Community Report 2Nd Quarter 2012 | Issue 22
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Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
C/C++ Programming with Qt 5.12.6 and Opencv 4.2.0
C/C++ programming with Qt 5.12.6 and OpenCV 4.2.0 Preparation of the computer • Download http://download.qt.io/archive/qt/5.12/5.12.6/qt-opensource-windows- x86-5.12.6.exe and http://www.ensta-bretagne.fr/lebars/Share/OpenCV4.2.0.zip (contains OpenCV with extra modules built for Visual Studio 2015, 2017, 2019, MinGW Qt 5.12.6 x86, MinGW 8 x64), run Qt installer and select Qt\Qt 5.12.6\MinGW 7.3.0 32 bit and Qt\Tools\MinGW 7.3.0 32 bit options and extract OpenCV4.2.0.zip in C:\ (check that the extraction did not create an additional parent folder (we need to get only C:\OpenCV4.2.0\ instead of C:\OpenCV4.2.0\OpenCV4.2.0\), right-click and choose Run as administrator if needed). For Linux or macOS, additional/different steps might be necessary depending on the specific versions (and the provided .pro might need to be tweaked), see https://www.ensta-bretagne.fr/lebars/Share/setup_opencv_Ubuntu.pdf ; corresponding OpenCV sources : https://github.com/opencv/opencv/archive/4.2.0.zip and https://github.com/opencv/opencv_contrib/archive/4.2.0.zip ; Qt Linux 64 bit : https://download.qt.io/archive/qt/5.12/5.12.6/qt-opensource-linux-x64-5.12.6.run (for Ubuntu you can try sudo apt install qtcreator qt5-default build-essential but the version will probably not be the same); Qt macOS : https://download.qt.io/archive/qt/5.12/5.12.6/qt-opensource-mac-x64-5.12.6.dmg . -
The Kmymoney Handbook
The KMyMoney Handbook for KMyMoney version 5.0 Michael T. Edwardes Thomas Baumgart Ace Jones Tony Bloomfield Robert Wadley Darin Strait Roger Lum Jack H. Ostroff Dawid Wróbel The KMyMoney Handbook 2 Contents 1 Introduction 14 1.1 What is KMyMoney? . 14 1.2 What KMyMoney is not . 14 2 What’s new in this release 15 2.1 Bug fixes and enhancements to functionality . 15 2.2 Updates to this Handbook . 15 3 Making the most of KMyMoney 17 3.1 Basic Accounting . 17 3.1.1 Defining the accounts (personal records) . 18 3.1.2 Defining the accounts (business records) . 18 3.2 Mapping your finances to KMyMoney . 18 3.2.1 Accounts . 18 3.2.1.1 Accounts - Asset . 18 3.2.1.2 Accounts - Liability . 19 3.2.2 Institutions . 19 3.2.3 Categories . 19 3.2.4 Sub-Categories . 19 3.2.5 Tags . 19 3.2.6 Payees . 19 3.2.7 Scheduled transactions . 20 3.3 Useful Tips . 20 4 Using KMyMoney for the first time 21 4.1 Running KMyMoney for the first time . 21 4.2 The main window . 22 4.3 Creating a new file . 23 4.4 Creating accounts . 28 4.5 Schedules . 28 4.6 Categories . 28 4.7 Tags.............................................. 29 The KMyMoney Handbook 4.8 Payees . 29 4.9 Quicken Interchange Format (QIF) Import . 29 4.10 Searching for transactions . 29 4.11 Reconciliation . 29 4.12 Backing up . 30 4.13 Launching KMyMoney . 30 4.14 How to move KMyMoney to a new computer . 30 4.14.1 Moving your data . -
Qt Long Term Support
Qt Long Term Support Jeramie disapprove chorally as moreish Biff jostling her canneries co-author impassably. Rudolfo never anatomise any redemptioner sauces appetizingly, is Torre lexical and overripe enough? Post-free Adolph usually stetted some basidiospores or flutes effeminately. Kde qt versions to the tests should be long qt term support for backing up qt company What will i, long qt term support for sale in the long. It is hard not even wonder what our cost whereas the Qt community or be. Please enter your support available to long term support available to notify others of the terms. What tests are needed? You should i restarted the terms were examined further development and will be supported for arrhythmia, or the condition? Define ad slots and config. Also, have a look at the comments below for new findings. You later need to compile your own Qt against a WEC SDK which is typically shipped by the BSP vendor. If system only involve half open the features of Qt Commercial, vision will not warrant the full price. Are you javer for long term support life cycles that supports the latter occurs earlier that opens up. Cmake will be happy to dry secretions, mutation will i could be seen at. QObjects can also send signals to themselves. Q_DECL_CONSTEXPR fix memory problem. Enables qt syndrome have long term in terms and linux. There has been lots of hype around the increasing role that machine learning, and artificial intelligence more broadly, will play in how we automate the management of IT systems. Vf noninducible at qt and long term in terms were performed at. -
Cómo Usar El Software Libre Para Hacer Tareas De Colegio. Ing
Cómo usar el software libre para hacer tareas de colegio. Ing. Ricardo Naranjo Faccini, M.Sc. 2020-10-20 Bogotá 2018 Bogotá 2019 https://www.skinait.com/tareas-opensource-Escritos-50/ ¿Han¿Han escuchadoescuchado sobre?sobre? ● FraudeFraude – Acción que resulta contraria a la verdad y a la rectitud en perjuicio de una persona u organización – Conducta deshonesta o engañosa con el fin de obtener alguna injusta ventaja sobre otra persona. ● PlagioPlagio – La acción de «copiar en lo sustancial obras ajenas, dándolas como propias» ¿Han¿Han escuchadoescuchado sobre?sobre? ● Piratería:Piratería: – AsaltoAsalto yy roborobo dede embarcacionesembarcaciones enen elel mar.mar. – InfracciónInfracción dede derechosderechos dede autor,autor, infraccióninfracción dede copyrightcopyright oo violaciónviolación dede copyrightcopyright > – UsoUso nono autorizadoautorizado oo prohibidoprohibido dede obrasobras cubiertascubiertas porpor laslas leyesleyes dede derechosderechos dede autorautor ● Copia. ● Reproducción. ● Hacer obras derivadas. ¡Pero¡Pero venimosvenimos aa hablarhablar dede LIB!"#$%&LIB!"#$%& ● SoftwareSoftware librelibre – Linux, GIMP, inkscape, pitivi, LibreOffice.org ● FormatosFormatos abiertosabiertos – Garantizar acceso a largo plazo – Fomentar la competencia – Open Document Format (ISO/IEC 26300) – PDF – ogv, ogg ● ProtocolosProtocolos dede comunicacióncomunicación estándarestándar – http – smtp; pop3/imap – smb – vnc ● Texto – HTML (formato estándar de las páginas web) – Office Open XML ISO/IEC 29500:20084 ● (para documentos de oficina) -
Kmymoney Pour Kmymoney Version 4.6
Manuel de KMyMoney pour KMyMoney version 4.6 Michael T. Edwardes Thomas Baumgart Ace Jones Tony Bloomfield Robert Wadley Darin Strait Roger Lum Jack H. Ostroff Traduction française : José Fournier Traduction française : Simon Depiets Manuel de KMyMoney 2 Table des matières 1 Introduction 14 1.1 Qu’est-ce que KMyMoney ? . 14 1.2 Qu’est-ce que KMyMoney n’est pas . 14 2 Quoi de neuf dans cette version 15 3 Tirer le meilleur profit de KMyMoney 16 3.1 Les bases de la comptabilité . 16 3.1.1 Création des comptes (comptes personnels) . 17 3.1.2 Création des comptes (comptes d’entreprise) . 17 3.2 Modéliser vos finances dans KMyMoney . 17 3.2.1 Comptes . 17 3.2.1.1 Comptes d’actif . 17 3.2.1.2 Comptes de passif . 18 3.2.2 Établissements . 18 3.2.3 Catégories . 18 3.2.4 Sous-catégories . 18 3.2.5 Bénéficiaires . 18 3.2.6 Opération récurrentes . 19 3.3 Conseils utiles . 19 4 Utiliser KMyMoney pour la première fois 20 4.1 Lancer KMyMoney pour la première fois . 20 4.2 La fenêtre principale . 21 4.3 Créer un nouveau fichier . 22 4.4 Créer les comptes . 26 4.5 Opérations récurrentes . 27 4.6 Catégories . 27 4.7 Bénéficiaires . 27 4.8 Importation depuis un fichier Quicken Interchange Format (QIF) . 27 4.9 Chercher des opérations . 27 4.10 Réconciliation . 28 Manuel de KMyMoney 4.11 Effectuer des copies de secours . 28 4.12 Lancer KMyMoney . 28 4.13 Contacter les Développeurs / Signaler des Bogues . -
Introduction to Linux
Presentation to U3A - Linux Introduction 8 June 2019 – Terry Schuster - [email protected] What is Linux? https://en.wikipedia.org/wiki/Linux https://www.iotforall.com/linux-operating-system-iot-devices/ In simple terms, Linux is an operating system which was developed to be a home-built version of UNIX, one of the first operating systems which could be run on different brands of mainframe computers with quite different types of hardware. Linux has developed to the extent that it is the leading operating system on servers and other big iron systems such as mainframe computers, and the only OS used on TOP500 supercomputers (since November 2017, having gradually eliminated all competitors). It is used by around 2.3 percent of desktop computers. The Chromebook, which runs the Linux kernel-based Chrome OS, dominates the US K–12 education market. In the mid 2000’s, Linux was quickly seen as a good building block for smartphones, as it provided an out- of-the-box modern, full-featured Operating System with very good device driver support, and that was considered both scalable for the new generation of devices and had the added benefit of being royalty free. It is now becoming very common in IoT devices, such as smart watches/refrigerators, home controllers, etc. etc. BTW, Tux is a penguin character and the official brand character of the Linux kernel. Originally created as an entry to a Linux logo competition, Tux is the most commonly used icon for Linux, although different Linux distributions depict Tux in various styles. The character is used in many other Linux programs and as a general symbol of Linux. -
Why Be a KDE Project? Martin Klapetek David Edmundson
Why be a KDE Project? Martin Klapetek David Edmundson What is KDE? KDE is not a desktop, it's a community „Community of technologists, designers, writers and advocates who work to ensure freedom for all people through our software“ --The KDE Manifesto What is a KDE Project? Project needs more than just good code What will you get as a KDE Project? Git repository Git repository plus „scratch repos“ (your personal playground) Creating a scratch repo git push –all kde:scratch/username/reponame Git repository plus web interface (using GitPHP) Git repository plus migration from Gitorious.org Bugzilla (the slightly prettier version) Review Board Integration of git with Bugzilla and Review Board Integration of git with Bugzilla and Review Board Using server-side commit hooks ● BUG: 24578 ● CCBUG: 29456 ● REVIEW: 100345 ● CCMAIL: [email protected] Communication tools Mailing lists Wiki pages Forums Single sign-on to all services Official IRC channels #kde-xxxxx (on Freenode) IRC cloak me@kde/developer/mklapetek [email protected] email address Support from sysadmin team Community support Development support Translations (71 translation teams) Testing support (Active Jenkins and EBN servers, plus Quality Team) Project continuation (when you stop developing it) KDE e.V. support Financial and organizational help Trademark security Project's licence defense via FLA Promo support Stories in official KDE News site (Got the Dot?) Your blog aggregated at Planet KDE Promo through social channels Web hosting under kde.org domain Association with one of the best -
Painting with Light: a Technical Overview of Implementing HDR Support in Krita
Painting with Light: A Technical Overview of Implementing HDR Support in Krita Executive Summary Krita, a leading open source application for artists, has become one of the first digital painting software to achieve true high dynamic range (HDR) capability. With more than two million downloads per year, the program enables users to create and manipulate illustrations, concept art, comics, matte paintings, game art, and more. With HDR, Krita now opens the door for professionals and amateurs to a vastly extended range of colors and luminance. The pioneering approach of the Krita team can be leveraged by developers to add HDR to other applications. Krita and Intel engineers have also worked together to enhance Krita performance through Intel® multithreading technology, while Intel’s built-in support of HDR provides further acceleration. This white paper gives a high-level description of the development process to equip Krita with HDR. A Revolution in the Display of Color and Brightness Before the arrival of HDR, displays were calibrated to comply with the D65 standard of whiteness, corresponding to average midday light in Western and Northern Europe. Possibilities of storing color, contrast, or other information about each pixel were limited. Encoding was limited to a depth of 8 bits; some laptop screens only handled 6 bits per pixel. By comparison, HDR standards typically define 10 bits per pixel, with some rising to 16. This extra capacity for storing information allows HDR displays to go beyond the basic sRGB color space used previously and display the colors of Recommendation ITU-R BT.2020 (Rec. 2020, also known as BT.2020). -
Kubuntu Desktop Guide
Kubuntu Desktop Guide Ubuntu Documentation Project <[email protected]> Kubuntu Desktop Guide by Ubuntu Documentation Project <[email protected]> Copyright © 2004, 2005, 2006 Canonical Ltd. and members of the Ubuntu Documentation Project Abstract The Kubuntu Desktop Guide aims to explain to the reader how to configure and use the Kubuntu desktop. Credits and License The following Ubuntu Documentation Team authors maintain this document: • Venkat Raghavan The following people have also have contributed to this document: • Brian Burger • Naaman Campbell • Milo Casagrande • Matthew East • Korky Kathman • Francois LeBlanc • Ken Minardo • Robert Stoffers The Kubuntu Desktop Guide is based on the original work of: • Chua Wen Kiat • Tomas Zijdemans • Abdullah Ramazanoglu • Christoph Haas • Alexander Poslavsky • Enrico Zini • Johnathon Hornbeck • Nick Loeve • Kevin Muligan • Niel Tallim • Matt Galvin • Sean Wheller This document is made available under a dual license strategy that includes the GNU Free Documentation License (GFDL) and the Creative Commons ShareAlike 2.0 License (CC-BY-SA). You are free to modify, extend, and improve the Ubuntu documentation source code under the terms of these licenses. All derivative works must be released under either or both of these licenses. This documentation is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE AS DESCRIBED IN THE DISCLAIMER. Copies of these licenses are available in the appendices section of this book. Online versions can be found at the following URLs: • GNU Free Documentation License [http://www.gnu.org/copyleft/fdl.html] • Attribution-ShareAlike 2.0 [http://creativecommons.org/licenses/by-sa/2.0/] Disclaimer Every effort has been made to ensure that the information compiled in this publication is accurate and correct. -
1 Australian Synchrotron
EPICS Qt Update Paul Martin 1 Australian Synchrotron • 3GeV, 216m circumference synchrotron • 8 Beamlines • 12 Software Engineers • IMBL – Worlds Widest Beam - MRT Clinical Program – Safety Critical • Melbourne, Australia • Nearest other facilities: Taiwan, Thailand, Japan • 16th Most Urbanized Country • World’s most livable cities • Hosting ICALEPCS in 2015 2 Qt • Qt is a cross-platform application and UI framework for developers using C++ – Windows,OS X, Linux, Embedded Linux, Android, iOS, vxWorks, Win CE, Amiga OS • Open Source (LPGL v2.1) Qt Designer • Trolltech -> Nokia -> Digia, • Development tools: Qt Creator, Qt Designer, Qmake, Qt Linguist, Qt Assistant, Integration into Visual Studio • Rich set of Widgets and other classes (1000+), Qwt (125+) • Very Good Documentation, help, examples • All Qt Objects contain powerful object communication Qt Creator mechanism (Signal+Slots) • GUI Layout widgets • Qt Project: www.qt-project.org 3 EPICS Qt – Team • Started 2009 – Anthony Owen, Andrew Rhyder, Glenn Jackson • Joined 2011 – Andy Starritt • Joined 2012 – Ricardo Fernandez • Joined 2013 – Zai Wang (1 year contract) 4 EPICS Qt – Rapid GUI Development • Adds Channel Access to standard Qt Widgets and Data Classes • Rapid GUI Dev – Drag and Drop EPICS aware components in Qt Designer • Macro Substitutions for PV names and other GUI functions Qt Designer Channel Access running at design time .ui file – presented using QEGui on any platform (windows / linux) 5 EPICS Qt – Other App Types QCaString Qt Creator QCaInteger QCaFloating QCaByteArray -
Multiplatformní GUI Toolkity GTK+ a Qt
Multiplatformní GUI toolkity GTK+ a Qt Jan Outrata KATEDRA INFORMATIKY UNIVERZITA PALACKÉHO V OLOMOUCI GUI toolkit (widget toolkit) (1) = programová knihovna (nebo kolekce knihoven) implementující prvky GUI = widgety (tlačítka, seznamy, menu, posuvník, bary, dialog, okno atd.) a umožňující tvorbu GUI (grafického uživatelského rozhraní) aplikace vlastní jednotný nebo nativní (pro platformu/systém) vzhled widgetů, možnost stylování nízkoúrovňové (Xt a Xlib v X Windows System a libwayland ve Waylandu na unixových systémech, GDI Windows API, Quartz a Carbon v Apple Mac OS) a vysokoúrovňové (MFC, WTL, WPF a Windows Forms v MS Windows, Cocoa v Apple Mac OS X, Motif/Lesstif, Xaw a XForms na unixových systémech) multiplatformní = pro více platforem (MS Windows, GNU/Linux, Apple Mac OS X, mobilní) nebo platformově nezávislé (Java) – aplikace může být také (většinou) událostmi řízené programování (event-driven programming) – toolkit v hlavní smyčce zachytává události (uživatelské od myši nebo klávesnice, od časovače, systému, aplikace samotné atd.) a umožňuje implementaci vlastních obsluh (even handler, callback function), objektově orientované programování (objekty = widgety aj.) – nevyžaduje OO programovací jazyk! Jan Outrata (Univerzita Palackého v Olomouci) Multiplatformní GUI toolkity duben 2015 1 / 10 GUI toolkit (widget toolkit) (2) language binding = API (aplikační programové rozhraní) toolkitu v jiném prog. jazyce než původní API a toolkit samotný GUI designer/builder = WYSIWYG nástroj pro tvorbu GUI s využitím toolkitu, hierarchicky skládáním prvků, z uloženého XML pak generuje kód nebo GUI vytvoří za běhu aplikace nekomerční (GNU (L)GPL, MIT, open source) i komerční licence např. GTK+ (C), Qt (C++), wxWidgets (C++), FLTK (C++), CEGUI (C++), Swing/JFC (Java), SWT (Java), JavaFX (Java), Tcl/Tk (Tcl), XUL (XML) aj.