OS X

About: OS X is a research topic. Over the lifetime, 425 publications have been published within this topic receiving 45485 citations.

UCSF Chimera--a visualization system for exploratory research and analysis.

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/.

Investigation of the freely available easy-to-use software 'EZR' for medical statistics.

Abstract: Although there are many commercially available statistical software packages, only a few implement a competing risk analysis or a proportional hazards regression model with time-dependent covariates, which are necessary in studies on hematopoietic SCT. In addition, most packages are not clinician friendly, as they require that commands be written based on statistical languages. This report describes the statistical software 'EZR' (Easy R), which is based on R and R commander. EZR enables the application of statistical functions that are frequently used in clinical studies, such as survival analyses, including competing risk analyses and the use of time-dependent covariates, receiver operating characteristics analyses, meta-analyses, sample size calculation and so on, by point-and-click access. EZR is freely available on our website (http://www.jichi.ac.jp/saitama-sct/SaitamaHP.files/statmed.html) and runs on both Windows (Microsoft Corporation, USA) and Mac OS X (Apple, USA). This report provides instructions for the installation and operation of EZR.

Open source clustering software

Abstract: Summary: We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. Availability: The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Tablet—next generation sequence assembly visualization

Abstract: Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides highquality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multicore aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk

Advanced Programming in the Unix Environment

Abstract: For more than twenty years, serious C programmers have relied on one book for practical, in-depth knowledge of the programming interfaces that drive the UNIX and Linux kernels: W Richard Stevens Advanced Programming in the UNIX Environment Now, once again, Richs colleague Steve Rago has thoroughly updated this classic work The new third edition supports todays leading platforms, reflects new technical advances and best practices, and aligns with Version 4 of the Single UNIX Specification Steve carefully retains the spirit and approach that have made this book so valuable Building on Richs pioneering work, he begins with files, directories, and processes, carefully laying the groundwork for more advanced techniques, such as signal handling and terminal I/O He also thoroughly covers threads and multithreaded programming, and socket-based IPC This edition covers more than seventy new interfaces, including POSIX asynchronous I/O, spin locks, barriers, and POSIX semaphores Most obsolete interfaces have been removed, except for a few that are ubiquitous Nearly all examples have been tested on four modern platforms: Solaris 10, Mac OS X version 1068 (Darwin 1080), FreeBSD 80, and Ubuntu version 1204 (based on Linux 32) As in previous editions, youll learn through examples, including more than ten thousand lines of downloadable, ISO C source code More than four hundred system calls and functions are demonstrated with concise, complete programs that clearly illustrate their usage, arguments, and return values To tie together what youve learned, the book presents several chapter-length case studies, each reflecting contemporary environments Advanced Programming in the UNIX Environment has helped generations of programmers write code with exceptional power, performance, and reliability Now updated for todays systems, this third edition will be even more valuable