Topic
Unix
About: Unix is a research topic. Over the lifetime, 5149 publications have been published within this topic receiving 201691 citations. The topic is also known as: UNIX & UnICS.
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TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.
35,698 citations
TL;DR: The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography.
Abstract: The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims and so there may be more than one program to cover each function. The programs are written mainly in standard Fortran77. They are from a wide variety of sources but are connected by standard data file formats. The package has been ported to all the major platforms under both Unix and VMS. The suite is distributed by anonymous ftp from Daresbury Laboratory and is widely used throughout the world.
17,220 citations
TL;DR: The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
Abstract: The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
13,804 citations
TL;DR: GMT allows users to manipulate (x,y,z) data, and generate PostScript illustrations, including simple x-y diagrams, contour maps, color images, and artificially illuminated, perspective, and/or shaded-relief plots using a variety of map projections.
Abstract: Version 31 of the Generic Mapping Tools (GMT) has been released More than 6000 scientists worldwide are currently using this free, public domain collection of UNIX tools that contains programs serving a variety of research functions GMT allows users to manipulate (x,y) and (x,y,z) data, and generate PostScript illustrations, including simple x-y diagrams, contour maps, color images, and artificially illuminated, perspective, and/or shaded-relief plots using a variety of map projections (see Wessel and Smith [1991] and Wessel and Smith [1995], for details) GMT has been installed under UNIX on most types of workstations and both IBM-compatible and Macintosh personal computers
6,819 citations
Book•
01 Jan 2002
TL;DR: PAUP* 4.0 Beta is a major upgrade of the bestselling software for the inference of evolutionary trees, for use in Macintosh or Windows/DOS-based formats.
Abstract: PAUP* 4.0 Beta is a major upgrade of the bestselling software for the inference of evolutionary trees, for use in Macintosh or Windows/DOS-based formats. This version is for use in Macintosh. Please note it is currently only available as a Beta version. For more information (and the Linux/UNIX version), visit www.sinauer.com/detail.php?id=8060
4,329 citations