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1954 1957 1960 1965 1970 1975 1980 1985 1990 1995 2000 2002 2003 2004 2005 2006 2007 2008 2009 2010 PostScript level 3 PostScript level 3 PostScript PostScript level 2 PostScript level 3 v 3016 v 3017 1982 1992 september 11, 1996 OO Forth 2003 september 11, 2005 1987 Forth FIG-Forth Forth-83 ANS Forth ISO Forth 1968 1978 1983 1986 1997 Logo Object Logo Tcl Tcl/Tk Tcl/Tk 8.1 Tcl/Tk 8.2.3 Tcl/Tk 8.3 Tcl/Tk 8.4 Tcl/Tk 8.4.1 Tcl/Tk 8.4.2 Tcl/Tk 8.4.3 Tcl/Tk 8.4.4 Tcl/Tk 8.4.5 Tcl/Tk 8.4.6 Tcl/Tk 8.4.7 Tcl/Tk 8.4.8 Tcl/Tk 8.4.9 Tcl/Tk 8.4.11 Tcl/Tk 8.4.12 Tcl/Tk 8.4.13 Tcl/Tk 8.4.14 Tcl/Tk 8.4.15 Tcl/Tk 8.5 Tcl/Tk 8.5.5 Tcl/Tk 8.5.6 Tcl/Tk 8.5.7 Tcl/Tk 8.5.9 1968 1986 mid 1988 end 1988 april 1999 dec. 16, 1999 october 22, 2001 september 10, 2002 october 22, 2002 march 3, 2003 may 20, 2003 july 22, 2003 november 24, 2003 march 1, 2004 july 25, 2004 nov. 22, 2004 december 7, 2004 june 28, 2005 december 6, 2005 april 19, 2006 october 19, 2006 may 25, 2007 december 20, 2007 october 15, 2008 january 2009 april 15, 2009 september 8, 2010 FORTRAN IV Fortran 2000 FORTRAN I FORTRAN II FORTRAN III FORTRAN IV FORTRAN V Fortran 90 ISO Fortran 2003 Fortran 2008 FORTRAN (Fortran 66 ANS) (Fortran 77 ANSI) Fortran 95 ISO (draft) november 1954 october 1956 1957 end-1958 1962 1991 december 15, 1997 november 30, 2004 september 2010 1966 april 1978 A A+ september 30, 2002 Prolog Prolog II Prolog III 1988 1992 Prolog IV 1970 october 1982 1984 1997 J K Sharp APL 1990 1996 JOSS TELCOMP MUMPS MUMPS (ANSI) MUMPS (FIPS) MUMPS ISO M M ANSI Open M M ISO M ISO 1964 1965 1966 september 15, 1977 1986 1992 1994 dec 8, 1995 dec 11, 1995 1999 january 6, 2005 Modula 3 Delphi Delphi 5 Delphi 6 Delphi 7 Delphi 8 Delphi 2005 Delphi 2006 Delphi 2007 Delphi 2009 Delphi 2010 1988 march 2007 august 2008 august 2009 march 2, 1995 APL96 august, 1999 may 1, 2001 august 6, 2002 november 2003 november 2004 october 30, 2005 Python 3.0a2 Python 3.1 APL APL 2 Python 3.0 Python 3.0.1 1960 august 1984 1996 december 7, 2007 february 13, 2009 june 27, 2009 B ABC december 3, 2008 1981 1987 Python Python 1.5.2 Python 1.6 Python 2.0 Python 2.1 Python 2.2 Python 2.2.1 Python 2.2.2 Python 2.3a2 Python 2.2.3 Python 2.3 Python 2.3.1 Python 2.3.2 Python 2.3.3 Python 2.3.4 Python 2.4 Python 2.4.1 Python 2.4.2 Python 2.5 Python 2.5.1 Python 2.6 Python 2.6.1 Python 2.6.2 Python 2.6.3 Python 2.7 1991 april 13, 1999 april 17, 2001 april 10, 2002 october 14, 2002 july 29, 2003 september 23, 2003 october 3, 2003 december 19, 2003 may 27, 2004 november 30, 2004 march 30, 2005 september 19, 2006 april 19, 2007 october 1, 2008 december 4, 2008 april 14, 2009 october 2, 2009 july 4, 2010 Object Pascal Borland september 5, 2000 october 16, 2000 december 21, 2001 february 19, 2003 may 30, 2003 september 28, 2005 1985 Turbo Pascal B-O Flow-Matic COBOL COBOL 61 COBOL 61 COBOL COBOL 68 ANS COBOL 74 ANSI COBOL 85 ISO/ANSI OO COBOL COBOL 2002 ISO/ANSI 1957 1958 1959 1961 Extended 1965 1968 1974 1985 1997 december 2002 1962 Rex 1.00 Rex 2.00 Rex 3.00 Rexx 3.20 ANSI Rexx Object Rexx may 1979 1980 1982 1984 february 25, 1997 Pascal Pascal AFNOR 1970 1983 Oberon Oberon-2 Active Oberon 1987 1991 2001 PL/M Modula 2 Modula-2 ISO Modula-2 ISO Modula Generic Extension 1972 1975 1979 june 1, 1996 Ada Ada 83 ANSI Ada ISO Ada 95 december 19, 1998 Ada 2006 (draft) Ada 2005 january 1983 1987 1995 2005 PL/I PL/1 ANS 1979 NetRexx NetRexx 1.150 C# C# C# 2.0 march 9, 2007 1991 C# (ECMA) (beta) C# 2.0 1964 1976 july 23, 1999 june 26, 2000 (ISO) november 2005 Concurrent C december 13, 2001 march 28, 2003 july 2003 1984 ISO C C# 3.0 CPL BCPL B C (K&R) ANSI C ISO C ISO C (C99) C# 3.5 C Classic C (C89) (C90) (C95) (beta) C# 3.0 C# 4.0 1963 july 1967 1969 1971 1978 december 1, 1999 november 6, 2006 november 19, 2007 april 12, 2010 1989 december 15, 1990 april 1, 1996 JScript JScript september 2005 JOVIAL JOVIAL I JOVIAL II JOVIAL 3 Objective-C may 1996 Objective-C 2.0 Objective-C 2.1 1959 august 28, 2009 1960 1961 1965 1983 JavaScript 2.0 JavaScript 2.0 august 7, 2006 Java 6 update 7 Cmm LiveScript JavaScript Java 2 (v6.0 beta) Java 6 Java 6 update 2 Java 6 update 11 Java 6 update 14 Java 6 update 22 1995 JavaScript 1.5 (draft 1) (draft 4) december 2004 july 5, 2007 july 11, 2008 december 2, 2008 june 10, 2009 CORAL 64 CORAL 66 1992 december 1995 C++03 ISO/IEC december 11, 2006 november 12, 2010 C with Classes C++ ARM C++ C++98 ANSI/ISO february 18, 1999 april 26, 2002 C++0x draft C++1x draft 1964 1966 april 1980 1989 1998 2003 2008 CLU july 1983 ECMAScript ECMAScript ed3 ECMAScript ed4 (draft) july 22, 2009 2002 Java 2 (v1.5.0) Simula 67 1974 june 1997 december 1999 Java 2 (v1.4) Java 2 Java 2 (v1.4.1_03) Java 2 (v5.0) (beta 2) Java 2 (v5.0) Java 2 (v5.0 update 3) Java 2 (v5.0 update 8) Java 2 (v5.0 update 12) Java 2 (v5.0 update 16) Java 2 (v5.0 update 17) Java 2 (v5.0 update 18) Java 2 (v5.0 update 21) Simula I Oak Java 1 Java 2 (v1.2) Java 2 (v1.3) Java 2 (v1.4.0_01) Java 2 (v1.4.1) (v1.4.1_02) (beta 1) july 11, 2008 1964 1967 may 8, 2000 early access june 11, 2003 june 28, 2004 september 30, 2004 april 28, 2005 august 11, 2006 may 31, 2007 december 2, 2008 march 24, 2009 september 11, 2009 Mesa june 1991 may 23, 1995 december 8, 1998 june 4, 2002 september 2002 february 27, 2003 Java 2 (v1.4.2) Java 2 (v1.4.2_01) Java 2 (v1.4.2_02) february 5, 2004 Java 2 (v1.4.2_18) ALGOL W february 6, 2002 Java 2 (v1.4.2_03) Java 2 (v1.4.2_04) Java 2 (v1.4.2_05) Java 2 (v1.4.2_06) Java 2 (v1.4.2_19) 1977 Ruby april 29, 2003 august 26, 2003 october 22, 2003 december 13, 2003 july 11, 2008 december 2, 2008 Ruby 1.9.2 preview 1 IAL ALGOL 58 ALGOL 60 1966 ALGOL 68 Cedar Ruby 0.95 Ruby 1.1 alpha 0 Ruby 1.3.2 Ruby 1.6.7 Ruby 1.6.8 march 8, 2004 june 30, 2004 november 23, 2004 Ruby 1.8.2 Ruby 1.8.3 Ruby 1.8.5 Ruby 1.8.6 Ruby 1.8.7 Ruby 1.9.1 Ruby 1.9.2 february 24, 1993 august 13, 1997 Ruby 1.6.1 Ruby 1.6.5 Ruby 1.8 Ruby 1.8.1 Ruby 1.8.4 july 18, 2009 1958 1958 1960 december 1983 december 1995 april 2, 1999 september 27, 2000 september 19, 2001 march 1, 2002 december 24, 2002 december 25, 2004 september 21, 2005 december 24, 2005 august 25, 2006 march 13, 2007 may 31, 2008 january 30, 2009 august 18, 2010 1968 august 4, 2003 december 25, 2003 GOGOL GOGOL III Smalltalk Smalltalk-72 Smalltalk-74 Smalltalk-76 Smalltalk-78 Smalltalk-80 ANSI Smalltalk 1964 1967 1971 1972 1974 1976 1978 1980 may 19, 1998 sed Self 4.0 Self 4.1 Self 4.1.6 Self 4.2.1 Self 4.3 Self april 3, 2004 Sail 1973 Mainsail Eiffel Eiffel 2 Eiffel 3 july 10, 1995 Eiffel 4 Eiffel 4.2 ISE Eiffel 5 august 7, 2001 september 2002 ECMA Eiffel june 30, 2006 1968 1975 1986 1988 1993 december 11, 1996 february 6, 1998 2001 june 2005 ISWIM awk nawk PHP/FI PHP 2.0 PHP 3.0 PHP 4.0 PHP 4.1.0 PHP 4.2.0 PHP 4.2.2 PHP 4.2.3 PHP 4.3.0 PHP 4.3.1 PHP 4.3.2 PHP 4.3.3 PHP 4.3.4 PHP 4.3.5 PHP 4.3.6 PHP 4.3.7 PHP 4.3.8 PHP 4.3.10 PHP 4.4.1 PHP 4.4.2 PHP 4.4.4 PHP 4.4.7 PHP 4.4.8 PHP 4.4.9 1966 1978 1985 1995 nov. 13, 1997 june 6, 1998 may 22, 2000 december 8, 2001 april 22, 2002 july 22, 2002 september 6, 2002 december 27, 2002 feb. 17, 2003 may 29, 2003 august 25, 2003 november 3, 2003 march 26, april 15, june 3, july 13, 2004 december 15, 2004 october 31, 2005 january 13, 2006 august 17, 2006 may 3, 2007 january 3, 2008 august 7, 2008 KRC Sather 0.1 Sather 1.0 Sather 1.1 Sather 1.2.1 2004 2004 2004 1981 june 1991 mid-1994 september 1995 november 4, 1999 PHP 5.0.0 csh PHP 5.0.3 PHP 5.0.4 PHP 5.0.5 PHP 5.1.0 PHP 5.1.6 PHP 5.2.0 PHP 5.2.3 PHP 5.2.4 PHP 5.2.5 PHP 5.2.6 PHP 5.2.7 PHP 5.2.8 PHP 5.3 PHP 5.3.3 july 13, 2004 december 15, 2004 PHP 5.2.9 october 1978 april 3, 2005 september 6, 2005 november 24, 2005 august 24, 2006 november 2, 2006 may 31, 2007 august 30, 2007 november 9, 2007 may 1, 2008 december 4, 2008 december 8, 2008 february 26, 2009 june 30, 2009 july 22, 2010 SASL Perl 2.000 Perl 3.000 Perl 4.000 Perl 5.000 Perl 5.005_50 Perl 5.6.0 Perl 5.7,0 Perl 5.8.0 Perl 5.8.1 Perl 5.8.2 Perl 5.8.3 Perl 5.8.4 Perl 5.8.5 Perl 5.8.8 Perl 5.11.0 Perl 1.000 july 26, 1998 Perl 5.8.6 Perl 5.8.7 Perl 5.10 Perl 5.12.0 1976 Miranda december 18, 1987 january 5, 1988 october 18, 1989 march 21, 1991 october 18, 1994 march 28, 2000 september 2, 2000 july 18, 2002 september 26, 2003 november 5, 2003 january 1, 2004 april 23, 2004 july 21, 2004 november 30, 2004 june 3, 2005 february 2, 2006 december 18, 2007 october 2, 2009 april 12, 2010 1982 Objective Caml O’Caml 2 O’Caml 3.00 O’Caml 3.02 O’Caml 3.03 O’Caml 3.04 O’Caml 3.05 O’Caml 3.06 O’Caml 3.08.0 O’Caml 3.08.2 O’Caml 3.09.2 O’Caml 3.10.0 O’Caml 3.10.2 O’Caml 3.11.0 O’Caml 3.11.1 O’Caml 3.12.0 sh 1996 O’Caml 1.0.7 O’Caml 3.07 1969 december 11, 1997 1998 june 2000 july 30, 2001 dec 10, 2001 dec 12, 2001 july 29, 2002 august 20, 2002 september 29, 2003 july 13, 2004 november 2004 april 14, 2006 may 16, 2007 february 29, 2008 december 4, 2008 june 12, 2009 august 2, 2010 MS Basic 2.0 BASICA GW-Basic QuickBasic 1.0 QuickBasic 4.5 MS Basic PDS 7.0 MS PDS 7.1 Visual Basic 3.0 Visual Basic 4.0 Visual Basic 5.0 Visual Basic 6.0 VB.NET BASIC 1989 Visual Basic 1.0 Visual Basic 2.0 may 1, 1964 july 1975 1981 1983 1985 1988 1990 may 20, 1991 march 1992 june 93 september 1995 april 1997 june 16, 1998 (Visual Basic 7.0) Clos 2001 Lisp Lisp 1 Lisp 1.5 Common Lisp 1989 Common Lisp ANSI 1958 1959 1962 1984 december 8, 1994 6 6 Scheme Scheme MIT Scheme 84 Scheme IEEE Scheme R5RS Scheme R RS (draft) Scheme R RS 1990 1998 september 14, 2006 august 28, 2007 1975 1978 1984 Haskell 1.3 Haskell 1.4 Haskell 98 Haskell 2010 Haskell HP 2010.2.0.0 Haskell 1.0 Haskell 1.1 Haskell 1.2 Haskell 98 (announced) 1987 april 1, 1990 march 1992 may 1996 april 1997 february 1999 (revised) july 2010 ML SML SML ‘90 SML ‘97 december 2002 november 2009 1973 1984 1990 1997 SL5 Icon Unicon Languages SNOBOL SNOBOL 2 SNOBOL 3 SNOBOL 4 1976 1977 Caml 2-6.1 2001 december 28, 2010 Caml Caml 3.1 1962 april 1964 1965 1967 1987 1991 1993 © Éric Lévénez 1999-2010 <http://www.levenez.com/lang/>.
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    An Introduction to Programming in Simula Rob Pooley This document, including all parts below hyperlinked directly to it, is copyright Rob Pooley ([email protected]). You are free to use it for your own non-commercial purposes, but may not copy it or reproduce all or part of it without including this paragraph. If you wish to use it for gain in any manner, you should contact Rob Pooley for terms appropriate to that use. Teachers in publicly funded schools, universities and colleges are free to use it in their normal teaching. Anyone, including vendors of commercial products, may include links to it in any documentation they distribute, so long as the link is to this page, not any sub-part. This is an .pdf version of the book originally published by Blackwell Scientific Publications. The copyright of that book also belongs to Rob Pooley. REMARK: This document is reassembled from the HTML version found on the web: https://web.archive.org/web/20040919031218/http://www.macs.hw.ac.uk/~rjp/bookhtml/ Oslo 20. March 2018 Øystein Myhre Andersen Table of Contents Chapter 1 - Begin at the beginning Basics Chapter 2 - And end at the end Syntax and semantics of basic elements Chapter 3 - Type cast actors Basic arithmetic and other simple types Chapter 4 - If only Conditional statements Chapter 5 - Would you mind repeating that? Texts and while loops Chapter 6 - Correct Procedures Building blocks Chapter 7 - File FOR future reference Simple input and output using InFile, OutFile and PrintFile Chapter 8 - Item by Item Item oriented reading and writing and for loops Chapter 9 - Classes as Records Chapter 10 - Make me a list Lists 1 - Arrays and simple linked lists Reference comparison Chapter 11 - Like parent like child Sub-classes and complex Boolean expressions Chapter 12 - A Language with Character Character handling, switches and jumps Chapter 13 - Let Us See what We Can See Inspection and Remote Accessing Chapter 14 - Side by Side Coroutines Chapter 15 - File For Immediate Use Direct and Byte Files Chapter 16 - With All My Worldly Goods..
  • A Command-Line Interface for Analysis of Molecular Dynamics Simulations

    A Command-Line Interface for Analysis of Molecular Dynamics Simulations

    taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. João M.C. Teixeira1, 2 1 Previous, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain 2 DOI: 10.21105/joss.02175 Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Software Canada • Review Summary • Repository • Archive Molecular dynamics (MD) simulations of biological molecules have evolved drastically since its application was first demonstrated four decades ago (McCammon, Gelin, & Karplus, 1977) and, nowadays, simulation of systems comprising millions of atoms is possible due to the latest Editor: Richard Gowers advances in computation and data storage capacity – and the scientific community’s interest Reviewers: is growing (Hospital, Battistini, Soliva, Gelpí, & Orozco, 2019). Academic groups develop most of the MD methods and software for MD data handling and analysis. The MD analysis • @amritagos libraries developed solely for the latter scope nicely address the needs of manipulating raw data • @luthaf and calculating structural parameters, such as: MDAnalysis (Gowers et al., 2016; Michaud- Agrawal, Denning, Woolf, & Beckstein, 2011); (McGibbon et al., 2015); (Romo, Submitted: 03 March 2020 MDTraj LOOS Published: 02 June 2020 Leioatts, & Grossfield, 2014); and PyTraj (Hai Nguyen, 2016; Roe & Cheatham, 2013), each with its advantages and drawbacks inherent to their implementation strategies. This diversity License enriches the field with a panoply of strategies that the community can utilize. Authors of papers retain copyright and release the work The MD analysis software libraries widely distributed and adopted by the community share under a Creative Commons two main characteristics: 1) they are written in pure Python (Rossum, 1995), or provide a Attribution 4.0 International Python interface; and 2) they are libraries: highly versatile and powerful pieces of software that, License (CC BY 4.0).