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Efficient Algorithms for Comparing, Storing, and Sharing
EFFICIENT ALGORITHMS FOR COMPARING, STORING, AND SHARING LARGE COLLECTIONS OF EVOLUTIONARY TREES A Dissertation by SUZANNE JUDE MATTHEWS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2012 Major Subject: Computer Science EFFICIENT ALGORITHMS FOR COMPARING, STORING, AND SHARING LARGE COLLECTIONS OF EVOLUTIONARY TREES A Dissertation by SUZANNE JUDE MATTHEWS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Tiffani L. Williams Committee Members, Nancy M. Amato Jennifer L. Welch James B. Woolley Head of Department, Hank W. Walker May 2012 Major Subject: Computer Science iii ABSTRACT Efficient Algorithms for Comparing, Storing, and Sharing Large Collections of Evolutionary Trees. (May 2012) Suzanne Jude Matthews, B.S.; M.S., Rensselaer Polytechnic Institute Chair of Advisory Committee: Dr. Tiffani L. Williams Evolutionary relationships between a group of organisms are commonly summarized in a phylogenetic (or evolutionary) tree. The goal of phylogenetic inference is to infer the best tree structure that represents the relationships between a group of organisms, given a set of observations (e.g. molecular sequences). However, popular heuristics for inferring phylogenies output tens to hundreds of thousands of equally weighted candidate trees. Biologists summarize these trees into a single structure called the consensus tree. The central assumption is that the information discarded has less value than the information retained. But, what if this assumption is not true? In this dissertation, we demonstrate the value of retaining and studying tree collections. -
PETER STEPHENS Current Technical Pursuits: Agile Practices, Cloud
PETER STEPHENS 512.778.6322 / cell 865.567.7173 1955 County Road 202 www.diligentsoftware.com/resume Liberty Hill, TX 78642 [email protected] Current Technical Pursuits: Agile Practices, Cloud Computing and Amazon Web Services, Cloud Automation, ASP.NET MVC, REST based web services, JavaScript and jQuery CURRENT SKILLS • Microsoft.NET Framework versions 1.0 – 4.5 » C#, LINQ, XML , Networking, Regular Expressions, Multithreading , Task Parallel Library, Encryption, etc. » Websites: ASP.NET WebForms and MVC » Thick Client: Windows Presentation Foundation (WPF) » Web Services: WCF, Web API (REST and RPC) , and OData • Cloud Computing » Amazon Web Services : EC2 , S3 , RDS , SQS, SNS, Cloud Formation, Route 53, etc. » Rackspace Cloud • Automation : Powershell, MSBuild, and T4 templating • Agile Practices : Continuous Integration with Team City and CruiseControl.NET, Test Driven Development (TDD ), NUnit, Rhino Mocks, MOQ, Autofac, and ReSharper • Microsoft SQL Server versions 7 – 2008. Extensive use of T-SQL , C# stored procedures, C# functions, management and database optimization • HTML , CSS , JavaScript , jQuery , HTTP, Web Design, SEO , and Microsoft Expression Studio, Report Viewer Control based RDLC reports • Domain Specific Languages: Irony • Deployment: WIX , InstallShield, and WebDeploy • Source Control : Git and Mercurial, Beyond Compare, KDIFF OPEN SOURCE AND SOCIAL • Stack Overflow: http://stackoverflow.com/users/72860/peter-stephens • Twitter: https://twitter.com/#!/peterastephens • Bitbucket: https://bitbucket.org/pstephens/ -
Higher Inductive Types (Hits) Are a New Type Former!
Git as a HIT Dan Licata Wesleyan University 1 1 Darcs Git as a HIT Dan Licata Wesleyan University 1 1 HITs 2 Generator for 2 equality of equality HITs Homotopy Type Theory is an extension of Agda/Coq based on connections with homotopy theory [Hofmann&Streicher,Awodey&Warren,Voevodsky,Lumsdaine,Garner&van den Berg] 2 Generator for 2 equality of equality HITs Homotopy Type Theory is an extension of Agda/Coq based on connections with homotopy theory [Hofmann&Streicher,Awodey&Warren,Voevodsky,Lumsdaine,Garner&van den Berg] Higher inductive types (HITs) are a new type former! 2 Generator for 2 equality of equality HITs Homotopy Type Theory is an extension of Agda/Coq based on connections with homotopy theory [Hofmann&Streicher,Awodey&Warren,Voevodsky,Lumsdaine,Garner&van den Berg] Higher inductive types (HITs) are a new type former! They were originally invented[Lumsdaine,Shulman,…] to model basic spaces (circle, spheres, the torus, …) and constructions in homotopy theory 2 Generator for 2 equality of equality HITs Homotopy Type Theory is an extension of Agda/Coq based on connections with homotopy theory [Hofmann&Streicher,Awodey&Warren,Voevodsky,Lumsdaine,Garner&van den Berg] Higher inductive types (HITs) are a new type former! They were originally invented[Lumsdaine,Shulman,…] to model basic spaces (circle, spheres, the torus, …) and constructions in homotopy theory But they have many other applications, including some programming ones! 2 Generator for 2 equality of equality Patches Patch a a 2c2 diff b d = < b c c --- > d 3 3 id a a b b -
Analysis of Devops Tools to Predict an Optimized Pipeline by Adding Weightage for Parameters
International Journal of Computer Applications (0975 – 8887) Volume 181 – No. 33, December 2018 Analysis of DevOps Tools to Predict an Optimized Pipeline by Adding Weightage for Parameters R. Vaasanthi V. Prasanna Kumari, PhD S. Philip Kingston Research Scholar, HOD, MCA Project Manager SCSVMV University Rajalakshmi Engineering Infosys, Mahindra City, Kanchipuram College, Chennai Chennai ABSTRACT cloud. Now-a-days more than ever, DevOps [Development + Operations] has gained a tremendous amount of attention in 2. SCM software industry. Selecting the tools for building the DevOps Source code management (SCM) is a software tool used for pipeline is not a trivial exercise as there are plethora’s of tools development, versioning and enables team working in available in market. It requires thought, planning, and multiple locations to work together more effectively. This preferably enough time to investigate and consult other plays a vital role in increasing team’s productivity. Some of people. Unfortunately, there isn’t enough time in the day to the SCM tools, considered for this study are GIT, SVN, CVS, dig for top-rated DevOps tools and its compatibility with ClearCase, Mercurial, TFS, Monotone, Bitkeeper, Code co- other tools. Each tool has its own pros/cons and compatibility op, Darcs, Endevor, Fossil, Perforce, Rational Synergy, of integrating with other tools. The objective of this paper is Source Safe, and GNU Bazaar. Table1 consists of SCM tools to propose an approach by adding weightage to each with weightage. parameter for the curated list of the DevOps tools. 3. BUILD Keywords Build is a process that enables source code to be automatically DevOps, SCM, dependencies, compatibility and pipeline compiled into binaries including code level unit testing to ensure individual pieces of code behave as expected [4]. -
Bluej Teamwork Repository Configuration
BlueJ Teamwork Repository Configuration Version 2.0 for BlueJ Version 2.5.0 (and 2.2.x) Davin McCall School of Engineering & IT, Deakin University 1 Introduction This document gives a brief description of how you might set up a version control repository for use with BlueJ’s teamwork features. It is intended mainly as a “quick start” guide and not as a complete reference – for that you should refer to the version control software documentation (i.e. the CVS manual or the Subversion manual) – but it does explain some BlueJ-specific concepts (such as how BlueJ supports the notion of student groups or teams). Setting up a repository usually requires a server to which you have “root” or administrator access. This may mean that you need to ask a Systems Administrator to set up the repository for you. Since BlueJ version 2.5.0, both Subversion and CVS are supported version control systems. BlueJ version 2.2.x supports only CVS. BlueJ versions prior to 2.2.0 did not support teamwork features. Chapters 2 and 3 explain how to set up and test a repository using CVS. Chapter 4 then covers the equivalent steps for using Subversion. 2 Setting up a simple single user CVS repository for testing the BlueJ teamwork features 2.1 Setting up the repository server On Unix / Linux / MacOS X: You must have the CVS software installed on the machine you intend to use as a server. There is a good chance that it is already installed, but if not, your vendor or distribution provider will almost certainly provide packages that can be installed. -
Software License Agreement (EULA)
Third-party Computer Software AutoVu™ ALPR cameras • angular-animate (https://docs.angularjs.org/api/ngAnimate) licensed under the terms of the MIT License (https://github.com/angular/angular.js/blob/master/LICENSE). © 2010-2016 Google, Inc. http://angularjs.org • angular-base64 (https://github.com/ninjatronic/angular-base64) licensed under the terms of the MIT License (https://github.com/ninjatronic/angular-base64/blob/master/LICENSE). © 2010 Nick Galbreath © 2013 Pete Martin • angular-translate (https://github.com/angular-translate/angular-translate) licensed under the terms of the MIT License (https://github.com/angular-translate/angular-translate/blob/master/LICENSE). © 2014 [email protected] • angular-translate-handler-log (https://github.com/angular-translate/bower-angular-translate-handler-log) licensed under the terms of the MIT License (https://github.com/angular-translate/angular-translate/blob/master/LICENSE). © 2014 [email protected] • angular-translate-loader-static-files (https://github.com/angular-translate/bower-angular-translate-loader-static-files) licensed under the terms of the MIT License (https://github.com/angular-translate/angular-translate/blob/master/LICENSE). © 2014 [email protected] • Angular Google Maps (http://angular-ui.github.io/angular-google-maps/#!/) licensed under the terms of the MIT License (https://opensource.org/licenses/MIT). © 2013-2016 angular-google-maps • AngularJS (http://angularjs.org/) licensed under the terms of the MIT License (https://github.com/angular/angular.js/blob/master/LICENSE). © 2010-2016 Google, Inc. http://angularjs.org • AngularUI Bootstrap (http://angular-ui.github.io/bootstrap/) licensed under the terms of the MIT License (https://github.com/angular- ui/bootstrap/blob/master/LICENSE). -
Windows Installer XML: Käyttöönotto Asennusohjelman Tekemisessä
Windows Installer XML: käyttöönotto asennusohjelman tekemisessä Koskina, Ekaterina 2012 Kerava Laurea-ammattikorkeakoulu Kerava Windows Installer XML: käyttöönotto asennusohjelman tekemisessä Ekaterina Koskina Tietojenkäsittelyn koulutusohjelma Opinnäytetyö Maaliskuu, 2012 Sisällys 1 Johdanto ............................................................................................. 6 2 Asennusohjelmat Windows- käyttöjärjestelmissä ............................................ 6 2.1 Windows Installer .......................................................................... 7 2.1.1 Synty, kehitys ja nykytilanne..................................................... 7 2.1.2 MSI- asennustiedoston rakenne .................................................. 8 2.2 WiX- työkalupaketti ja sen kilpailijat................................................... 9 3 WiX:in käyttöönotto ............................................................................. 11 4 WiX- teknologia ................................................................................... 13 4.1 Rungon Elementit ........................................................................ 14 4.1.1 Tuote- elementti ................................................................. 15 4.1.2 Pakkaus- elementti............................................................... 15 4.1.3 Media- elementti ................................................................. 16 4.2 Hakemistot ................................................................................ 17 4.3 Komponentti- elementit -
FAKULTÄT FÜR INFORMATIK Leveraging Traceability Between Code and Tasks for Code Reviews and Release Management
FAKULTÄT FÜR INFORMATIK DER TECHNISCHEN UNIVERSITÄT MÜNCHEN Master’s Thesis in Informatics Leveraging Traceability between Code and Tasks for Code Reviews and Release Management Jan Finis FAKULTÄT FÜR INFORMATIK DER TECHNISCHEN UNIVERSITÄT MÜNCHEN Master’s Thesis in Informatics Leveraging Traceability between Code and Tasks for Code Reviews and Release Management Einsatz von Nachvollziehbarkeit zwischen Quellcode und Aufgaben für Code Reviews und Freigabemanagement Author: Jan Finis Supervisor: Prof. Bernd Brügge, Ph.D. Advisors: Maximilian Kögel, Nitesh Narayan Submission Date: May 18, 2011 I assure the single-handed composition of this master’s thesis only supported by declared resources. Sydney, May 10th, 2011 Jan Finis Acknowledgments First, I would like to thank my adviser Maximilian Kögel for actively supporting me with my thesis and being reachable for my frequent issues even at unusual times and even after he left the chair. Furthermore, I would like to thank him for his patience, as the surrounding conditions of my thesis, like me having an industrial internship and finishing my thesis abroad, were sometimes quite impedimental. Second, I want to thank my other adviser Nitesh Narayan for helping out after Max- imilian has left the chair. Since he did not advise me from the start, he had more effort working himself into my topic than any usual adviser being in charge of a thesis from the beginning on. Third, I want to thank the National ICT Australia for providing a workspace, Internet, and library access for me while I was finishing my thesis in Sydney. Finally, my thanks go to my supervisor Professor Bernd Brügge, Ph.D. -
DVCS Or a New Way to Use Version Control Systems for Freebsd
Brief history of VCS FreeBSD context & gures Is Arch/baz suited for FreeBSD? Mercurial to the rescue New processes & policies needed Conclusions DVCS or a new way to use Version Control Systems for FreeBSD Ollivier ROBERT <[email protected]> BSDCan 2006 Ottawa, Canada May, 12-13th, 2006 Ollivier ROBERT <[email protected]> DVCS or a new way to use Version Control Systems for FreeBSD Brief history of VCS FreeBSD context & gures Is Arch/baz suited for FreeBSD? Mercurial to the rescue New processes & policies needed Conclusions Agenda 1 Brief history of VCS 2 FreeBSD context & gures 3 Is Arch/baz suited for FreeBSD? 4 Mercurial to the rescue 5 New processes & policies needed 6 Conclusions Ollivier ROBERT <[email protected]> DVCS or a new way to use Version Control Systems for FreeBSD Brief history of VCS FreeBSD context & gures Is Arch/baz suited for FreeBSD? Mercurial to the rescue New processes & policies needed Conclusions The ancestors: SCCS, RCS File-oriented Use a subdirectory to store deltas and metadata Use lock-based architecture Support shared developments through NFS (fragile) SCCS is proprietary (System V), RCS is Open Source a SCCS clone exists: CSSC You can have a central repository with symlinks (RCS) Ollivier ROBERT <[email protected]> DVCS or a new way to use Version Control Systems for FreeBSD Brief history of VCS FreeBSD context & gures Is Arch/baz suited for FreeBSD? Mercurial to the rescue New processes & policies needed Conclusions CVS, the de facto VCS for the free world Initially written as shell wrappers over RCS then rewritten in C Centralised server Easy UI Use sandboxes to avoid locking Simple 3-way merges Can be replicated through CVSup or even rsync Extensive documentation (papers, websites, books) Free software and used everywhere (SourceForge for example) Ollivier ROBERT <[email protected]> DVCS or a new way to use Version Control Systems for FreeBSD Brief history of VCS FreeBSD context & gures Is Arch/baz suited for FreeBSD? Mercurial to the rescue New processes & policies needed Conclusions CVS annoyances and aws BUT.. -
Opinnäytetyö Ohjeet
Lappeenrannan–Lahden teknillinen yliopisto LUT School of Engineering Science Tietotekniikan koulutusohjelma Kandidaatintyö Mikko Mustonen PARHAITEN OPETUSKÄYTTÖÖN SOVELTUVAN VERSIONHALLINTAJÄRJESTELMÄN LÖYTÄMINEN Työn tarkastaja: Tutkijaopettaja Uolevi Nikula Työn ohjaaja: Tutkijaopettaja Uolevi Nikula TIIVISTELMÄ LUT-yliopisto School of Engineering Science Tietotekniikan koulutusohjelma Mikko Mustonen Parhaiten opetuskäyttöön soveltuvan versionhallintajärjestelmän löytäminen Kandidaatintyö 2019 31 sivua, 8 kuvaa, 2 taulukkoa Työn tarkastajat: Tutkijaopettaja Uolevi Nikula Hakusanat: versionhallinta, versionhallintajärjestelmä, Git, GitLab, SVN, Subversion, oppimateriaali Keywords: version control, version control system, Git, GitLab, SVN, Subversion, learning material LUT-yliopistossa on tietotekniikan opetuksessa käytetty Apache Subversionia versionhallintaan. Subversionin käyttö kuitenkin johtaa ylimääräisiin ylläpitotoimiin LUTin tietohallinnolle. Lisäksi Subversionin julkaisun jälkeen on tullut uusia versionhallintajärjestelmiä ja tässä työssä tutkitaankin, olisiko Subversion syytä vaihtaa johonkin toiseen versionhallintajärjestelmään opetuskäytössä. Työn tavoitteena on löytää opetuskäyttöön parhaiten soveltuva versionhallintajärjestelmä ja tuottaa sille opetusmateriaalia. Työssä havaittiin, että Git on suosituin versionhallintajärjestelmä ja se on myös suhteellisen helppo käyttää. Lisäksi GitLab on tutkimuksen mukaan Suomen yliopistoissa käytetyin ja ominaisuuksiltaan ja hinnaltaan sopivin Gitin web-käyttöliittymä. Näille tehtiin -
Darcs 2.0.0 (2.0.0 (+ 75 Patches)) Darcs
Darcs 2.0.0 (2.0.0 (+ 75 patches)) Darcs David Roundy April 23, 2008 2 Contents 1 Introduction 7 1.1 Features . 9 1.2 Switching from CVS . 11 1.3 Switching from arch . 12 2 Building darcs 15 2.1 Prerequisites . 15 2.2 Building on Mac OS X . 16 2.3 Building on Microsoft Windows . 16 2.4 Building from tarball . 16 2.5 Building darcs from the repository . 17 2.6 Building darcs with git . 18 2.7 Submitting patches to darcs . 18 3 Getting started 19 3.1 Creating your repository . 19 3.2 Making changes . 20 3.3 Making your repository visible to others . 20 3.4 Getting changes made to another repository . 21 3.5 Moving patches from one repository to another . 21 3.5.1 All pulls . 21 3.5.2 Send and apply manually . 21 3.5.3 Push . 22 3.5.4 Push —apply-as . 22 3.5.5 Sending signed patches by email . 23 3.6 Reducing disk space usage . 26 3.6.1 Linking between repositories . 26 3.6.2 Alternate formats for the pristine tree . 26 4 Configuring darcs 29 4.1 prefs . 29 4.2 Environment variables . 32 4.3 General-purpose variables . 33 4.4 Remote repositories . 34 3 4 CONTENTS 4.5 Highlighted output . 36 4.6 Character escaping and non-ASCII character encodings . 36 5 Best practices 39 5.1 Introduction . 39 5.2 Creating patches . 39 5.2.1 Changes . 40 5.2.2 Keeping or discarding changes . 40 5.2.3 Unrecording changes . -
Bazaar, Das DVCS
Bazaar, das DVCS Marek Kubica 20. November 2008 Marek Kubica Bazaar, das DVCS Vorweg ein paar Infos Mit was ich so spiele Bazaar in der Arbeit Mercurial für Python-Projekte Git für den Rest Welche Spielzeuge lass ich links liegen CVS wozu noch wo es SVN gibt? SVN wozu noch wenn es DVCS gibt? darcs lohnt sich nicht mehr monotone, codeville, arch obsolete das selbsgehackte, tolle DVCS deines Nachbarn ;) Marek Kubica Bazaar, das DVCS Geschichte In the beginning, there was GNU Arch Marek Kubica Bazaar, das DVCS GNU Arch Die Anfänge von DVCS CVS stinkt, wir brauchen was besseres SVN ist Evolution, keine Revolution GNU Arch war das erste DVCS mit dem ich in Kontakt kam (larch) fürchterlich kompliziert wurde dann von tla ersetzt immer noch fürchterlich Canonical hat tla 1.2 geforkt und Bazaar, baz genannt Paralell dazu: revc = Arch 2.0 Marek Kubica Bazaar, das DVCS Baz als Rettung? Von heiÿen Kartoeln baz war in C Was passiert: Canonical ruft Bazaar-NG ins Leben, bzr, lässt baz fallen Bazaar-NG wird in Bazaar umgetauft baz ist tot, tla ist tot, larch ist tot, revc ist bedeutungslos Hurra, GNU Arch ist endlich tot, es lebe bzr! Marek Kubica Bazaar, das DVCS bzr, der Retter Was bietet Bazaar? in Python geschrieben, mit einigen Speedups in Pyrex (C) reguläre Releases (quasi jeden Monat) Einfache Bedienung Meist ausreichende Performance Umfangreiche Dokumentation: Programmmeldungen, Manpages, Wiki, IRC-Channel (wenn man Geduld hat) Flexible Einsatzmöglichkeiten (verschiedene Workows) 1 Git mit Bazaar simulieren 2 SVN in Bazaar nachbauen (für Nostalgiker) freier Hoster wo man Code hochladen kann (Launchpad) Marek Kubica Bazaar, das DVCS Zeitleiste 2005 war eine aufregende Zeit 26.