VSI TCP/IP Messages, Logicals, & Decnet Applications
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Multinet for Openvms Messages, Logicals, and Decnet Applications
MultiNet for OpenVMS Messages, Logicals, and DECnet Applications Part Number: N-0703-54-NN-A November 2011 This guide lists common messages encountered when running MultiNet as well as a comprehensive list of MultiNet logicals with descriptions, and information on using TCP/IP Services for DECnet Applications. Revision/Update: This manual supersedes the MultiNet Messages and Logicals Reference, V5.3 Operating System/Version: VAX/VMS V5.5-2 or later, OpenVMS VAX V6.2 or later, OpenVMS Alpha V6.2 or later, OpenVMS I64 V8.2 or later Software Version: MultiNet V5.4 Process Software Framingham, Massachusetts USA The material in this document is for informational purposes only and is subject to change without notice. It should not be construed as a commitment by Process Software. Process Software assumes no responsibility for any errors that may appear in this document. Use, duplication, or disclosure by the U.S. Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. The following third-party software may be included with your product and will be subject to the software license agreement. Network Time Protocol (NTP). Copyright © 1992-2004 by David L. Mills. The University of Delaware makes no representations about the suitability of this software for any purpose. Point-to-Point Protocol. Copyright © 1989 by Carnegie-Mellon University. All rights reserved. The name of the University may not be used to endorse or promote products derived from this software without specific prior written permission. Redistribution and use in source and binary forms are permitted provided that the above copyright notice and this paragraph are duplicated in all such forms and that any documentation, advertising materials, and other materials related to such distribution and use acknowledge that the software was developed by Carnegie Mellon University. -
Grace FAQ (For Grace-5.1.23)
Grace FAQ (for Grace-5.1.23) by the Grace Team 12.06.2010 This document contains Frequently Asked Questions (FAQ) about Grace, a WYSIWYG 2D plotting tool for scientic data. (A German translation of this document, made by Tobias Brinkert, is available here: Grace FAQ <http://www.semibyte.de/dokuwiki/informatik:linux:xmgrace:grace_faq> .) Contents 1 General Questions 5 1.1 What is Grace?...........................................5 1.2 Where can I get Grace?.......................................5 1.3 Where can I get the most recent information about Grace?...................5 1.4 What is the dierence between Xmgr and Grace?........................5 1.5 Why did you change the name?..................................6 1.6 Is Grace free?............................................6 1.7 Who wrote Grace?.........................................6 1.8 Is there a PostscriptjLaTeXjHTMLjSGML version of this document?.............6 2 Getting Help 6 2.1 Are there any books about Grace?.................................6 2.2 Is there a User's Guide available for Grace?...........................7 2.3 Is there a Tutorial available for Grace?..............................7 2.4 Where do I get support for Grace?................................7 2.5 Is there a newsgroup devoted to Grace?..............................7 2.6 Is there a mailing list for Grace?..................................7 2.7 Is there a forum for Grace?.....................................8 3 Providing Help: Finding and Reporting Bugs8 3.1 I think I found a bug in Grace! How do I report -
VMD User's Guide
VMD User’s Guide Version 1.9.4a48 October 13, 2020 NIH Biomedical Research Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group1 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 N. Mathews Urbana, IL 61801 http://www.ks.uiuc.edu/Research/vmd/ Description The VMD User’s Guide describes how to run and use the molecular visualization and analysis program VMD. This guide documents the user interfaces displaying and grapically manipulating molecules, and describes how to use the scripting interfaces for analysis and to customize the behavior of VMD. VMD development is supported by the National Institutes of Health grant numbers NIH P41- GM104601. 1http://www.ks.uiuc.edu/ Contents 1 Introduction 11 1.1 Contactingtheauthors. ....... 12 1.2 RegisteringVMD.................................. 12 1.3 CitationReference ............................... ...... 12 1.4 Acknowledgments................................. ..... 13 1.5 Copyright and Disclaimer Notices . .......... 13 1.6 For information on our other software . .......... 15 2 Hardware and Software Requirements 17 2.1 Basic Hardware and Software Requirements . ........... 17 2.2 Multi-core CPUs and GPU Acceleration . ......... 17 2.3 Parallel Computing on Clusters and Supercomputers . .............. 18 3 Tutorials 19 3.1 RapidIntroductiontoVMD. ...... 19 3.2 Viewing a molecule: Myoglobin . ........ 19 3.3 RenderinganImage ................................ 21 3.4 AQuickAnimation................................. 21 3.5 An Introduction to Atom Selection . ......... 22 3.6 ComparingTwoStructures . ...... 22 3.7 SomeNiceRepresenations . ....... 23 3.8 Savingyourwork.................................. 24 3.9 Tracking Script Command Versions of the GUI Actions . ............ 24 4 Loading A Molecule 26 4.1 Notes on common molecular file formats . ......... 26 4.2 Whathappenswhenafileisloaded? . ....... 27 4.3 Babelinterface ................................. -
“Infectious” Open Source Software: Spreading Incentives Or Promoting Resistance?
“INFECTIOUS” OPEN SOURCE SOFTWARE: SPREADING INCENTIVES OR PROMOTING RESISTANCE? Greg R. Vetter* ABSTRACT Some free or open source software infects other software with its licensing terms. Popularly, this is called a viral license, but the software is not a computer virus. Free or open source software is a copyright-based licensing system. It typically allows modification and distribution on conditions such as source code availability, royalty free use and other requirements. Some licenses require distribution of modifications under the same terms. A license is infectious when it has a strong scope for the modifications provision. The scope arises from a broad conception of software derivative works. A strong infectious ambit would apply itself to modified software, and to software intermixed or coupled with non-open-source software. Popular open source software, including the * Assistant Professor of Law, University of Houston Law Center (UHLC); Co-Director, Institute for Intellectual Property and Information Law (IPIL) at UHLC; biography and additional background available at: www.law.uh.edu/faculty/gvetter. Relevant to this Article is that my background includes a Master’s degree in Computer Science and full-time work experience in the business-to-business software industry from 1987 to 1996. Research for this Article was supported by summer research grants from the University of Houston Law Foundation and a grant from the University of Houston’s New Faculty Research Program. I also thank UHLC’s IPIL Institute and its sponsors for support of my endeavors at UHLC. My thanks to UHLC students Jason Williams, Cuong Lam Nguyen, Stacey R. Vause and Nivine Zakhari for research assistance. -
Scientific Computing with Free Software on GNU/Linux HOWTO
Scientific Computing with Free software on GNU/Linux HOWTO Manoj Warrier <m_war (at) users.sourceforge.net> Shishir Deshpande <shishir (at) ipr.res.in> V. S. Ashoka <ashok (at) rri.res.in> 2003−10−03 Revision History Revision 1.2 2004−10−19 Revised by: M. W 1 Correction and new additional links Revision 1.1 2004−06−21 Revised by: M. W Updates and evaluated distros Revision 1.0 2003−11−18 Revised by: JP Document Reviewed by LDP. Revision 0.0 2003−10−01 Revised by: M. W first draft proposed This document aims to show how a PC running GNU/Linux can be used for scientific computing. It lists the various available free software and also links on the world wide web to tutorials on getting started with the tools. Scientific Computing with Free software on GNU/Linux HOWTO Table of Contents 1. Preamble..........................................................................................................................................................1 1.1. Copyright and License......................................................................................................................1 1.2. Disclaimer.........................................................................................................................................1 1.3. Motivation.........................................................................................................................................1 1.4. Credits / Contributors........................................................................................................................1 -
GROMACS Introductory Tutorial
GROMACS Tutorial GROMACS Introductory Tutorial Gromacs ver 3.3.1 Author: John E. Kerrigan, Ph.D. AST/IST, University of Medicine and Dentistry of NJ 675 Hoes Lane Piscataway, NJ 08554 Phone: (732) 2354473 Fax: (732) 2355252 Email: [email protected] 1 GROMACS Tutorial GROMACS Tutorial for Solvation Study of Spider Toxin Peptide. Yu, H., Rosen, M. K., Saccomano, N. A., Phillips, D., Volkmann, R. A., Schreiber, S. L.: Sequential assignment and structure determination of spider toxin omegaAgaIVB. Biochemistry 32 pp. 13123 (1993) GROMACS is a highend, high performance research tool designed for the study of protein dynamics using classical molecular dynamics theory. [1] This versatile software package is Gnu public license free software. You may download it from http://www.gromacs.org . GROMACS runs on linux, unix, and on Windows (a recent development). Synopsis. In this tutorial, you will study a toxin isolated from the venom of the funnel web spider. Venom toxins have been used in the past to identify cation channels. Calcium ion channels regulate the entry of this ion into cells. Nerve signals are highly governed by the balance of ions in neuronal cells. It is hypothesized that exposed positively charged residues in venoms like the spider toxin here bind favorably to the negatively charged entrance of the cell’s ion channel. The spider toxin in this tutorial has its positively charged residues pointing predominantly to one side of the peptide. The ion channel is blocked, resulting in blocked nerve signal leading to paralysis and ultimately to death (presumably via respiratory failure). -
The Openvms Frequently Asked Questions (FAQ)
The OpenVMS Frequently Asked Questions (FAQ) ABSTRACT This document contains answers to many common questions on the OpenVMS operating system, and covers OpenVMS, and OpenVMS running on Itanium, Alpha, and VAX hardware. While this document is available in multiple formats, the text-format version is far and away generally the easiest format to search. Revision/Update Information OpenVMS V8.3 Revision/Update Information: Revision Date/September 2006 FAQ Contents PREFACE i OPENVMS FREQUENTLY ASKED QUESTIONS (FAQ) iii CHAPTER 1 INTRODUCTION 1–1 1.1 WHAT CORE OPENVMS URLS DO YOU NEED TO KNOW? 1–1 1.2 WHAT ARE THE OPENVMS USENET NEWSGROUPS? 1–2 1.2.1 What is the scope of the comp.os.vms newsgroup? 1–2 1.2.2 What newsgroups carry VMS-related information? 1–2 1.2.3 What newsgroup archives are available? 1–3 1.2.4 What is the INFO-VAX mailing list? 1–3 1.2.4.1 How do I subscribe to or unsubscribe from INFO-VAX? • 1–3 1.3 WHAT IS [N]ETIQUETTE? 1–4 1.4 WHAT OPENVMS USER GROUP(S) ARE AVAILABLE? 1–5 1.5 OPENVMS SUPPORT, QUESTIONS AND COMMENTS? 1–5 1.5.1 Corporate contacts for OpenVMS Business Issues? 1–6 1.5.2 OpenVMS Ambassadors? 1–6 1.5.3 Contact for OpenVMS Marketing Issues and Questions? 1–6 1.5.4 Contact URLs for OpenVMS Technical Issues? 1–7 CHAPTER 2 GENERAL INFORMATION 2–1 2.1 WHAT IS OPENVMS? WHAT IS ITS HISTORY? 2–1 2.2 WHAT IS THE DIFFERENCE BETWEEN VMS AND OPENVMS? 2–2 iii Contents 2.3 WHAT’S IN A NAME? TERMINOLOGY AND PRODUCTS? 2–3 2.3.1 How do I port from VMS to OpenVMS? 2–4 2.4 WHICH IS BETTER, OPENVMS OR UNIX? 2–4 2.5 IS HP CONTINUING -
Opentext Exceed User's Guide
OpenText™ Exceed™ User's Guide User’s Guide Version 15 OpenText™ Exceed™ User's Guide Rev.: 2/27/15 This documentation has been created for software version 15.0. It is also valid for subsequent software versions as long as no new document version is shipped with the product or is published at https://knowledge.opentext.com. Open Text SA 40 Avenue Monterey, Luxembourg, Luxembourg L-2163 Tel: 35 2 264566 1 Open Text Corporation 275 Frank Tompa Drive, Waterloo, Ontario, Canada, N2L 0A1 Tel: +1-519-888-7111 Toll Free Canada/USA: 1-800-499-6544 International: +800-4996-5440 Fax: +1-519-888-0677 Support: http://support.opentext.com For more information, visit https://www.opentext.com Copyright © 2015 Open Text SA and/or Open Text ULC (in Canada). All Rights Reserved. Trademarks owned by Open Text SA or Open Text ULC (in Canada). All rights reserved. Exceed onDemand includes the following third-party software: Portions of the code have been contributed by Massachusetts Institute of Technology OpenGL is a registered trademark of Silicon Graphics Inc. This product includes software developed by the OpenSSL Project for use in the OpenSSL Toolkit. (http://www.openssl.org/) Copyright© 1998- 2005 The OpenSSL Project. All rights reserved. This product includes cryptographic software written by Eric Young ([email protected]) Copyright © 1995-1998 Eric Young ([email protected]) Portions of the code are based on the work of the VirtualGL Project. Portions of the code are based on the work of the FLTK Project. Exceed includes the following third-party software: Portions of the code have been contributed by Massachusetts Institute of Technology. -
Tcpware for Openvms Installation & Configuration Guide
TCPware® for OpenVMS Installation & Configuration Guide Part Number: N-6000-60-NN-A January 2014 This document provides the system manager with the procedures for installing, configuring, and starting up the TCPware for OpenVMS Product. Revision/Update: This is a revised manual. Operating System/Version: VAX/VMS V5.5-2 or later, OpenVMS VAX V6.0 or later, OpenVMS Alpha V6.1 or later, or OpenVMS I64 V8.2 or later Software Version: 6.0 Process Software Framingham, Massachusetts USA i The material in this document is for informational purposes only and is subject to change without notice. It should not be construed as a commitment by Process Software. Process Software assumes no responsibility for any errors that may appear in this document. Use, duplication, or disclosure by the U.S. Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. The following third-party software may be included with your product and will be subject to the software license agreement. Network Time Protocol (NTP). Copyright © 1992 by David L. Mills. The University of Delaware makes no representations about the suitability of this software for any purpose. Point-to-Point Protocol.Copyright © 1989 by Carnegie-Mellon University. All rights reserved. The name of the University may not be used to endorse or promote products derived from this software without specific prior written permission. Redistribution and use in source and binary forms are permitted provided that the above copyright notice and this paragraph are duplicated in all such forms and that any documentation, advertising materials, and other materials related to such distribution and use acknowledge that the software was developed by Carnegie Mellon University. -
ITC Lab Software List
ITC Lab Software List This list contains the software available on ITC Lab machines as of Spring 2018. It is categorized by operating system; a brief description of the software is available as well. Table of Contents Windows-only ................................................................................................................................ 2 Linux-only ........................................................................................................................................ 6 Both .................................................................................................................................................. 11 1 Windows-only 7-Zip: file archiver ActivePerl: commercial version of the Perl scripting language ActiveTCL: TCL distribution Adobe Acrobat Reader: PDF reading and editing software Adobe Creative Suite: graphic art, web, video, and document design programs • Animate • Audition • Bridge • Dreamweaver • Edge Animate • Fuse • Illustrator • InCopy • InDesign • Media Encoder • Muse • Photoshop • Prelude • Premiere • SpeedGrade ANSYS: engineering simulation software ArcGIS: mapping software Arena: discrete event simulation Autocad: CAD and drafting software Avogadro: molecular visualization/editor CDFplayer: software for Computable Document Format files ChemCAD: chemical process simulator • ChemDraw 2 Chimera: molecular visualization CMGL: oil/gas reservoir simulation software Cygwin: approximate Linux behavior/functionality on Windows deltaEC: simulation and design environment for thermoacoustic -
HMMER User's Guide
HMMER User’s Guide Biological sequence analysis using profile hidden Markov models Sean R. Eddy and the HMMER development team http://hmmer.org Version 3.3.2; Nov 2020 Copyright (C) 2020 Howard Hughes Medical Institute. HMMER and its documentation are freely distributed under the 3-Clause BSD open source license. For a copy of the license, see opensource.org/licenses/BSD-3-Clause. HMMER development is supported in part by the National Human Genome Research Institute of the US National Institutes of Health under grant number R01HG009116. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Contents Introduction 7 How to avoid reading this manual.......................... 7 Background and brief history............................. 8 Problems HMMER is designed for.......................... 9 HMMER uses ensemble algorithms, not optimal alignment............ 10 Assumptions and limitations of profile HMMs................... 12 How to learn more................................... 12 How to cite HMMER.................................. 12 How to report a bug.................................. 13 When’s HMMER4 coming?.............................. 13 What’s still missing................................... 15 How to avoid using this software (links to similar software)........... 15 Installation 17 Quickest: install a precompiled binary package.................. 17 Quick-ish: compile the source code.......................... 17 Geeky: compile source from our