Gourt > Science > Biology > Genetics > Software (1)
Computer software (or simply software) is the programs and procedures that enable a computer to perform a specific task, as opposed to the physical components of the system (hardware). This includes application software such as a word processor, which enables a user to perform a task, and system software such as an operating system, which enables other software to run properly, by interfacing with hardware and with other software.
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 reading different sequences of instructions into the memory of a device to control computations was invented by Charles Babbage as part of his difference engine. The theory that is the basis for most modern software was first proposed by Alan Turing in his 1935 essay Computable numbers with an application to the Entscheidungsproblem. Hally, Mike (2005:79). Electronic brains/Stories from the dawn of the computer age. British Broadcasting Corporation and Granta Books, London. ISBN 1-86-207663-4.
Relationship to hardware
Computer software is so called in contrast to computer hardware, which encompasses the physical interconnections and devices required to store and execute (or run) the software. In computers, software is loaded into RAM and executed in the central processing unit. At the lowest level, software consists of a machine language specific to an individual processor. A machine language consists of groups of binary values signifying processor instructions (object code), which change the state of the computer from its preceding state. Software is an ordered sequence of instructions for changing the state of the computer hardware in a particular sequence. It is generally written in high-level programming languages that are easier and more efficient for humans to use (closer to natural language) than machine language. High-level languages are compiled or interpreted into machine language object code. Software may also be written in an assembly language, essentially, a mnemonic representation of a machine language using a natural language alphabet. Assembly language must be assembled into object code via an assembler. More on [ Computer software ]
Genetic Programming :: Artificial Intelligence
Bioinformatics :: Biology
Software :: Biology
Software :: Science
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Alice Software - Database system to build and publish synonymised checklists of species. Species descriptions include pre-established fields and detailed descriptions employing any number of user-defined fields.
Alternative Splice Site Predictor - ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons.
BioConstructor Molecular Cloning Software - BioConstructor is a bioinformatics solution focussing on molecular cloning. Runs on Windows, Mac OS X, Linux.
Broad Institute Genetics Software - Offers a wide range of software for genome sequence analysis, genetic variation, linkage analysis, expression analysis, and PCR primer selection.
Meta Description: [ Access to the software, protocols and data of Broad Institute.
]
CounterTrace II DNA Sequencing - Software and reagent for improving the quality and read length of DNA sequence traces collected on the ABI 3730 DNA sequencer.
Meta Description: [ CounterTrace II DNA sequencing software & reagents for improving the read length and increasing the base call quality of the ABI KB base caller ]
CREME: Cis-REgulatory Module Explorer - Identifies modules of putative transcription factor binding sites that are specific to promoters of co-expressed human genes. Provides a resource for decoding microarray experiments.
Gene Array Analyzer Software - Software for the efficient management, analysis and visualization of large amounts of gene expression data.
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Gene Expression Open Source System - Open source database and analysis package used to archive and analyze expression data from gene chip experiments. Includes microarray center workflow management, and researcher tools to analyze final data.
Meta Description: [ GEOSS is an Open Source Gene Expression Database supporting storage and analysis of Affymetrix� GeneChip� technology, with planned support for two color spotted arrays and other gene expression measurement technologies. GEOSS is designed to serve as a secure repository and archive for many re... ]
GeneSifter - Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation from public databases. Product overview in pdf format.
Genetic Linkage Analysis - Offers links and other resources for genetic analysis software from the Rockefeller University.
Meta Description: [ we, the laboratory of
statistical genetics at rockefeller university, are providing
information on genetic linkage analysis ]
Genetic Network Maps as Java Applets - Genetic networks controlling development in Sea Urchin represented as Java applets. Formal scheme. Molecular interactions modelled as Petri Net.
Meta Description: [ Genetic Network Maps ]
Genex Open Source Gene Expression Database - Genex is an open source database for storing, processing, and analyzing gene expression microarray data.It is intended for local installation by medium sized laboratories with some system administration support. No activity since 2003.
GENtle - GPL software for viewing and editing DNA and amino acid sequences. Integrated alignment, PCR, BLAST searches, and shared databases. Windows version is available for download (English and German).
Hands on Genetics - Instructional software for basic genetics, such as DNA, PCR, Mendel, Hardy-Weinberg, meiosis and computer simulations. Freeware for Mac and Windows.
Meta Description: [ Genetics teaching: DNA, PCR, Mendel and meiosis. We offer interactive computer simulation to teach genetics. Our programs offer learning to students with and without prior genetics knowledge. ]
MapMakerDrawer - Program that draws chromosome maps (as EMF files) using the output of MapMaker EXP. Delphi source code is freely available upon request. The software is available under the MIT licence.
MuStaR Sequence Variant Database Software - Designed to create a database of mutation loci, to make this information available to as many people as possible. No longer being maintained.
Mutation Explorer - Software to automatically detect mutations from DNA sequence data, including homozygous, heterozygous, insertion and deletion.
Pegasys - Open source software for executing and integrating analyses of biological sequences. Includes documentation and installation instructions.
Meta Description: [ University of British Columbia Bioinformatics Centre : Pegasys: workflow management for bioinformatics ]
PyMoods - A software application for visualizing genomic data. Can be used to analyze and display relations between complete genomes, genomic fragments, proteins, ESTs, full length cDNAs, and gene expression data.
STRand - Open-source Windows program to automate or speed up the analysis of DNA fragment length polymorphism samples run on ABI3730, 3700 and 377 sequencers. Instructions for use and program download available.
Synopsis - Commercial Windows software for visualization and annotation of genomic data.
TagSorter - Database application designed to simplify the collation, sorting, comparison and identification of SAGE tag sequences.
Meta Description: [ tagsorter.com ]
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The BioCatalog - Software directory of general interest in molecular biology and genetics. Not updated since 2000.
The Sequence Manipulation Suite - The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.
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