memory and RAM).

Once the software is loaded, the computer is able to operate the software. Computers operate by executing the computer program. This involves passing instructions from the application software, through the system software, to the hardware which ultimately receives the instruction as machine code. Each instruction causes the computer to carry out an operation -- moving data, carrying out a computation, or altering the flow of instructions.

Kinds of software by operation: computer program as executable, source code or script, configuration.

Software quality and reliability

Software reliability considers the errors, faults, and failures related to the creation and operation of software.

See Software quality, Software testing, and Software reliability.

Software patents

The issue of software patents is very controversial, since while patents protect the ideas of "inventors", they are widely believed to hinder software development. See Hacker ethic

See also

This article is based on the article "Software" from Wikipedia - the free encyclopedia created and edited by online user community. This article is distributed under the terms of GNU Free Documentation License. Here you find the list of authors of this article. The article can only edited within Wikipedia. Edit this article in Wikipedia.