Teaching an ODE Course with Cocalc, Sage, Jupyter Notebooks, and LATEX
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Sagemath and Sagemathcloud
Viviane Pons Ma^ıtrede conf´erence,Universit´eParis-Sud Orsay [email protected] { @PyViv SageMath and SageMathCloud Introduction SageMath SageMath is a free open source mathematics software I Created in 2005 by William Stein. I http://www.sagemath.org/ I Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 2 / 7 SageMath Source and language I the main language of Sage is python (but there are many other source languages: cython, C, C++, fortran) I the source is distributed under the GPL licence. Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 3 / 7 SageMath Sage and libraries One of the original purpose of Sage was to put together the many existent open source mathematics software programs: Atlas, GAP, GMP, Linbox, Maxima, MPFR, PARI/GP, NetworkX, NTL, Numpy/Scipy, Singular, Symmetrica,... Sage is all-inclusive: it installs all those libraries and gives you a common python-based interface to work on them. On top of it is the python / cython Sage library it-self. Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 4 / 7 SageMath Sage and libraries I You can use a library explicitly: sage: n = gap(20062006) sage: type(n) <c l a s s 'sage. interfaces .gap.GapElement'> sage: n.Factors() [ 2, 17, 59, 73, 137 ] I But also, many of Sage computation are done through those libraries without necessarily telling you: sage: G = PermutationGroup([[(1,2,3),(4,5)],[(3,4)]]) sage : G . g a p () Group( [ (3,4), (1,2,3)(4,5) ] ) Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 5 / 7 SageMath Development model Development model I Sage is developed by researchers for researchers: the original philosophy is to develop what you need for your research and share it with the community. -
Jupyter Notebooks—A Publishing Format for Reproducible Computational Workflows
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elpub digital library Jupyter Notebooks—a publishing format for reproducible computational workflows Thomas KLUYVERa,1, Benjamin RAGAN-KELLEYb,1, Fernando PÉREZc, Brian GRANGERd, Matthias BUSSONNIERc, Jonathan FREDERICd, Kyle KELLEYe, Jessica HAMRICKc, Jason GROUTf, Sylvain CORLAYf, Paul IVANOVg, Damián h i d j AVILA , Safia ABDALLA , Carol WILLING and Jupyter Development Team a University of Southampton, UK b Simula Research Lab, Norway c University of California, Berkeley, USA d California Polytechnic State University, San Luis Obispo, USA e Rackspace f Bloomberg LP g Disqus h Continuum Analytics i Project Jupyter j Worldwide Abstract. It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents. Keywords. Notebook, reproducibility, research code 1. Introduction Researchers today across all academic disciplines often need to write computer code in order to collect and process data, carry out statistical tests, run simulations or draw figures. The widely applicable libraries and tools for this are often developed as open source projects (such as NumPy, Julia, or FEniCS), but the specific code researchers write for a particular piece of work is often left unpublished, hindering reproducibility. Some authors may describe computational methods in prose, as part of a general description of research methods. -
Running Sagemath (With Or Without Installation)
Running SageMath (with or without installation) http://www.sagemath.org/ Éric Gourgoulhon Running SageMath 9 Feb. 2017 1 / 5 Various ways to install/access SageMath 7.5.1 Install on your computer: 2 options: install a compiled binary version for Linux, MacOS X or Windows1 from http://www.sagemath.org/download.html compile from source (Linux, MacOS X): check the prerequisites (see here for Ubuntu) and run git clone git://github.com/sagemath/sage.git cd sage MAKE=’make -j8’ make Run on your computer without installation: Sage Debian Live http://sagedebianlive.metelu.net/ Bootable USB flash drive with SageMath (boosted with octave, scilab), Geogebra, LaTeX, gimp, vlc, LibreOffice,... Open a (free) account on SageMathCloud https://cloud.sagemath.com/ Run in SageMathCell Single cell mode: http://sagecell.sagemath.org/ 1requires VirtualBox; alternatively, a full Windows installer is in pre-release stage at https://github.com/embray/sage-windows/releases Éric Gourgoulhon Running SageMath 9 Feb. 2017 2 / 5 Example 1: installing on Ubuntu 16.04 1 Download the archive sage-7.5.1-Ubuntu_16.04-x86_64.tar.bz2 from one the mirrors listed at http://www.sagemath.org/download-linux.html 2 Run the following commands in a terminal: bunzip2 sage-7.5.1-Ubuntu_16.04-x86_64.tar.bz2 tar xvf sage-7.5.1-Ubuntu_16.04-x86_64.tar cd SageMath ./sage -n jupyter A Jupyter home page should then open in your browser. Click on New and select SageMath 7.5.1 to open a Jupyter notebook with a SageMath kernel. Éric Gourgoulhon Running SageMath 9 Feb. 2017 3 / 5 Example 2: using the SageMathCloud 1 Open a free account on https://cloud.sagemath.com/ 2 Create a new project 3 In the second top menu, click on New to create a new file 4 Select Jupyter Notebook for the file type 5 In the Jupyter menu, click on Kernel, then Change kernel and choose SageMath 7.5 Éric Gourgoulhon Running SageMath 9 Feb. -
Deep Dive on Project Jupyter
A I M 4 1 3 Deep dive on Project Jupyter Dr. Brian E. Granger Principal Technical Program Manager Co-Founder and Leader Amazon Web Services Project Jupyter © 2019, Amazon Web Services, Inc. or its affiliates. All rights reserved. © 2019, Amazon Web Services, Inc. or its affiliates. All rights reserved. Project Jupyter exists to develop open-source software, open standards and services for interactive and reproducible computing. https://jupyter.org/ Overview • Project Jupyter is a multi-stakeholder, open source project. • Jupyter’s flagship application is the Text Math Jupyter Notebook. • Notebook document format: • Live code, narrative text, equations, images, visualizations, audio. • ~100 programming languages supported. Live code • Over 500 contributors across >100 GitHub repositories. • Part of the NumFOCUS Foundation: • Along with NumPy, Pandas, Julia, Matplotlib,… Charts Who uses Jupyter and how? Students/Teachers Data science Data Engineers Machine learning Data Scientists Scientific computing Researchers Data cleaning and transformation Scientists Exploratory data analysis ML Engineers Analytics ML Researchers Simulation Analysts Algorithm development Reporting Data visualization Jupyter has a large and diverse user community • Many millions of Jupyter users worldwide • Thousands of AWS customers • Highly international • Over 5M public notebooks on GitHub alone Example: Dive into Deep Learning • Dive into Deep Learning is a free, open-source book about deep learning. • Zhang, Lipton, Li, Smola from AWS • All content is Jupyter Notebooks on GitHub. • 890 page PDF, hundreds of notebooks • https://d2l.ai/ © 2019, Amazon Web Services, Inc. or its affiliates. All rights reserved. Common threads • Jupyter serves an extremely broad range of personas, usage cases, industries, and applications • What do these have in common? Ideas of Jupyter • Computational narrative • “Real-time thinking” with a computer • Direct manipulation user interfaces that augment the writing of code “Computers are good at consuming, producing, and processing data. -
Some Effective Methods for Teaching Mathematics Courses in Technological Universities
International Journal of Education and Information Studies. ISSN 2277-3169 Volume 6, Number 1 (2016), pp. 11-18 © Research India Publications http://www.ripublication.com Some Effective Methods for Teaching Mathematics Courses in Technological Universities Dr. D. S. Sankar Professor, School of Applied Sciences and Mathematics, Universiti Teknologi Brunei, Jalan Tungku Link, BE1410, Brunei Darussalam E-mail: [email protected] Dr. Rama Rao Karri Principal Lecturer, Petroleum and Chemical Engineering Programme Area, Faculty of Engineering, Universiti Teknologi Brunei, Jalan Tungku Link, Gadong BE1410, Brunei Darussalam E-mail: [email protected] Abstract This article discusses some effective and useful methods for teaching various mathematics topics to the students of undergraduate and post-graduate degree programmes in technological universities. These teaching methods not only equip the students to acquire knowledge and skills for solving real world problems efficiently, but also these methods enhance the teacher’s ability to demonstrate the mathematical concepts effectively along with suitable physical examples. The exposure to mathematical softwares like MATLAB, SCILAB, MATHEMATICA, etc not only increases the students confidential level to solve variety of typical problems which they come across in their respective disciplines of study, but also it enables them to visualize the surfaces of the functions of several variable. Peer learning, seminar based learning and project based learning are other methods of learning environment to the students which makes the students to learn mathematics by themselves. These are higher level learning methods which enhances the students understanding on the mathematical concepts and it enables them to take up research projects. It is noted that the teaching and learning of mathematics with the support of mathematical softwares is believed to be more effective when compared to the effects of other methods of teaching and learning of mathematics. -
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 -
2015 Program for Women and Mathematics
2015 Program for Women and Mathematics SageMath Installation Instructions Below are instructions for configuring your personal computer to run SageMath. Since one of the files that you need to download is quite large in size, we recommended that you complete the steps below on your personal computer prior to the start of the 2015 Program for Women and Mathematics. If you run into any issues with these instructions on your personal computer, please contact the School of Mathematics Help Desk at [email protected] or visit the SageMath website (http://www.sagemath.org/). Fedora 21 Operating System 1. Download and unpack the Fedora 21 pre-built SageMath binary tarball from the following location: http://www.sagemath.org/download-linux.html. 2. Create a symbolic link in /usr/local/bin that points to the path where you unpacked the pre-built SageMath binary in Step 1. For example, ln -s /path/to/sage-x.y.z-x86_64-Linux/sage /usr/local/bin/sage 3. Navigate to /usr/local/bin. 4. Type sage and press the Enter button. 5. You will be prompted to install “sagemath”. Enter y. Please wait for all required packages to be downloaded and installed. 6. Once the installation is complete, type sage. 7. Type notebook() to launch the browser-based notebook interface. 8. Type in a new password for the SageMath Notebook “admin” account twice. 9. The SageMath browser-based notebook should now be displayed. How to exit the Sage appliance 1. Click on the Sign out link at the top of the SageMath browser based notebook interface. -
SENTINEL-2 DATA PROCESSING USING R Case Study: Imperial Valley, USA
TRAINING KIT – R01 DFSDFGAGRIAGRA SENTINEL-2 DATA PROCESSING USING R Case Study: Imperial Valley, USA Research and User Support for Sentinel Core Products The RUS Service is funded by the European Commission, managed by the European Space Agency and operated by CSSI and its partners. Authors would be glad to receive your feedback or suggestions and to know how this material was used. Please, contact us on [email protected] Cover image credits: ESA The following training material has been prepared by Serco Italia S.p.A. within the RUS Copernicus project. Date of publication: November 2020 Version: 1.1 Suggested citation: Serco Italia SPA (2020). Sentinel-2 data processing using R (version 1.1). Retrieved from RUS Lectures at https://rus-copernicus.eu/portal/the-rus-library/learn-by-yourself/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. DISCLAIMER While every effort has been made to ensure the accuracy of the information contained in this publication, RUS Copernicus does not warrant its accuracy or will, regardless of its or their negligence, assume liability for any foreseeable or unforeseeable use made of this publication. Consequently, such use is at the recipient’s own risk on the basis that any use by the recipient constitutes agreement to the terms of this disclaimer. The information contained in this publication does not purport to constitute professional advice. 2 Table of Contents 1 Introduction to RUS ........................................................................................................................ -
Final Report for the Redus Project
FINAL REPORT FOR THE REDUS PROJECT Reduced Uncertainty in Stock Assessment Erik Olsen (HI), Sondre Aanes Norwegian Computing Center, Magne Aldrin Norwegian Computing Center, Olav Nikolai Breivik Norwegian Computing Center, Edvin Fuglebakk, Daisuke Goto, Nils Olav Handegard, Cecilie Hansen, Arne Johannes Holmin, Daniel Howell, Espen Johnsen, Natoya Jourdain, Knut Korsbrekke, Ono Kotaro, Håkon Otterå, Holly Ann Perryman, Samuel Subbey, Guldborg Søvik, Ibrahim Umar, Sindre Vatnehol og Jon Helge Vølstad (HI) RAPPORT FRA HAVFORSKNINGEN NR. 2021-16 Tittel (norsk og engelsk): Final report for the REDUS project Sluttrapport for REDUS-prosjektet Undertittel (norsk og engelsk): Reduced Uncertainty in Stock Assessment Rapportserie: År - Nr.: Dato: Distribusjon: Rapport fra havforskningen 2021-16 17.03.2021 Åpen ISSN:1893-4536 Prosjektnr: Forfatter(e): 14809 Erik Olsen (HI), Sondre Aanes Norwegian Computing Center, Magne Aldrin Norwegian Computing Center, Olav Nikolai Breivik Norwegian Program: Computing Center, Edvin Fuglebakk, Daisuke Goto, Nils Olav Handegard, Cecilie Hansen, Arne Johannes Holmin, Daniel Howell, Marine prosesser og menneskelig Espen Johnsen, Natoya Jourdain, Knut Korsbrekke, Ono Kotaro, påvirkning Håkon Otterå, Holly Ann Perryman, Samuel Subbey, Guldborg Søvik, Ibrahim Umar, Sindre Vatnehol og Jon Helge Vølstad (HI) Forskningsgruppe(r): Godkjent av: Forskningsdirektør(er): Geir Huse Programleder(e): Bentiske ressurser og prosesser Frode Vikebø Bunnfisk Fiskeridynamikk Pelagisk fisk Sjøpattedyr Økosystemakustikk Økosystemprosesser -
Using Octave and Sagemath on Taito
Using Octave and SageMath on Taito Sampo Sillanpää 17 October 2017 CSC – Finnish research, education, culture and public administration ICT knowledge center Octave ● Powerful mathematics-oriented syntax with built- in plotting and visualization tools. ● Free software, runs on GNU/Linux, macOS, BSD, and Windows. ● Drop-in compatible with many Matlab scripts. ● https://www.gnu.org/software/octave/ SageMath ● SageMath is a free open-source mathematics software system licensed under the GPL. ● Builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. ● http://www.sagemath.org/ Octave on Taito ● Latest version 4.2.1 module load octave-env octave Or octave --no-gui ● Interactive sessions on Taito-shell via NoMachine client https://research.csc.5/-/nomachine Octave Forge ● A central location for development of packages for GNU Octave. ● Packages can be installed on Taito module load octave-env octave --no-gui octave:> pkg install -forge package_name octave:> pkg load package_name SageMath on Taito ● installed version 7.6. module load sagemath sage ● Interactive sessions on Taito-shell via NoMachine client. ● Browser-based notebook sage: notebook() Octave Batch Jobs #!/bin/bash -l #mytest.sh #SBATCH --constraint="snb|hsw" #SBATCH -o output.out #SBATCH -e stderr.err #SBATCH -p serial #SBATCH -n 1 #SBATCH -t 00:05:00 #SBATCH --mem-per-cpu=1000 module load octave-env octave --no-gui/wrk/user_name/example.m used_slurm_resources.bash [user@taito-login1]$ sbatch mytest.sh SageMath Batch Jobs #!/bin/bash -l #mytest.sh #SBATCH --constraint="snb|hsw" #SBATCH -o output.out #SBATCH -e stderr.err #SBATCH -p serial #SBATCH -n 1 #SBATCH -t 00:05:00 #SBATCH --mem-per-cpu=1000 module load sagemath sage /wrk/user_name/example.sage used_slurm_resources.bash [user@taito-login1]$ sbatch mytest.sh Instrucons and Documentaon ● Octave – https://research.csc.5/-/octave – https://www.gnu.org/software/octave/doc/interp reter/ ● SageMath – https://research.csc.5/-/sagemath – http://doc.sagemath.org/ [email protected]. -
Exploratory Data Science Using a Literate Programming Tool Mary Beth Kery1 Marissa Radensky2 Mahima Arya1 Bonnie E
The Story in the Notebook: Exploratory Data Science using a Literate Programming Tool Mary Beth Kery1 Marissa Radensky2 Mahima Arya1 Bonnie E. John3 Brad A. Myers1 1Human-Computer Interaction Institute 2Amherst College 3Bloomberg L. P. Carnegie Mellon University Amherst, MA New York City, NY Pittsburgh, PA [email protected] [email protected] mkery, mahimaa, bam @cs.cmu.edu ABSTRACT engineers, many of whom never receive formal training in Literate programming tools are used by millions of software engineering [30]. programmers today, and are intended to facilitate presenting data analyses in the form of a narrative. We interviewed 21 As even more technical novices engage with code and data data scientists to study coding behaviors in a literate manipulations, it is key to have end-user programming programming environment and how data scientists kept track tools that address barriers to doing effective data science. For of variants they explored. For participants who tried to keep instance, programming with data often requires heavy a detailed history of their experimentation, both informal and exploration with different ways to manipulate the data formal versioning attempts led to problems, such as reduced [14,23]. Currently even experts struggle to keep track of the notebook readability. During iteration, participants actively experimentation they do, leading to lost work, confusion curated their notebooks into narratives, although primarily over how a result was achieved, and difficulties effectively through cell structure rather than markdown explanations. ideating [11]. Literate programming has recently arisen as a Next, we surveyed 45 data scientists and asked them to promising direction to address some of these problems [17]. -
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