Gourt > Science > Biology > Bioinformatics > 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 ]
RT tabebuia: Why CIOs are enumeration yes to open source software - silicon j. mp20OnFe opensource governance !
airliakkcl (Maria Reedypl) Wed, 16 Dec 2009 12:29:22 -0000
RT tabebuia: Why CIOs are enumeration yes to open source software - silicon j. mp20OnFe opensource governance !
[new blog post] Judge: DVD-copying software is illegal http://bit.ly/7F8Jlj
19thHole (Jim Odom) Wed, 16 Dec 2009 12:29:18 -0000
[new blog post] Judge: DVD-copying software is illegal http://bit.ly/7F8Jlj
Avoiding Holiday Disk-asters | Data Recovery Service and Software ... http://bit.ly/75wj2M
Earthyman (Howard Bright) Wed, 16 Dec 2009 12:29:06 -0000
Avoiding Holiday Disk-asters | Data Recovery Service and Software ... http://bit.ly/75wj2M
@randyball I was going to but realized some other software I use would need to be upgraded and paid. Eventually :)
necker47 (Jonathan Longnecker) Wed, 16 Dec 2009 12:28:46 -0000
@randyball I was going to but realized some other software I use would need to be upgraded and paid. Eventually :)
Zicron Software introduces Gift Box 1.0 for iPhone and iPod Touch http://bit.ly/6PNFne
musicchio (Antonio Angelicchio) Wed, 16 Dec 2009 12:28:46 -0000
Zicron Software introduces Gift Box 1.0 for iPhone and iPod Touch http://bit.ly/6PNFne
RT: @meneame_net: Adobe Reader el 'software' más inseguro y 'hackeado' del año http://menea.me/hwps <-- mira juanlublancom
leyresoyyo (leyre) Wed, 16 Dec 2009 12:28:39 -0000
RT: @meneame_net: Adobe Reader el 'software' más inseguro y 'hackeado' del año http://menea.me/hwps <-- mira juanlublancom
EMBOSS - The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.
ADF MAGE-ML - Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
Meta Description: [ ADF MAGE-ML Tool: Tool for conversion from ADF to MAGE-ML and reverse ]
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AlmaKnowledgeServer - Text mining tool for genomics, proteomics platforms and drug discovery.
AnnHyb - Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
Meta Description: [ AnnHyb's home page ]
APBioKnoppix - Knoppix based bioinformatics software tools. Bootable from CD.
ARCiB -- Accessible Retired Computers in Biology - NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
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BioEdit - Free Windows biological sequence alignment editor.
biOpen - Commercial Mac OS X sequence analysis and structure visualization software.
Meta Description: [ hebergement mutualise, hebergement professionnel, nom de domaine, hebergement, professionnel, PHP, paiement securise, boutique en ligne, hebergeur, afnic ]
Darwin - An interactive tool for peptide and nucleotide sequence analysis.
Meta Description: [ ETH Zuerich ]
DNAMAN - Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
Meta Description: [ DNAMAN - Sequence analysis software for Windows and Macintosh ]
DNPTrapper - An Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Expression Profiler - An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics, machine-learning algorithms and visualization.
500
FASTA - William Pearson's package for fast sequence comparison tools.
GDE - An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
Meta Description: [ An integrated sequence alignment linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Download GDE for Linux. ]
GeneRunner - A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now abandonware.
Meta Description: [ runner treadmill walking shoes track and field running marathon triathlon ]
Genespotter - Commercial Windows software for analyzing biochip image data.
Genome-tools Web Interface - Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
Meta Description: [ The world's largest development and download repository of Open Source code and applications ]
Gints - Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
GoCore - GoCore is an free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
HMMER - Profiles protein sequence data using hidden Markov models of a statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
INCA - INteractive Codon Analysis - Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the possibility to export graphics or text files for further analysis. Free for academic users.
JAligner - Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
Meta Description: [ JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model. ]
JSTRING - Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
Keck Computational Systems Biology Software - Software for simulating metabolic, signal and genetic networks. Home of Jarnac, JDesigner and SCAMP.
Meta Description: [ Home of the Systems Biology Workbench, a modular framework for Systems Biology. ]
limmaGUI - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
404
MAFFT - Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies.
Meta Description: [ Multiple sequence alignment software. ]
MaGe (Magnifying Genomes) - Microbial genome Annotation System - The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.
Meta Description: [ MaGe (Magnifying Genomes) - Microbial Genome Annotation System ]
404
MARBL - MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
Mauve - Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
Meta Description: [ The Genome Evolution Laboratory, directed by Prof. Nicole T. Perna, performs research into rates and patterns of adaptive genome evolution in animal and plant associated microbes. Our research involves experimental characterization of pathogens and computational modeling of genome evolution. ]
MedScan - Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
Meta Description: [ MedScan is natural language processing technology that harvests information from the literature and saves it in a database available for computational analysis. ]
MELTING - Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
Meta-MEME - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
MIRA - A sequence assembly suite with SNP detection for hard projects.
Meta Description: [ Website of Bastien Chevreux, home of the MIRA genome and EST sequence assembler ]
Nano+Bio-Centre - Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
500
PathwayStudio - Pathway analysis software for interpreting experimental data in the context of pathways, gene regulation networks and protein interaction maps.
pDRAW32 - Freeware DNA cloning, analysis and visualization software.
Meta Description: [ Scientific software for the molecular biologist. Performs virtual DNA cloning, analyses DNA for restriction enzymes, homing enzymes and primer sites, dam and dcm methylation sites, finds and translates open reading frames. Calculates annealing temperatures for PCR. Generates DNA/plasmid plots, vi... ]
Phrap/Consed - DNA sequence assembler and finishing tools from the UW Genome Center.
PHRED - A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.
Premier Biosoft International - Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics.
Meta Description: [ Free and commercial software that reduce your time and cost of experimentation. Primer design tools for PCR, real time PCR & microarrays, dual labeled probe design such as TaqMan®, molecular beacons and FRET. Cloning simulation and plasmid map drawing. Statistical tool for tissue microarray anal... ]
RGBG Analyzer - Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 XP.
Seqtools - Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
Meta Description: [ SEQtools is a comprehensive software package for handling and analysis of nucleotide and protein sequences. ]
Sequence Analysis - A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
SeWeR - An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
Meta Description: [ SeWeR: Sequence Analysis using Web Resources is an integrated
portal to commonly used bioinformatics tools on Internet and World Wide Web. Nucleic Acid sequence
analysis, Protein sequence analysis, Sequence Alignment, PCR and related analysis,
Database searches, Bookmarklets for bioinformatics... ]
500
Sfold - Predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
Meta Description: [ Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. ]
Sockeye - 3D visualisation platform for Comparative Genomics visualisation.
STRAP - Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
STRING - Search for Tandem Repeats IN Genomes. Includes C source code and examples.
Tandem Repeats Finder - Locates and displays tandem repeats in DNA sequences.
The ARB Project - A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
WU-BLAST - The Washington University improved version of BLAST. Free for academic users.
Meta Description: [ BLAST 2.0 from Washington University is the original gapped BLAST with statistics. It offers increased speed, sensitivity, flexibility and reliability over competing solutions. ]
XDigitize - A Linux/Unix visualization software system for evaluation of hybridisation experiments.
Meta Description: [ Xdigitise is a visualization software system for evaluation of hybridisation experiments. ]
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