SUGI 26: That Mysterious Colon
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An Overview of Gut Microbiota and Colon Diseases with a Focus on Adenomatous Colon Polyps
International Journal of Molecular Sciences Review An Overview of Gut Microbiota and Colon Diseases with a Focus on Adenomatous Colon Polyps Oana Lelia Pop 1 , Dan Cristian Vodnar 1 , Zorita Diaconeasa 1 , Magdalena Istrati 2, 3 4 1, Adriana Bint, int, an , Vasile Virgil Bint, int, an , Ramona Suharoschi * and Rosita Gabbianelli 5,* 1 Department of Food Science, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania; [email protected] (O.L.P.); [email protected] (D.C.V.); [email protected] (Z.D.) 2 Regional Institute of Gastroenterology and Hepatology “Prof. Dr. Octavian Fodor”, 400158 Cluj-Napoca, Romania; [email protected] 3 1st Medical Clinic, Department of Gastroenterology, Emergency County Hospital, 400006 Cluj Napoca, Romania; [email protected] 4 1st Surgical Clinic, Department of Surgery, University of Medicine and Pharmacy Cluj Napoca, 400006 Cluj Napoca, Romania; [email protected] 5 Unit of Molecular Biology, School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy * Correspondence: [email protected] (R.S.); [email protected] (R.G.) Received: 6 August 2020; Accepted: 2 October 2020; Published: 5 October 2020 Abstract: It is known and accepted that the gut microbiota composition of an organism has an impact on its health. Many studies deal with this topic, the majority discussing gastrointestinal health. Adenomatous colon polyps have a high prevalence as colon cancer precursors, but in many cases, they are hard to diagnose in their early stages. Gut microbiota composition correlated with the presence of adenomatous colon polyps may be a noninvasive and efficient tool for diagnosis with a high impact on human wellbeing and favorable health care costs. -
A First Course to Openfoam
Basic Shell Scripting Slides from Wei Feinstein HPC User Services LSU HPC & LON [email protected] September 2018 Outline • Introduction to Linux Shell • Shell Scripting Basics • Variables/Special Characters • Arithmetic Operations • Arrays • Beyond Basic Shell Scripting – Flow Control – Functions • Advanced Text Processing Commands (grep, sed, awk) Basic Shell Scripting 2 Linux System Architecture Basic Shell Scripting 3 Linux Shell What is a Shell ▪ An application running on top of the kernel and provides a command line interface to the system ▪ Process user’s commands, gather input from user and execute programs ▪ Types of shell with varied features o sh o csh o ksh o bash o tcsh Basic Shell Scripting 4 Shell Comparison Software sh csh ksh bash tcsh Programming language y y y y y Shell variables y y y y y Command alias n y y y y Command history n y y y y Filename autocompletion n y* y* y y Command line editing n n y* y y Job control n y y y y *: not by default http://www.cis.rit.edu/class/simg211/unixintro/Shell.html Basic Shell Scripting 5 What can you do with a shell? ▪ Check the current shell ▪ echo $SHELL ▪ List available shells on the system ▪ cat /etc/shells ▪ Change to another shell ▪ csh ▪ Date ▪ date ▪ wget: get online files ▪ wget https://ftp.gnu.org/gnu/gcc/gcc-7.1.0/gcc-7.1.0.tar.gz ▪ Compile and run applications ▪ gcc hello.c –o hello ▪ ./hello ▪ What we need to learn today? o Automation of an entire script of commands! o Use the shell script to run jobs – Write job scripts Basic Shell Scripting 6 Shell Scripting ▪ Script: a program written for a software environment to automate execution of tasks ▪ A series of shell commands put together in a file ▪ When the script is executed, those commands will be executed one line at a time automatically ▪ Shell script is interpreted, not compiled. -
Punctuation Guide
Punctuation guide 1. The uses of punctuation Punctuation is an art, not a science, and a sentence can often be punctuated correctly in more than one way. It may also vary according to style: formal academic prose, for instance, might make more use of colons, semicolons, and brackets and less of full stops, commas, and dashes than conversational or journalistic prose. But there are some conventions you will need to follow if you are to write clear and elegant English. In earlier periods of English, punctuation was often used rhetorically—that is, to represent the rhythms of the speaking voice. The main function of modern English punctuation, however, is logical: it is used to make clear the grammatical structure of the sentence, linking or separating groups of ideas and distinguishing what is important in the sentence from what is subordinate. It can also be used to break up a long sentence into more manageable units, but this may only be done where a logical break occurs; Jane Austen's sentence ‗No one who had ever seen Catherine Morland in her infancy, would ever have supposed her born to be a heroine‘ would now lose its comma, since there is no logical break between subject and verb (compare: ‗No one would have supposed …‘). 2. The main stops and their functions The full stop, exclamation mark, and question mark are used to mark off separate sentences. Within the sentence, the colon (:) and semicolon (;) are stronger marks of division than the comma, brackets, and the dash. Properly used, the stops can be a very effective method of marking off the divisions and subdivisions of your argument; misused, they can make it barely intelligible, as in this example: ‗Donne starts the poem by poking fun at the Petrarchan convention; the belief that one's mistress's scorn could make one physically ill, he carries this one step further…‘. -
Punctuation: Program 8-- the Semicolon, Colon, and Dash
C a p t i o n e d M e d i a P r o g r a m #9994 PUNCTUATION: PROGRAM 8-- THE SEMICOLON, COLON, AND DASH FILMS FOR THE HUMANITIES & SCIENCES, 2000 Grade Level: 8-13+ 22 mins. DESCRIPTION How does a writer use a semicolon, colon, or dash? A semicolon is a bridge that joins two independent clauses with the same basic idea or joins phrases in a series. To elaborate a sentence with further information, use a colon to imply “and here it is!” The dash has no specific rules for use; it generally introduces some dramatic element into the sentence or interrupts its smooth flow. Clear examples given. ACADEMIC STANDARDS Subject Area: Language Arts–Writing • Standard: Uses grammatical and mechanical conventions in written compositions Benchmark: Uses conventions of punctuation in written compositions (e.g., uses commas with nonrestrictive clauses and contrasting expressions, uses quotation marks with ending punctuation, uses colons before extended quotations, uses hyphens for compound adjectives, uses semicolons between independent clauses, uses dashes to break continuity of thought) (See INSTRUCTIONAL GOALS 1-4.) INSTRUCTIONAL GOALS 1. To explain the proper use of a semicolon to combine independent clauses and in lists with commas. 2. To show the correct use of colons for combining information and in sentence fragments. 3. To illustrate the use of a dash in sentences. 4. To show some misuses of the semicolon, colon, and dash. BACKGROUND INFORMATION The semicolon, colon, and dash are among the punctuation marks most neglected by students and, sad to say, teachers. However, professional writers—and proficient writers in business—use them all to good effect. -
Bash Guide for Beginners
Bash Guide for Beginners Machtelt Garrels Garrels BVBA <tille wants no spam _at_ garrels dot be> Version 1.11 Last updated 20081227 Edition Bash Guide for Beginners Table of Contents Introduction.........................................................................................................................................................1 1. Why this guide?...................................................................................................................................1 2. Who should read this book?.................................................................................................................1 3. New versions, translations and availability.........................................................................................2 4. Revision History..................................................................................................................................2 5. Contributions.......................................................................................................................................3 6. Feedback..............................................................................................................................................3 7. Copyright information.........................................................................................................................3 8. What do you need?...............................................................................................................................4 9. Conventions used in this -
Lecture 17 the Shell and Shell Scripting Simple Shell Scripts
Lecture 17 The Shell and Shell Scripting In this lecture • The UNIX shell • Simple Shell Scripts • Shell variables • File System commands, IO commands, IO redirection • Command Line Arguments • Evaluating Expr in Shell • Predicates, operators for testing strings, ints and files • If-then-else in Shell • The for, while and do loop in Shell • Writing Shell scripts • Exercises In this course, we need to be familiar with the "UNIX shell". We use it, whether bash, csh, tcsh, zsh, or other variants, to start and stop processes, control the terminal, and to otherwise interact with the system. Many of you have heard of, or made use of "shell scripting", that is the process of providing instructions to shell in a simple, interpreted programming language . To see what shell we are working on, first SSH into unix.andrew.cmu.edu and type echo $SHELL ---- to see the working shell in SSH We will be writing our shell scripts for this particular shell (csh). The shell scripting language does not fit the classic definition of a useful language. It does not have many of the features such as portability, facilities for resource intensive tasks such as recursion or hashing or sorting. It does not have data structures like arrays and hash tables. It does not have facilities for direct access to hardware or good security features. But in many other ways the language of the shell is very powerful -- it has functions, conditionals, loops. It does not support strong data typing -- it is completely untyped (everything is a string). But, the real power of shell program doesn't come from the language itself, but from the diverse library that it can call upon -- any program. -
Review of Set-Theoretic Notations and Terminology A.J
Math 347 Review of Set-theoretic Notations and Terminology A.J. Hildebrand Review of Set-theoretic Notations and Terminology • Sets: A set is an unordered collection of objects, called the elements of the set. The standard notation for a set is the brace notation f::: g, with the elements of the set listed inside the pair of braces. • Set builder notation: Notation of the form f::: : ::: g, where the colon (:) has the meaning of \such that", the dots to the left of the colon indicate the generic form of the element in the set and the dots to 2 the right of the colon denote any constraints on the element. E.g., fx 2 R : x < 4g stands for \the set of 2 all x 2 R such that x < 4"; this is the same as the interval (−2; 2). Other examples of this notation are f2k : k 2 Zg (set of all even integers), fx : x 2 A and x 2 Bg (intersection of A and B, A \ B). 2 Note: Instead of a colon (:), one can also use a vertical bar (j) as a separator; e.g., fx 2 R j x < 4g. Both notations are equally acceptable. • Equality of sets: Two sets are equal if they contain the same elements. E.g., the sets f3; 4; 7g, f4; 3; 7g, f3; 3; 4; 7g are all equal since they contain the same three elements, namely 3, 4, 7. • Some special sets: • Empty set: ; (or fg) • \Double bar" sets: 1 ∗ Natural numbers: N = f1; 2;::: g (note that 0 is not an element of N) ∗ Integers: Z = f:::; −2; −1; 0; 1; 2;::: g ∗ Rational numbers: Q = fp=q : p; q 2 Z; q 6= 0g ∗ Real numbers: R • Intervals: ∗ Open interval: (a; b) = fx 2 R : a < x < bg ∗ Closed interval: [a; b] = fx 2 R : a ≤ x ≤ bg ∗ Half-open interval: [a; b) = fx 2 R : a ≤ x < bg • Universe: U (\universe", a \superset" of which all sets under consideration are assumed to be a subset). -
ASCII Delimited Format Plug-In User’S Guide
ASCII Delimited Format Plug-in User’s Guide Version 3.4 ASCII DELIMITED ......................................................................................................... 4 CREATING AN ASCII DELIMITED MESSAGE ....................................................... 4 ASCII DELIMITED EXTERNAL MESSAGE UI........................................................ 6 DEFINING AN ASCII DELIMITED MESSAGE FORMAT...................................... 7 ASCII DELIMITED FORMAT OPTIONS .............................................................................. 7 Delimiter ..................................................................................................................... 8 Message Options......................................................................................................... 9 Treat Entire Input/Output as a Single Message (Message Mode) ...................... 9 Treat Each Record as a Separate Message (Batch Mode) ................................ 10 Single Record Mode ......................................................................................... 10 Header/Trailer Option.............................................................................................. 11 ADDING A NEW FIELD.................................................................................................... 12 SPECIFYING FIELD PROPERTIES...................................................................................... 13 The Required Property..................................................................................... -
STAT579: SAS Programming
Note on homework for SAS date formats I'm getting error messages using the format MMDDYY10D. even though this is listed on websites for SAS date formats. Instead, MMDDYY10 and similar (without the D seems to work for both hyphens and slashes. Also note that a date format such as MMDDYYw. means that the w is replaced by a number indicating the width of the string (e.g., 8 or 10). SAS Programming SAS data sets (Chapter 4 of Cody book) SAS creates data sets internally once they are read in from a Data Step. The data sets can be stored in different locations and accessed later on. The default is to store them in WORK, so if you create a data set using data adress; the logfile will say that it created a SAS dataset called WORK.ADDRESS. You can nagivate to the newly created SAS dataset. In SAS Studio, go to the Libraries Tab on the left (Usually appears toward the bottom until you click on it). Then WORK.ADDRESS should appear. SAS Programming SAS data sets SAS Programming SAS data sets SAS Programming Making datasets permanent You can also make SAS datasets permanent. This is done using the libname statement. E.g. SAS Programming Permanent SAS datasets The new dataset should be available to be accessed directly from other SAS programs without reading in original data. This can save a lot of time for large datasets. If the SAS dataset is called mydata, the SAS dataset will be called mydata.sas7bdat, where the 7 refers to the datastructures used in version 7 (and which hasn't changed up to version 9). -
International Language Environments Guide
International Language Environments Guide Sun Microsystems, Inc. 4150 Network Circle Santa Clara, CA 95054 U.S.A. Part No: 806–6642–10 May, 2002 Copyright 2002 Sun Microsystems, Inc. 4150 Network Circle, Santa Clara, CA 95054 U.S.A. All rights reserved. This product or document is protected by copyright and distributed under licenses restricting its use, copying, distribution, and decompilation. No part of this product or document may be reproduced in any form by any means without prior written authorization of Sun and its licensors, if any. Third-party software, including font technology, is copyrighted and licensed from Sun suppliers. Parts of the product may be derived from Berkeley BSD systems, licensed from the University of California. UNIX is a registered trademark in the U.S. and other countries, exclusively licensed through X/Open Company, Ltd. Sun, Sun Microsystems, the Sun logo, docs.sun.com, AnswerBook, AnswerBook2, Java, XView, ToolTalk, Solstice AdminTools, SunVideo and Solaris are trademarks, registered trademarks, or service marks of Sun Microsystems, Inc. in the U.S. and other countries. All SPARC trademarks are used under license and are trademarks or registered trademarks of SPARC International, Inc. in the U.S. and other countries. Products bearing SPARC trademarks are based upon an architecture developed by Sun Microsystems, Inc. SunOS, Solaris, X11, SPARC, UNIX, PostScript, OpenWindows, AnswerBook, SunExpress, SPARCprinter, JumpStart, Xlib The OPEN LOOK and Sun™ Graphical User Interface was developed by Sun Microsystems, Inc. for its users and licensees. Sun acknowledges the pioneering efforts of Xerox in researching and developing the concept of visual or graphical user interfaces for the computer industry. -
Positive Pay Format Guide
Positive Pay Format Guide Check File Import Contents Contents ........................................................................................................................................................ 1 I. Supported File Types ............................................................................................................................. 2 A. Delimited Text Files ........................................................................................................................... 2 B. Microsoft Excel Files.......................................................................................................................... 2 C. Fixed-width Text Files ....................................................................................................................... 2 D. Header and Trailer Records .............................................................................................................. 2 II. File Data Requirements ......................................................................................................................... 3 A. Required Columns ............................................................................................................................. 3 B. Optional Columns.............................................................................................................................. 3 Positive Pay 1 of 3 BankFinancial, NA Format Guide 11-2016-1 I. Supported File Types Positive Pay supports the following three types of issued files: A. Delimited -
Teach Yourself Perl 5 in 21 Days
Teach Yourself Perl 5 in 21 days David Till Table of Contents: Introduction ● Who Should Read This Book? ● Special Features of This Book ● Programming Examples ● End-of-Day Q& A and Workshop ● Conventions Used in This Book ● What You'll Learn in 21 Days Week 1 Week at a Glance ● Where You're Going Day 1 Getting Started ● What Is Perl? ● How Do I Find Perl? ❍ Where Do I Get Perl? ❍ Other Places to Get Perl ● A Sample Perl Program ● Running a Perl Program ❍ If Something Goes Wrong ● The First Line of Your Perl Program: How Comments Work ❍ Comments ● Line 2: Statements, Tokens, and <STDIN> ❍ Statements and Tokens ❍ Tokens and White Space ❍ What the Tokens Do: Reading from Standard Input ● Line 3: Writing to Standard Output ❍ Function Invocations and Arguments ● Error Messages ● Interpretive Languages Versus Compiled Languages ● Summary ● Q&A ● Workshop ❍ Quiz ❍ Exercises Day 2 Basic Operators and Control Flow ● Storing in Scalar Variables Assignment ❍ The Definition of a Scalar Variable ❍ Scalar Variable Syntax ❍ Assigning a Value to a Scalar Variable ● Performing Arithmetic ❍ Example of Miles-to-Kilometers Conversion ❍ The chop Library Function ● Expressions ❍ Assignments and Expressions ● Other Perl Operators ● Introduction to Conditional Statements ● The if Statement ❍ The Conditional Expression ❍ The Statement Block ❍ Testing for Equality Using == ❍ Other Comparison Operators ● Two-Way Branching Using if and else ● Multi-Way Branching Using elsif ● Writing Loops Using the while Statement ● Nesting Conditional Statements ● Looping Using