A Command-Line Interface for Analysis of Molecular Dynamics Simulations
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The Molecular Sciences Software Institute
The Molecular Sciences Software Institute T. Daniel Crawford, Cecilia Clementi, Robert Harrison, Teresa Head-Gordon, Shantenu Jha*, Anna Krylov, Vijay Pande, and Theresa Windus http://molssi.org S2I2 HEP/CS Workshop at NCSA/UIUC 07 Dec, 2016 1 Outline • Space and Scope of Computational Molecular Sciences. • “State of the art and practice” • Intellectual drivers • Conceptualization Phase: Identifying the community and needs • Bio-molecular Simulations (BMS) Conceptualization • Quantum Mechanics/Chemistry (QM) Conceptualization • Execution Phase. • Structure and Governance Model • Resource Distribution • Work Plan 2 The Molecular Sciences Software Institute (MolSSI) • New project (as of August 1st, 2016) funded by the National Science Foundation. • Collaborative effort by Virginia Tech, Rice U., Stony Brook U., U.C. Berkeley, Stanford U., Rutgers U., U. Southern California, and Iowa State U. • Total budget of $19.42M for five years, potentially renewable to ten years. • Joint support from numerous NSF divisions: Advanced Cyberinfrastructure (ACI), Chemistry (CHE), Division of Materials Research (DMR), Office of Multidisciplinary Activities (OMA) • Designed to serve and enhance the software development efforts of the broad field of computational molecular science. 3 Computational Molecular Sciences (CMS) • The history of CMS – the sub-fields of quantum chemistry, computational materials science, and biomolecular simulation – reaches back decades to the genesis of computational science. • CMS is now a “full partner with experiment”. • For an impressive array of chemical, biochemical, and materials challenges, our community has developed simulations and models that directly impact: • Development of new chiral drugs; • Elucidation of the functionalities of biological macromolecules; • Development of more advanced materials for solar-energy storage, technology for CO2 sequestration, etc. -
Easyaccess: Enhanced SQL Command Line Interpreter for Astronomical Surveys
easyaccess: Enhanced SQL command line interpreter for astronomical surveys Matias Carrasco Kind1, Alex Drlica-Wagner2, Audrey Koziol1, and Don Petravick1 1 National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign. 1205 W Clark St, Urbana, IL USA 61801 2 Fermi National Accelerator Laboratory, P. O. Box 500, DOI: 00.00000/joss.00000 Batavia,IL 60510, USA Software • Review Summary • Repository • Archive easyaccess is an enhanced command line interpreter and Python package created to Submitted: 00 January 0000 facilitate access to astronomical catalogs stored in SQL Databases. It provides a custom Published: 00 January 0000 interface with custom commands and was specifically designed to access data from the License Dark Energy Survey Oracle database, although it can easily be extended to another survey Authors of papers retain copyright or SQL database. The package was completely written in Python and support customized and release the work under a Cre- addition of commands and functionalities. Visit https://github.com/mgckind/easyaccess ative Commons Attribution 4.0 In- to view installation instructions, tutorials, and the Python source code for easyaccess. ternational License (CC-BY). The Dark Energy Survey The Dark Energy Survey (DES) (DES Collaboration 2005; DES Collaboration 2016) is an international, collaborative effort of over 500 scientists from 26 institutions in seven countries. The primary goals of DES are reveal the nature of the mysterious dark energy and dark matter by mapping hundreds of millions of galaxies, detecting thousands of supernovae, and finding patterns in the large-scale structure of the Universe. Survey operations began on on August 31, 2013 and will conclude in early 2019. -
Ed 060 620 Author Title Institution Spons Agency Pub Date
DOCUMENT RESUME ED 060 620 EM 009 626 AUTHOR Bork, Alfred M. TITLE Introduction to Computer Programming Languages. INSTITUTION California Univ., Irvine. Physics Computer Development Project. SPONS AGENCY National Science Foundation, Washington, D-C. PUB DATE Dec 71 NOTE 5p. JOURNAL CIT JCST; P 12-16 December 1971 EDRS PRICE MF-$0.65 HC-$3.29 DESCRIPTORS Computer Assisted Instruction; Computer Science Education; *Guides; *Programing; *Programing Languages ABSTRACT A brief introduction to computer programing explains the basic grammar of ccmputer language as well as fundamental computer techniques. What constitutes a computer program is made clear, then three simple kinds of statements basic to the computational computer are defined: assignment statements, input-output statements, and branching statements. A short description of several available computer languages is given along with an explanation of how the newcomer would make use of basic computer software. Finally, five different versions of a simple program (for solving the harmonic oscillator numerically) are given with comparison. (RB) 74.-E U.S. DEPARTMENT OF HEALTH. F749 EDUCATION & WELFARE erP\ e-"ri". "79' - A ott, Tritl OFFICE OF EDUCATION t,.4 taicta- THIS DOCUMENT HAS BEEN REPRO- DUCED EXACTLY AS RECEIVED FROM THE PERSON OR ORGANIZATION ORIG- '14r- C-1"?Fig ErtrIgf7t Or>re!9,1 2 INATING IT. POINTS OF VIEW OR OPIN- 616 ti LiS kC..".4 .2) szyj /ONS STATED DO NOT NECESSARILY cp-S.e REPRESENT OFFICIAL OFFICE OF EDU- CATION POSITION OR POLICY. By Affred M. Bork r,9 he digital computer is a powerful, calculating. andwhat the programmer wants it to do. For convenience, L logical device. -
EPSRC Service Level Agreement with STFC for Computational Science Support
CoSeC Computational Science Centre for Research Communities EPSRC Service Level Agreement with STFC for Computational Science Support FY 2016/17 Report and Update on FY 2017/18 Work Plans This document contains the 2016/17 plans, 2016/17 summary reports, and 2017/18 plans for the programme in support of CCP and HEC communities delivered by STFC and funded by EPSRC through a Service Level Agreement. Notes in blue are in-year updates on progress to the tasks included in the 2016/17 plans. Text highlighted in yellow shows changes to the draft 2017/18 plans that we submitted in January 2017. Contents CCP5 – Computer Simulation of Condensed Phases .......................................................................... 4 CCP5 – 2016 / 17 Plans (1 April 2016 – 31 March 2017) ...................................................... 4 CCP5 – Summary Report (1 April 2016 – 31 March 2017) .................................................... 7 CCP5 –2017 / 18 Plans (1 April 2017 – 31 March 2018) ....................................................... 8 CCP9 – Electronic Structure of Solids .................................................................................................. 9 CCP9 – 2016 / 17 Plans (1 April 2016 – 31 March 2017) ...................................................... 9 CCP9 – Summary Report (1 April 2016 – 31 March 2017) .................................................. 11 CCP9 – 2017 / 18 Plans (1 April 2017 – 31 March 2018) .................................................... 12 CCP-mag – Computational Multiscale -
A GTK+ Binding to Build Graphical User Interfaces in Fortran Vincent Magnin, James Tappin, Jens Hunger, Jerry De Lisle
gtk-fortran: a GTK+ binding to build Graphical User Interfaces in Fortran Vincent Magnin, James Tappin, Jens Hunger, Jerry de Lisle To cite this version: Vincent Magnin, James Tappin, Jens Hunger, Jerry de Lisle. gtk-fortran: a GTK+ binding to build Graphical User Interfaces in Fortran. Journal of Open Source Software, Open Journals, 2019, 4 (34), pp.1109. 10.21105/joss.01109. hal-02113675 HAL Id: hal-02113675 https://hal.archives-ouvertes.fr/hal-02113675 Submitted on 29 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License gtk-fortran: a GTK+ binding to build Graphical User Interfaces in Fortran Vincent MAGNIN1, James TAPPIN2, Jens HUNGER3, and Jerry DE LISLE4 1 Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520 - IEMN, F-59000 Lille, France 2 RAL Space, STFC Rutherford Appleton Laboratory, Harwell Campus ,Didcot,Oxfordshire OX11 0QX, United Kingdom 3 Technische Universität Dresden, Department of Chemistry and Food Chemistry, Dresden, Germany 4 GFortran Team, USA DOI: 10.21105/joss.01109 Software • Review Summary • Repository • Archive Fortran is still much used in research because it is suited by design to scientific computing Submitted: 11 October 2018 and there is a lot of legacy code written in this language. -
1. with Examples of Different Programming Languages Show How Programming Languages Are Organized Along the Given Rubrics: I
AGBOOLA ABIOLA CSC302 17/SCI01/007 COMPUTER SCIENCE ASSIGNMENT 1. With examples of different programming languages show how programming languages are organized along the given rubrics: i. Unstructured, structured, modular, object oriented, aspect oriented, activity oriented and event oriented programming requirement. ii. Based on domain requirements. iii. Based on requirements i and ii above. 2. Give brief preview of the evolution of programming languages in a chronological order. 3. Vividly distinguish between modular programming paradigm and object oriented programming paradigm. Answer 1i). UNSTRUCTURED LANGUAGE DEVELOPER DATE Assembly Language 1949 FORTRAN John Backus 1957 COBOL CODASYL, ANSI, ISO 1959 JOSS Cliff Shaw, RAND 1963 BASIC John G. Kemeny, Thomas E. Kurtz 1964 TELCOMP BBN 1965 MUMPS Neil Pappalardo 1966 FOCAL Richard Merrill, DEC 1968 STRUCTURED LANGUAGE DEVELOPER DATE ALGOL 58 Friedrich L. Bauer, and co. 1958 ALGOL 60 Backus, Bauer and co. 1960 ABC CWI 1980 Ada United States Department of Defence 1980 Accent R NIS 1980 Action! Optimized Systems Software 1983 Alef Phil Winterbottom 1992 DASL Sun Micro-systems Laboratories 1999-2003 MODULAR LANGUAGE DEVELOPER DATE ALGOL W Niklaus Wirth, Tony Hoare 1966 APL Larry Breed, Dick Lathwell and co. 1966 ALGOL 68 A. Van Wijngaarden and co. 1968 AMOS BASIC FranÇois Lionet anConstantin Stiropoulos 1990 Alice ML Saarland University 2000 Agda Ulf Norell;Catarina coquand(1.0) 2007 Arc Paul Graham, Robert Morris and co. 2008 Bosque Mark Marron 2019 OBJECT-ORIENTED LANGUAGE DEVELOPER DATE C* Thinking Machine 1987 Actor Charles Duff 1988 Aldor Thomas J. Watson Research Center 1990 Amiga E Wouter van Oortmerssen 1993 Action Script Macromedia 1998 BeanShell JCP 1999 AngelScript Andreas Jönsson 2003 Boo Rodrigo B. -
Using GNU Make to Manage the Workflow of Data Analysis Projects
JSS Journal of Statistical Software June 2020, Volume 94, Code Snippet 1. doi: 10.18637/jss.v094.c01 Using GNU Make to Manage the Workflow of Data Analysis Projects Peter Baker University of Queensland Abstract Data analysis projects invariably involve a series of steps such as reading, cleaning, summarizing and plotting data, statistical analysis and reporting. To facilitate repro- ducible research, rather than employing a relatively ad-hoc point-and-click cut-and-paste approach, we typically break down these tasks into manageable chunks by employing sep- arate files of statistical, programming or text processing syntax for each step including the final report. Real world data analysis often requires an iterative process because many of these steps may need to be repeated any number of times. Manually repeating these steps is problematic in that some necessary steps may be left out or some reported results may not be for the most recent data set or syntax. GNU Make may be used to automate the mundane task of regenerating output given dependencies between syntax and data files. In addition to facilitating the management of and documenting the workflow of a complex data analysis project, such automation can help minimize errors and make the project more reproducible. It is relatively simple to construct Makefiles for small data analysis projects. As projects increase in size, difficulties arise because GNU Make does not have inbuilt rules for statistical and related software. Without such rules, Makefiles can become unwieldy and error-prone. This article addresses these issues by providing GNU Make pattern rules for R, Sweave, rmarkdown, SAS, Stata, Perl and Python to streamline management of data analysis and reporting projects. -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape. Permalink https://escholarship.org/uc/item/4sm897jh Journal Chemical reviews, 121(8) ISSN 0009-2665 Authors Kowalski, Karol Bair, Raymond Bauman, Nicholas P et al. Publication Date 2021-04-01 DOI 10.1021/acs.chemrev.0c00998 Peer reviewed eScholarship.org Powered by the California Digital Library University of California From NWChem to NWChemEx: Evolving with the computational chemistry landscape Karol Kowalski,y Raymond Bair,z Nicholas P. Bauman,y Jeffery S. Boschen,{ Eric J. Bylaska,y Jeff Daily,y Wibe A. de Jong,x Thom Dunning, Jr,y Niranjan Govind,y Robert J. Harrison,k Murat Keçeli,z Kristopher Keipert,? Sriram Krishnamoorthy,y Suraj Kumar,y Erdal Mutlu,y Bruce Palmer,y Ajay Panyala,y Bo Peng,y Ryan M. Richard,{ T. P. Straatsma,# Peter Sushko,y Edward F. Valeev,@ Marat Valiev,y Hubertus J. J. van Dam,4 Jonathan M. Waldrop,{ David B. Williams-Young,x Chao Yang,x Marcin Zalewski,y and Theresa L. Windus*,r yPacific Northwest National Laboratory, Richland, WA 99352 zArgonne National Laboratory, Lemont, IL 60439 {Ames Laboratory, Ames, IA 50011 xLawrence Berkeley National Laboratory, Berkeley, 94720 kInstitute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794 ?NVIDIA Inc, previously Argonne National Laboratory, Lemont, IL 60439 #National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373 @Department of Chemistry, Virginia Tech, Blacksburg, VA 24061 4Brookhaven National Laboratory, Upton, NY 11973 rDepartment of Chemistry, Iowa State University and Ames Laboratory, Ames, IA 50011 E-mail: [email protected] 1 Abstract Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. -
Measure to Fund Upgrades
In Sports... In Forum... Spartans upset On the bus in 10th-ranked SPARTAN San Jose: 49ers, win two of sights, sounds three games in and smells. weekend series. FORUM & OPINION See story on page 4. See column on page 2. 1'111,11,11yd for AIStith' tucr 1414 Volume 102, Number 49 Monday. April 18, 1994 Measure to fund upgrades New building By Laurel Anderson The money will be divided almost oumi, associate executive vice presi- The $901; ntillion to fund the pro- in the works siranan Daily Staff Writer equally among the three systems. dent of facilities development and jects comes In the state's selling of genti.t1 /bligation bonds to investors By Laurel Anderson A bond measure to fund Califor- The CSU's project list covers an operations. Sintruui Day St41 Writer nia college campus improvements estimated 80 projects at all 20 Bentley-Adler said, "In who earn interest on the money they will be on the June 1994 ballot. The campuses. 1990 when Proposition 143 loan to the state. The total cost to the A plan to construct and renovate campus projects include modernization and "The bond measure is the ALIFORNIA failed, that set us back a cou- state is $1.6 billion, because an addi- facilities will proceed if SJSU receives funding remodeling of facilities, updating only way to remodel and ple years in building and tional $700 million will be paid in from a $900 million bond measure. safety standards and replacing aging repair some of our facilities," TATE remodeling projects, so if interest. -
PLUMED User's Guide
PLUMED User’s Guide A portable plugin for free-energy calculations with molecular dynamics Version 1.3.0 – Nov 2011 Contents 1 Introduction 5 1.1 What is PLUMED?.........................5 1.2 Supported codes . .6 1.3 Features . .7 1.4 New in version 1.3 . .8 1.5 Restrictions . .9 1.6 The PLUMED package . .9 1.7 Online resources . 10 1.8 Credits . 11 1.9 Citing PLUMED ........................... 11 1.10 License . 11 2 Installation 13 2.1 Compiling PLUMED ......................... 13 2.1.1 Compiling the ACEMD plugin with PLUMED ...... 17 2.2 Including reconnaissance metadynamics . 18 2.3 Testing the installation . 19 2.4 Back to the original code . 21 2.5 The Python interface to PLUMED ................. 21 3 Running free-energy simulations 23 3.1 How to activate PLUMED ..................... 23 3.2 The input file . 25 3.3 A note on units . 27 3.4 Metadynamics . 27 3.4.1 Typical output . 27 3.4.2 Bias potential . 28 3.4.3 Well-tempered metadynamics . 29 1 3.4.4 Restarting a metadynamics run . 30 3.4.5 Using GRID ........................ 30 3.4.6 Multiple walkers . 35 3.4.7 Monitoring a collective variable without biasing it . 35 3.4.8 Defining an interval . 36 3.4.9 Inversion condition . 38 3.5 Running in parallel . 40 3.6 Replica exchange methods . 40 3.6.1 Parallel tempering metadynamics . 41 3.6.2 Bias exchange simulations . 42 3.7 Umbrella sampling . 45 3.8 Steered MD . 46 3.8.1 Steerplan . 46 3.9 Adiabatic Bias MD . -
The Logo Lineage
id302705 pdfMachine by Broadgun Software - a great PDF writer! - a great PDF creator! - http://www.pdfmachine.com http://www.broadgun.com THE LOGO LINEAGE by Wallace Feurzeig Wallace Feurzeig is a division scientist in information sciences for Bolt Beranek and Newman. His favorite implementation of Logo is still Logo-S for minicomputers. L ogo was created in 1966 at Bolt Beranek and Newman, a Cambridge research firm. Its intellectual roots are in artificial intelligence, mathematical logic and developmental psychology. The first four years of Logo research, development and teaching work was done at BBN. During the early 1960s, BBN had become a major center of computer science research and innovative applications. I joined the firm in 1962 to work with its newly available facilities in the Artificial Intelligence Department, one of the earliest AI organizations. My colleagues were actively engaged in some of the pioneering AI work in computer pattern recognition, natural language understanding, theorem proving, LISP language development and robot problem solving. Much of this work was done in collaboration with distinguished researchers at M.I.T. such as Marvin Minsky and John McCarthy, who were regular BBN consultants during the early 1960s. Other groups at BBN were doing original work in cognitive science, instructional research and man- computer communication. Some of the first work on knowledge representation (semantic networks), question-answering, interactive graphics and computer- aided instruction was actively underway. J. C. R. Licklider was the spiritual as well as the scientific leader of much of this work, championing the cause of on- line interaction during an era when almost all computation was being done via batch processing. -
Assessing the Feasibility of Genome-Wide DNA Methylation Profiling
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.04.455090; this version posted August 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling Federico Rossi1,13*, Alessandro Crnjar2, Federico Comitani3,4, Rodrigo Feliciano5,6, Leonie Jahn1,7, George Malim2, Laura Southgate8, Emily Kay1,9, Rebecca Oakey1, Richard Buggs8.10, Andy Moir11, Logan Kistler12, Ana Rodriguez Mateos5, Carla Molteni2*, Reiner Schulz1*, 1 King's College London, Department of Medical and Molecular Genetics, London, UK 2 King's College London, Department of Physics, London, UK 3 University College London, Department of Chemistry, London, UK 4 The Hospital for Sick Children, Toronto, Ontario, Canada 5 King's College London, Department of Nutrition, London, UK 6 University of Dusseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, Dusseldorf, Germany 7 Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kemitorvet, Denmark 8 Royal Botanical Gardens, Department of Natural Capital and Plant Health, Richmond, UK 9 CRUK Beatson Institute, Glasgow, UK 10 Queen Mary University of London, School of Biological and Chemical Sciences, London, UK 11 Tree-Ring Services Limited, Mitcheldean, UK 12 National Museum Of Natural History, Smithsonian Institution, Department of Anthropology, Washington, DC, USA 13 IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy * Corresponding author Abstract Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions.