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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 . -
Plotting Direction Fields in Matlab and Maxima – a Short Tutorial
Plotting direction fields in Matlab and Maxima – a short tutorial Luis Carvalho Introduction A first order differential equation can be expressed as dx x0(t) = = f(t; x) (1) dt where t is the independent variable and x is the dependent variable (on t). Note that the equation above is in normal form. The difficulty in solving equation (1) depends clearly on f(t; x). One way to gain geometric insight on how the solution might look like is to observe that any solution to (1) should be such that the slope at any point P (t0; x0) is f(t0; x0), since this is the value of the derivative at P . With this motivation in mind, if you select enough points and plot the slopes in each of these points, you will obtain a direction field for ODE (1). However, it is not easy to plot such a direction field for any function f(t; x), and so we must resort to some computational help. There are many computational packages to help us in this task. This is a short tutorial on how to plot direction fields for first order ODE’s in Matlab and Maxima. Matlab Matlab is a powerful “computing environment that combines numeric computation, advanced graphics and visualization” 1. A nice package for plotting direction field in Matlab (although resourceful, Matlab does not provide such facility natively) can be found at http://math.rice.edu/»dfield, contributed by John C. Polking from the Dept. of Mathematics at Rice University. To install this add-on, simply browse to the files for your version of Matlab and download them. -
CAS (Computer Algebra System) Mathematica
CAS (Computer Algebra System) Mathematica- UML students can download a copy for free as part of the UML site license; see the course website for details From: Wikipedia 2/9/2014 A computer algebra system (CAS) is a software program that allows [one] to compute with mathematical expressions in a way which is similar to the traditional handwritten computations of the mathematicians and other scientists. The main ones are Axiom, Magma, Maple, Mathematica and Sage (the latter includes several computer algebras systems, such as Macsyma and SymPy). Computer algebra systems began to appear in the 1960s, and evolved out of two quite different sources—the requirements of theoretical physicists and research into artificial intelligence. A prime example for the first development was the pioneering work conducted by the later Nobel Prize laureate in physics Martin Veltman, who designed a program for symbolic mathematics, especially High Energy Physics, called Schoonschip (Dutch for "clean ship") in 1963. Using LISP as the programming basis, Carl Engelman created MATHLAB in 1964 at MITRE within an artificial intelligence research environment. Later MATHLAB was made available to users on PDP-6 and PDP-10 Systems running TOPS-10 or TENEX in universities. Today it can still be used on SIMH-Emulations of the PDP-10. MATHLAB ("mathematical laboratory") should not be confused with MATLAB ("matrix laboratory") which is a system for numerical computation built 15 years later at the University of New Mexico, accidentally named rather similarly. The first popular computer algebra systems were muMATH, Reduce, Derive (based on muMATH), and Macsyma; a popular copyleft version of Macsyma called Maxima is actively being maintained. -
Perfeccionamiento De Un Nuevo Simulador Interactivo, Bajo Software
Perfeccionamiento de un nuevo simulador interactivo, bajo software libre gnu/linux, como desarrollo de una nueva herramienta en la enseñanza y aprendizaje de la física Harley J. Orjuela Ballesteros1, Alejandro Hurtado Márquez1 1Grupo de Investigación Física e Informática Fisinfor, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas,, Carrera 3 No.26 A - 40, Bogotá, Colombia. E-mail: [email protected], [email protected] (Recibido el 22 de Diciembre de 2009; aceptado el 23 de Enero de 2010) Resumen Con el fin de proponer nuevos mecanismos e instrumentos en la enseñanza de la física este documento pretende divulgar el simulador físico Interactivo STEP, creado bajo ambiente GNU/Linux (código abierto), por el grupo The KDE Education Project (Kde-Edu) y modificado e implementado (bajo la autorización y cooperación de Kde-Edu) por el grupo de investigación colombiano Fisinfor, pues con el fin de lograr comprender y explicar las ciencias físicas se requiere el manejo adecuado de diferentes aspectos como lo son: el lenguaje verbal y matemático, los implementos de laboratorio, aplicación, manejo y desarrollo de nuevas herramientas didácticas como aplicativos, "fislet" (physlet) y software educativo. Palabras clave: Física General, Enseñanza, Software. Abstract With the purpose of proposing new mechanisms and instruments in the teaching of the physics this document it seeks to disclose the Interactive physical pretender STEP, created ambient first floor GNU/Linux (open code), for the group The KDE Education Project (Kde-Edu) and modified and implemented (under the authorization and cooperation of Kde-Edu) for the group of investigate-ción Colombian Fisinfor, because with the purpose of being able to understand and to explain the physical sciences the appropriate handling of different aspects it is required like they are it: the verbal and mathematical language, the laboratory implements, application, handling and development of new didactic tools as application, "fislet" (physlet) and educational software. -
Anexaminationofthebenefitsofus
An Examination 1 Running head: AN EXAMINATION OF THE BENEFITS OF USING OPEN SOURCE An Examination of the Benefits of Using Open Source Software in Schools Charles E. Craig, Jr. Tennessee Tech University July 21, 2011 An Examination 2 Abstract This research is an examination of ways that open source software can bring educational value and significant cost savings to K-12 schools. Existing case studies and other research are examined. Particular attention is given to K-12 schools which have implemented the free and open source Linux operating system to replace Microsoft Windows on older computers, as well as schools which have replaced Microsoft Office with OpenOffice. An Examination 3 Table of Contents Abstract …………………………………………………………………………………………2 List of Tables/Figures ………………………………………………………………………….. 4 Chapter I. Introduction …………………………………………………………………………..5 Chapter II. Methodology ………………………………………………………………………...8 Chapter III. A Comparison and Contrast of Proprietary Software and Open Source Software …9 Chapter IV. Educational Benefits of Open Source Software …………………………………..12 Chapter V. Cost Benefits of Open Source Software ……………………………………….…..29 Chapter VI. Summary, Conclusions, Recommendations …………...………………………….33 References ……………………………………………………………………………………...38 An Examination 4 List of Tables/Figures TABLES: Table 1. A Comparison of RAM and CPU Usage in Various Linux Desktop Environments and Window Managers …………………………………………………………………...….14 FIGURES: Figure 1. The Ubuntu Linux desktop……………………………………………………………13 Figure 2. A screenshot of the LibreOffice Writer word processor running in Linux……………17 Figure 3. A screenshot of the Kalzium periodic table software ..……………………………….18 Figure 4. Kanagram ……………………………………………………………………………..19 Figure 5. KGeography ………………………………………………………………………..…20 Figure 6. The KStars desktop planetarium ………………………………………………..…….21 Figure 7. The TuxMath interactive educational game …………………………………………..22 Figure 8. TuxPaint ……………………………………………………………………………....23 Figure 9. Peppermint OS Two running on an eight year old Dell desktop ……………………..35 Figure 10. -
Establishing Your School's First Computer System
COMPUTER SYSTEM SUSTAINABILITY TOOLKIT UNIT 3: Establishing Your School’s First Computer System: Planning for Success 3 UNIT 3: ESTABLISHING YOUR SCHOOL’S FIRST COMPUTER SYSTEM: PLANNING FOR SUCCESS Page 3 This unit will help the leadership and staff at schools that do not yet have a computer system or lab make decisions about establishing a new computer system at their school. This unit may also be useful for SPTs at schools that already have computers and are thinking about buying more computer equipment or establishing additional computer labs. If your school already has a computer system and you are not considering expanding it at this time, you may wish to skip Unit 3 and jump to Unit 4. Why do we want to establish a computer effectively, you may want to stop the small system or lab at our school? group discussions and have each group This is an important question for the SPT briefly present the main points and answers to discuss and answer. At first, the answer to the questions its members have discussed. to this question may appear to be simple. Members of the SPT may answer, “Yes, we The questions that follow should help you should establish a computer system at our determine if your school should establish a school.” However, before you jump to this computer system or lab. Before starting the conclusion, it is important for you and the discussion, it would be helpful to present SPT to consider, discuss, and answer a few this list of questions to the SPT and ask if other related questions. -
KDE Galaxy 4.13
KDE Galaxy 4.13 - Devaja Shah About Me ●3rd Year Alienatic Student at DA- !"# Gandhinagar ●Dot-editor %or KDE &romo "ea' ●Member of KDE e.(. ●&a))ion for Technology# Literature ●+un the Google Developer Group in !olle$e ●-rganizin$ Tea' of KDE Meetup# con%./de.in 14 -/ay, sooooo....... ●Ho1 many of you are %an) of Science Fiction3 ●Astronomy3 ● 0o1 is it Related to KDE3 ●That i) precisely 1hat the talk is about. ●Analogy to $et you to kno1 everythin$ that you should about ● “Galaxy KDE 4.13” 4ait, isn't it 4.14? ●KDE5) late)t ver)ion S! 4.14 6 7ove'ber 8914 ●KDE Soft1are !o',ilation ::.xx ●Significance o% +elea)e) ●- -r$ani.ed# )y)te'atic co',ilation o% %eature) < develo,'ent) ●- 2ive )erie) of relea)e) till date. ●7o Synchronized +elea)e) Any lon$er: ● - KDE 2ra'e1ork) > ?'onthly@ ● - KDE &la)'a > ?3 'onth)@ ● - KDE Ap,lication) ?date ba)ed@ ●Au)t *i/e Ap, (er)ion) But, 1hat am I to do o% the Galaxy 7umber? ●4ork in a "eam ●4ork acros) a Deadline ●-%;ce Space Si'ulation ●Added 'petus %or Deliverin$ your 2eature) ●You 1ork a) a ,art of the C!oreD Developer "ea' ● nstils Discipline ●Better +e),onse# Better 2eedbac/ ●Better Deliverance ●Synchronized 1ork with other C)ea)onedD developer) Enough of the bore....... ●Ho1 do $et started3 ● - Hope you didn't )nooze yesterday ● +!# Subscribe to Mailing Lists ●Mentoring Progra') ●GsoC# Season of KDE, O2W Progra') ●Bootstra,pin$ Training Session) Strap yourself onto the Rocket ●And Blast O%%......... ● ● ● Entered A 4ormhole and Ea,ped into the KDE Galaxy ●No1 what? ●Pick a Planet to nhabit ●But.... -
Sage Tutorial (Pdf)
Sage Tutorial Release 9.4 The Sage Development Team Aug 24, 2021 CONTENTS 1 Introduction 3 1.1 Installation................................................4 1.2 Ways to Use Sage.............................................4 1.3 Longterm Goals for Sage.........................................5 2 A Guided Tour 7 2.1 Assignment, Equality, and Arithmetic..................................7 2.2 Getting Help...............................................9 2.3 Functions, Indentation, and Counting.................................. 10 2.4 Basic Algebra and Calculus....................................... 14 2.5 Plotting.................................................. 20 2.6 Some Common Issues with Functions.................................. 23 2.7 Basic Rings................................................ 26 2.8 Linear Algebra.............................................. 28 2.9 Polynomials............................................... 32 2.10 Parents, Conversion and Coercion.................................... 36 2.11 Finite Groups, Abelian Groups...................................... 42 2.12 Number Theory............................................. 43 2.13 Some More Advanced Mathematics................................... 46 3 The Interactive Shell 55 3.1 Your Sage Session............................................ 55 3.2 Logging Input and Output........................................ 57 3.3 Paste Ignores Prompts.......................................... 58 3.4 Timing Commands............................................ 58 3.5 Other IPython -
Děti a Linux
DĚTI A LINUX. RND R. ŠÁRKA VAVREČKOVÁ , PHD. Ústav informatiky, Filozoficko-přírodovědecká fakulta Slezské univerzity v Opavě, tel. +420 553 684 366, e-mail: [email protected], web: http://fpf.slu.cz/~vav10ui Na počítačích ve většině škol a domácích počítačích využívaných dětmi najdeme většinou Windows. V tomto článku se zamýšlíme nad tím, zda by v některých případech nebylo lepší místo Windows používat Linux. Je všeobecně známo, že po finanční stránce Linux vítězí, ale pořád se objevují argumenty poukazující na složitost Linuxu, nedostatek výukových prog- ramů a her, a také odlišnost od „majoritního“ operačního systému. V textu se budeme zabývat vztahem dětí k Linuxu, volbou vhodné distribuce Linuxu a grafického prostředí, problematikou správy zaměřenou na školství a především nabídkou výuko- vých programů a didaktických her pro tento operační systém. Kľúčové slová : Linux, distribuce, KDE, GNOME, výukový software, didaktická hra, SMART Board Devizou Linuxu vzhledem k dětem je nepřeberné 1. ÚVOD množství programů včetně výukového softwaru V současné době se děti dostávají do kontaktu a her, které se nainstalují už při instalaci operačního s počítačem velmi brzy, ať už doma, u kamaráda systému. Je pravda, že některé z nich nejsou dosud nebo ve škole. Tento fakt nelze moc ovlivňovat, lokalizované do češtiny nebo slovenštiny, nebo sice souvisí s dobou, ve které děti vyrůstají, ano, ale kromě nápovědy, ale v současné době se a s požadavky, které jsou na ně kladeny ve vyšším děti už na prvním stupni základních škol učí anglic- věku. Rodiče a učitelé však mají možnost ovlivnit ky (s problémy se setkáváme spíše u vyučujících alespoň to, k čemu má dítě na počítači přístup. -
Highlighting Wxmaxima in Calculus
mathematics Article Not Another Computer Algebra System: Highlighting wxMaxima in Calculus Natanael Karjanto 1,* and Husty Serviana Husain 2 1 Department of Mathematics, University College, Natural Science Campus, Sungkyunkwan University Suwon 16419, Korea 2 Department of Mathematics Education, Faculty of Mathematics and Natural Science Education, Indonesia University of Education, Bandung 40154, Indonesia; [email protected] * Correspondence: [email protected] Abstract: This article introduces and explains a computer algebra system (CAS) wxMaxima for Calculus teaching and learning at the tertiary level. The didactic reasoning behind this approach is the need to implement an element of technology into classrooms to enhance students’ understanding of Calculus concepts. For many mathematics educators who have been using CAS, this material is of great interest, particularly for secondary teachers and university instructors who plan to introduce an alternative CAS into their classrooms. By highlighting both the strengths and limitations of the software, we hope that it will stimulate further debate not only among mathematics educators and software users but also also among symbolic computation and software developers. Keywords: computer algebra system; wxMaxima; Calculus; symbolic computation Citation: Karjanto, N.; Husain, H.S. 1. Introduction Not Another Computer Algebra A computer algebra system (CAS) is a program that can solve mathematical problems System: Highlighting wxMaxima in by rearranging formulas and finding a formula that solves the problem, as opposed to Calculus. Mathematics 2021, 9, 1317. just outputting the numerical value of the result. Maxima is a full-featured open-source https://doi.org/10.3390/ CAS: the software can serve as a calculator, provide analytical expressions, and perform math9121317 symbolic manipulations. -
Master Thesis Innovation Dynamics in Open Source Software
Master thesis Innovation dynamics in open source software Author: Name: Remco Bloemen Student number: 0109150 Email: [email protected] Telephone: +316 11 88 66 71 Supervisors and advisors: Name: prof. dr. Stefan Kuhlmann Email: [email protected] Telephone: +31 53 489 3353 Office: Ravelijn RA 4410 (STEPS) Name: dr. Chintan Amrit Email: [email protected] Telephone: +31 53 489 4064 Office: Ravelijn RA 3410 (IEBIS) Name: dr. Gonzalo Ord´o~nez{Matamoros Email: [email protected] Telephone: +31 53 489 3348 Office: Ravelijn RA 4333 (STEPS) 1 Abstract Open source software development is a major driver of software innovation, yet it has thus far received little attention from innovation research. One of the reasons is that conventional methods such as survey based studies or patent co-citation analysis do not work in the open source communities. In this thesis it will be shown that open source development is very accessible to study, due to its open nature, but it requires special tools. In particular, this thesis introduces the method of dependency graph analysis to study open source software devel- opment on the grandest scale. A proof of concept application of this method is done and has delivered many significant and interesting results. Contents 1 Open source software 6 1.1 The open source licenses . 8 1.2 Commercial involvement in open source . 9 1.3 Opens source development . 10 1.4 The intellectual property debates . 12 1.4.1 The software patent debate . 13 1.4.2 The open source blind spot . 15 1.5 Litterature search on network analysis in software development . -
Programming for Computations – Python
15 Svein Linge · Hans Petter Langtangen Programming for Computations – Python Editorial Board T. J.Barth M.Griebel D.E.Keyes R.M.Nieminen D.Roose T.Schlick Texts in Computational 15 Science and Engineering Editors Timothy J. Barth Michael Griebel David E. Keyes Risto M. Nieminen Dirk Roose Tamar Schlick More information about this series at http://www.springer.com/series/5151 Svein Linge Hans Petter Langtangen Programming for Computations – Python A Gentle Introduction to Numerical Simulations with Python Svein Linge Hans Petter Langtangen Department of Process, Energy and Simula Research Laboratory Environmental Technology Lysaker, Norway University College of Southeast Norway Porsgrunn, Norway On leave from: Department of Informatics University of Oslo Oslo, Norway ISSN 1611-0994 Texts in Computational Science and Engineering ISBN 978-3-319-32427-2 ISBN 978-3-319-32428-9 (eBook) DOI 10.1007/978-3-319-32428-9 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2016945368 Mathematic Subject Classification (2010): 26-01, 34A05, 34A30, 34A34, 39-01, 40-01, 65D15, 65D25, 65D30, 68-01, 68N01, 68N19, 68N30, 70-01, 92D25, 97-04, 97U50 © The Editor(s) (if applicable) and the Author(s) 2016 This book is published open access. Open Access This book is distributed under the terms of the Creative Commons Attribution-Non- Commercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, a link is provided to the Creative Commons license and any changes made are indicated.