An Introduction to Perl for Bioinformatics
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Perl Baseless Myths & Startling Realities
http://xkcd.com/224/ 1 Perl Baseless Myths & Startling Realities by Tim Bunce, February 2008 2 Parrot and Perl 6 portion incomplete due to lack of time (not lack of myths!) Realities - I'm positive about Perl Not negative about other languages - Pick any language well suited to the task - Good developers are always most important, whatever language is used 3 DISPEL myths UPDATE about perl Who am I? - Tim Bunce - Author of the Perl DBI module - Using Perl since 1991 - Involved in the development of Perl 5 - “Pumpkin” for 5.4.x maintenance releases - http://blog.timbunce.org 4 Perl 5.4.x 1997-1998 Living on the west coast of Ireland ~ Myths ~ 5 http://www.bleaklow.com/blog/2003/08/new_perl_6_book_announced.html ~ Myths ~ - Perl is dead - Perl is hard to read / test / maintain - Perl 6 is killing Perl 5 6 Another myth: Perl is slow: http://www.tbray.org/ongoing/When/200x/2007/10/30/WF-Results ~ Myths ~ - Perl is dead - Perl is hard to read / test / maintain - Perl 6 is killing Perl 5 7 Perl 5 - Perl 5 isn’t the new kid on the block - Perl is 21 years old - Perl 5 is 14 years old - A mature language with a mature culture 8 How many times Microsoft has changed developer technologies in the last 14 years... 9 10 You can guess where thatʼs leading... From “The State of the Onion 10” by Larry Wall, 2006 http://www.perl.com/pub/a/2006/09/21/onion.html?page=3 Buzz != Jobs - Perl5 hasn’t been generating buzz recently - It’s just getting on with the job - Lots of jobs - just not all in web development 11 Web developers tend to have a narrow focus. -
Linux Lunacy V & Perl Whirl
SPEAKERS Linux Lunacy V Nicholas Clark Scott Collins & Perl Whirl ’05 Mark Jason Dominus Andrew Dunstan Running Concurrently brian d foy Jon “maddog” Hall Southwestern Caribbean Andrew Morton OCTOBER 2ND TO 9TH, 2005 Ken Pugh Allison Randal Linux Lunacy V and Perl Whirl ’05 run concurrently. Attendees can mix and match, choosing courses from Randal Schwartz both conferences. Doc Searls Ted Ts’o Larry Wall Michael Warfield DAY PORT ARRIVE DEPART CONFERENCE SESSIONS Sunday, Oct 2 Tampa, Florida — 4:00pm 7:15pm, Bon Voyage Party Monday, Oct 3 Cruising The Caribbean — — 8:30am – 5:00pm Tuesday, Oct 4 Grand Cayman 7:00am 4:00pm 4:00pm – 7:30pm Wednesday, Oct 5 Costa Maya, Mexico 10:00am 6:00pm 6:00pm – 7:30pm Thursday, Oct 6 Cozumel, Mexico 7:00am 6:00pm 6:00pm – 7:30pm Friday, Oct 7 Belize City, Belize 7:30am 4:30pm 4:30pm – 8:00pm Saturday, Oct 8 Cruising The Caribbean — — 8:30am – 5:00pm Sunday, Oct 9 Tampa, Florida 8:00am — Perl Whirl ’05 and Linux Lunacy V Perl Whirl ’05 are running concurrently. Attendees can mix and match, choosing courses Seminars at a Glance from both conferences. You may choose any combination Regular Expression Mastery (half day) Programming with Iterators and Generators of full-, half-, or quarter-day seminars Speaker: Mark Jason Dominus Speaker: Mark Jason Dominus (half day) for a total of two-and-one-half Almost everyone has written a regex that failed Sometimes you’ll write a function that takes too (2.5) days’ worth of sessions. The to match something they wanted it to, or that long to run because it produces too much useful conference fee is $995 and includes matched something they thought it shouldn’t, and information. -
When Geeks Cruise
COMMUNITY Geek Cruise: Linux Lunacy Linux Lunacy, Perl Whirl, MySQL Swell: Open Source technologists on board When Geeks Cruise If you are on one of those huge cruising ships and, instead of middle-aged ladies sipping cocktails, you spot a bunch of T-shirt touting, nerdy looking guys hacking on their notebooks in the lounges, chances are you are witnessing a “Geek Cruise”. BY ULRICH WOLF eil Baumann, of Palo Alto, Cali- and practical tips on application develop- The dedicated Linux track comprised a fornia, has been organizing geek ment – not only for Perl developers but meager spattering of six lectures, and Ncruises since 1999 (http://www. for anyone interested in programming. though there was something to suit geekcruises.com/), Neil always finds everyone’s taste, the whole thing tended enough open source and programming Perl: Present and to lack detail. Ted T’so spent a long time celebrities to hold sessions on Linux, (Distant?) Future talking about the Ext2 and Ext3 file sys- Perl, PHP and other topics dear to geeks. In contrast, Allison Randal’s tutorials on tems, criticizing ReiserFS along the way, Parrot Assembler and Perl6 features were but had very little to say about network Open Source Celebs hardcore. Thank goodness Larry Wall file systems, an increasingly vital topic. on the Med summed up all the major details on Perl6 Developers were treated to a lecture on I was lucky enough to get on board the in a brilliant lecture that was rich with developing shared libraries, and admins first Geek Cruise on the Mediterranean, metaphors and bursting with informa- enjoyed sessions on Samba and hetero- scaring the nerds to death with my tion. -
Minimal Perl for UNIX and Linux People
Minimal Perl For UNIX and Linux People BY TIM MAHER MANNING Greenwich (74° w. long.) For online information and ordering of this and other Manning books, please visit www.manning.com. The publisher offers discounts on this book when ordered in quantity. For more information, please contact: Special Sales Department Manning Publications Co. Cherokee Station PO Box 20386 Fax: (609) 877-8256 New York, NY 10021 email: [email protected] ©2007 by Manning Publications Co. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by means electronic, mechanical, photocopying, or otherwise, without prior written permission of the publisher. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in the book, and Manning Publications was aware of a trademark claim, the designations have been printed in initial caps or all caps. Recognizing the importance of preserving what has been written, it is Manning’s policy to have the books we publish printed on acid-free paper, and we exert our best efforts to that end. Manning Publications Co. Copyeditor: Tiffany Taylor 209 Bruce Park Avenue Typesetters: Denis Dalinnik, Dottie Marsico Greenwich, CT 06830 Cover designer: Leslie Haimes ISBN 1-932394-50-8 Printed in the United States of America 12345678910–VHG–1009080706 To Yeshe Dolma Sherpa, whose fortitude, endurance, and many sacrifices made this book possible. To my parents, Gloria Grady Washington and William N. Maher, who indulged my early interests in literature. To my limbic system, with gratitude for all the good times we’ve had together. -
Cancer Immunology of Cutaneous Melanoma: a Systems Biology Approach
Cancer Immunology of Cutaneous Melanoma: A Systems Biology Approach Mindy Stephania De Los Ángeles Muñoz Miranda Doctoral Thesis presented to Bioinformatics Graduate Program at Institute of Mathematics and Statistics of University of São Paulo to obtain Doctor of Science degree Concentration Area: Bioinformatics Supervisor: Prof. Dr. Helder Takashi Imoto Nakaya During the project development the author received funding from CAPES São Paulo, September 2020 Mindy Stephania De Los Ángeles Muñoz Miranda Imunologia do Câncer de Melanoma Cutâneo: Uma abordagem de Biologia de Sistemas VERSÃO CORRIGIDA Esta versão de tese contém as correções e alterações sugeridas pela Comissão Julgadora durante a defesa da versão original do trabalho, realizada em 28/09/2020. Uma cópia da versão original está disponível no Instituto de Matemática e Estatística da Universidade de São Paulo. This thesis version contains the corrections and changes suggested by the Committee during the defense of the original version of the work presented on 09/28/2020. A copy of the original version is available at Institute of Mathematics and Statistics at the University of São Paulo. Comissão Julgadora: • Prof. Dr. Helder Takashi Imoto Nakaya (Orientador, Não Votante) - FCF-USP • Prof. Dr. André Fujita - IME-USP • Profa. Dra. Patricia Abrão Possik - INCA-Externo • Profa. Dra. Ana Carolina Tahira - I.Butantan-Externo i FICHA CATALOGRÁFICA Muñoz Miranda, Mindy StephaniaFicha de Catalográfica los Ángeles M967 Cancer immunology of cutaneous melanoma: a systems biology approach = Imuno- logia do câncer de melanoma cutâneo: uma abordagem de biologia de sistemas / Mindy Stephania de los Ángeles Muñoz Miranda, [orientador] Helder Takashi Imoto Nakaya. São Paulo : 2020. 58 p. -
Programming Perl (Nutshell Handbooks) Randal L. Schwartz
[PDF] Programming Perl (Nutshell Handbooks) Randal L. Schwartz, Larry Wall - pdf download free book Programming Perl (Nutshell Handbooks) PDF, Programming Perl (Nutshell Handbooks) Download PDF, Programming Perl (Nutshell Handbooks) by Randal L. Schwartz, Larry Wall Download, Programming Perl (Nutshell Handbooks) Full Collection, Read Best Book Online Programming Perl (Nutshell Handbooks), Read Online Programming Perl (Nutshell Handbooks) Ebook Popular, Download Free Programming Perl (Nutshell Handbooks) Book, Download PDF Programming Perl (Nutshell Handbooks), pdf free download Programming Perl (Nutshell Handbooks), by Randal L. Schwartz, Larry Wall Programming Perl (Nutshell Handbooks), the book Programming Perl (Nutshell Handbooks), Download Programming Perl (Nutshell Handbooks) Online Free, Read Online Programming Perl (Nutshell Handbooks) Book, Read Programming Perl (Nutshell Handbooks) Full Collection, Programming Perl (Nutshell Handbooks) PDF read online, Programming Perl (Nutshell Handbooks) Ebooks, Programming Perl (Nutshell Handbooks) Free Download, Programming Perl (Nutshell Handbooks) Free PDF Download, Programming Perl (Nutshell Handbooks) Books Online, PDF Download Programming Perl (Nutshell Handbooks) Free Collection, CLICK HERE FOR DOWNLOAD pdf, mobi, epub, azw, kindle Description: About the Author Randal L. Schwartz is a two-decade veteran of the software industry. He is skilled in software design, system administration, security, technical writing, and training. Randal has coauthored the "must-have" standards: Programming Perl, Learning Perl, Learning Perl for Win32 Systems, and Effective Perl Learning, and is a regular columnist for WebTechniques, PerformanceComputing, SysAdmin, and Linux magazines. He is also a frequent contributor to the Perl newsgroups, and has moderated comp.lang.perl.announce since its inception. His offbeat humor and technical mastery have reached legendary proportions worldwide (but he probably started some of those legends himself). -
Table of Contents • Index • Reviews • Reader Reviews • Errata Perl 6 Essentials by Allison Randal, Dan Sugalski, Leopold Tötsch
• Table of Contents • Index • Reviews • Reader Reviews • Errata Perl 6 Essentials By Allison Randal, Dan Sugalski, Leopold Tötsch Publisher: O'Reilly Pub Date: June 2003 ISBN: 0-596-00499-0 Pages: 208 Slots: 1 Perl 6 Essentials is the first book that offers a peek into the next major version of the Perl language. Written by members of the Perl 6 core development team, the book covers the development not only of Perl 6 syntax but also Parrot, the language-independent interpreter developed as part of the Perl 6 design strategy. This book is essential reading for anyone interested in the future of Perl. It will satisfy their curiosity and show how changes in the language will make it more powerful and easier to use. 1 / 155 • Table of Contents • Index • Reviews • Reader Reviews • Errata Perl 6 Essentials By Allison Randal, Dan Sugalski, Leopold Tötsch Publisher: O'Reilly Pub Date: June 2003 ISBN: 0-596-00499-0 Pages: 208 Slots: 1 Copyright Preface How This Book Is Organized Font Conventions We'd Like to Hear from You Acknowledgments Chapter 1. Project Overview Section 1.1. The Birth of Perl 6 Section 1.2. In the Beginning . Section 1.3. The Continuing Mission Chapter 2. Project Development Section 2.1. Language Development Section 2.2. Parrot Development Chapter 3. Design Philosophy Section 3.1. Linguistic and Cognitive Considerations Section 3.2. Architectural Considerations Chapter 4. Syntax Section 4.1. Variables Section 4.2. Operators Section 4.3. Control Structures Section 4.4. Subroutines Section 4.5. Classes and Objects Section 4.6. -
Perl Baseless Myths & Startling Realities
http://xkcd.com/224/ Perl Baseless Myths & Startling Realities by Tim Bunce, July 2008 Prefer ‘Good Developers’ over ‘Good Languages’ “For all program aspects investigated, the performance variability that derives from differences among programmers of the same language—as described by the bad-to-good ratios—is on average as large or larger than the variability found among the different languages.” — An empirical comparison of C, C++, Java, Perl, Python, Rexx, and Tcl. IEEE Computer Journal October 2000 Who am I? - Tim Bunce - Author of the Perl DBI module - Using Perl since 1991 - Involved in the development of Perl 5 - “Pumpkin” for 5.4.x maintenance releases - http://blog.timbunce.org ~ Myths ~ ~ Myths ~ - Perl is dead - Perl is hard to read / test / maintain - Perl 6 is killing Perl 5 ~ Myths ~ - Perl is dead - Perl is hard to read / test / maintain - Perl 6 is killing Perl 5 Perl 5 - Perl 5 isn’t the new kid on the block - Perl is 21 years old - Perl 5 is 14 years old - A mature language with a mature culture Buzz != Jobs - Perl5 hasn’t been generating buzz recently - It’s just getting on with the job - Lots of jobs - - just not all in web development Guess the Languages “web developer” Yes, Perl is growing more slowly than others but these are just “web developer” jobs “software engineer” Perl is mentioned in many more software engineer/developer jobs. “foo developer” Perl is the primary focus of more developer jobs. Want a fun new job? Become a Perl developer! Massive Module Market - Large and vibrant developer community - Over 15,000 distributions (58,000 modules) - Over 6,700 ‘authors’ (who make releases) - One quarter of all CPAN distributions have been updated in the last 4 months! - Half of all updated in the last 17 months! Top Modules -Many gems, including.. -
Learning Perl. 5Th Edition [PDF]
Learning Perl ,perlroadmap.24755 Page ii Tuesday, June 17, 2008 8:15 AM Other Perl resources from O’Reilly Related titles Advanced Perl Programming Perl Debugger Pocket Intermediate Perl Reference Mastering Perl Perl in a Nutshell Perl 6 and Parrot Essentials Perl Testing: A Developer’s Perl Best Practices Notebook Perl Cookbook Practical mod-perl Perl Books perl.oreilly.com is a complete catalog of O’Reilly’s books on Perl Resource Center and related technologies, including sample chapters and code examples. Perl.com is the central web site for the Perl community. It is the perfect starting place for finding out everything there is to know about Perl. Conferences O’Reilly brings diverse innovators together to nurture the ideas that spark revolutionary industries. We specialize in document- ing the latest tools and systems, translating the innovator’s knowledge into useful skills for those in the trenches. Visit conferences.oreilly.com for our upcoming events. Safari Bookshelf (safari.oreilly.com) is the premier online refer- ence library for programmers and ITprofessionals. Conduct searches across more than 1,000 books. Subscribers can zero in on answers to time-critical questions in a matter of seconds. Read the books on your Bookshelf from cover to cover or sim- ply flip to the page you need. Try it today with a free trial. main.title Page iii Monday, May 19, 2008 11:21 AM FIFTH EDITION LearningTomcat Perl™ The Definitive Guide Randal L. Schwartz,Jason Tom Brittain Phoenix, and and Ian brian F. Darwin d foy Beijing • Cambridge • Farnham • Köln • Sebastopol • Taipei • Tokyo Learning Perl, Fifth Edition by Randal L. -
Chapter 11 the Perl Scripting Language Dr
Chapter 11 The Perl Scripting Language Dr. Marjan Trutschl [email protected] Louisiana State University, Shreveport, LA 71115 Chapter 11 The Perl Scripting Language ¤ Intro to Perl ¤ Working with Files ¤ Help ¤ Sort ¤ Terminology ¤ Subroutines ¤ Running a Perl Program ¤ Regular Expressions ¤ Syntax ¤ CPAN Modules ¤ Variables ¤ Examples ¤ Control Structures Intro to Perl ¤ The Perl motto is "There's more than one way to do it." Divining how many more is left as an exercise to the reader. ¤ Originally created by Larry Wall as a tool to process reports Yep. This guy. at NASA, AKA the Practical Extraction and Report Language ¤ Perl is easy, flexible and processes text information quickly ¤ Since most graphics are text at some level, Perl has been adapted to CGI pretty widely ¤ It’s also great at RegExp and works very well with Linux by allowing embedded bash in a Perl script or Perl in a bash script Help ¤ Help ¤ There are numerous resources for Perl, so please don’t stop with just the text ¤ Try reading the documentation…it’s actually very well written and provides sound advice ¤ Also, if you’re in a hurry, try this tutorial: ¤ http://www.perl.com/pub/2008/04/23/a-beginners- introduction-to-perl-510.html Perl is already installed on the Sun servers or any OSX system, but some Linux distributions (like raspbian) don’t ship with it. Simply install it with ‘apt-get’ or your favorite package manager. Help ¤ Documentation ¤ Because Perl’s restrictions can be turned off, it’s easy to use it for simple tasks with sloppy code ¤ Turn on ‘strict’ and ‘warnings’ to tighten up your code ¤ Perl supports object oriented code, though there is no special syntax for it, feel free to write good code ¤ Constructors can be created using the ‘bless’ function ¤ Use the ‘perldoc’ utility to document Larry is very religious, and has a good sense of humor about it. -
Pragmaticperl-Interviews-A4.Pdf
Pragmatic Perl Interviews pragmaticperl.com 2013—2015 Editor and interviewer: Viacheslav Tykhanovskyi Covers: Marko Ivanyk Revision: 2018-03-02 11:22 © Pragmatic Perl Contents 1 Preface .......................................... 1 2 Alexis Sukrieh (April 2013) ............................... 2 3 Sawyer X (May 2013) .................................. 10 4 Stevan Little (September 2013) ............................. 17 5 chromatic (October 2013) ................................ 22 6 Marc Lehmann (November 2013) ............................ 29 7 Tokuhiro Matsuno (January 2014) ........................... 46 8 Randal Schwartz (February 2014) ........................... 53 9 Christian Walde (May 2014) .............................. 56 10 Florian Ragwitz (rafl) (June 2014) ........................... 62 11 Curtis “Ovid” Poe (September 2014) .......................... 70 12 Leon Timmermans (October 2014) ........................... 77 13 Olaf Alders (December 2014) .............................. 81 14 Ricardo Signes (January 2015) ............................. 87 15 Neil Bowers (February 2015) .............................. 94 16 Renée Bäcker (June 2015) ................................ 102 17 David Golden (July 2015) ................................ 109 18 Philippe Bruhat (Book) (August 2015) . 115 19 Author .......................................... 123 i Preface 1 Preface Hello there! You have downloaded a compilation of interviews done with Perl pro- grammers in Pragmatic Perl journal from 2013 to 2015. Since the journal itself is in Russian -
Bio::Graphics HOWTO Lincoln Stein Cold Spring Harbor Laboratory1 [email protected]
Bio::Graphics HOWTO Lincoln Stein Cold Spring Harbor Laboratory1 [email protected] This HOWTO describes how to render sequence data graphically in a horizontal map. It applies to a variety of situations ranging from rendering the feature table of a GenBank entry, to graphing the positions and scores of a BLAST search, to rendering a clone map. It describes the programmatic interface to the Bio::Graphics module, and discusses how to create dynamic web pages using Bio::DB::GFF and the gbrowse package. Table of Contents Introduction ...........................................................................................................................3 Preliminaries..........................................................................................................................3 Getting Started ......................................................................................................................3 Adding a Scale to the Image ...............................................................................................5 Improving the Image............................................................................................................7 Parsing Real BLAST Output...............................................................................................8 Rendering Features from a GenBank or EMBL File ....................................................12 A Better Version of the Feature Renderer ......................................................................14 Summary...............................................................................................................................18