Scientific Writing with LaTeX

Transcription

1 Scientific Writing with LaTeX

2 One Possible Workflow in Scientific Writing

3 Document Preparation: LaTeX typesetting was conceived and developed by Donald A. Knuth between 1977 and 1986 in collaboration with his students and with advice from typesetters and calligraphers. TeX is a typesetting system for technical texts. is a collection of TeX macros written by L. Lamport From

4 It s All About Typography From ETH-Bib s e-collection, a disseration in Word from 2012

5 TeX Philosophy I Enter one-dimensional instructions (the.tex input file) in the well weathered (platform-independent) ASCII format for the eventually two-dimensional page layout. The logical structure of document-, page-, paragraph-, word-, and finally letterdesign proceeds via boxes: The same way a classical typesetter would work: TeX solves many optimization problems of penalty-functions which are formulated for all kinds of typographical rules. The result of the optimization process should finally lead to a «aesthetically pleasing typeset document» (Knuth)

6 TeX Philosophy II TeX acts as a high-level programming language The type-setting instructions are interspersed within the actual text which is to be typeset. The parser of the.tex files identifies the commands by their specific structure \commandname{arg1}{arg2}{arg3}

7 TeX s Strength From its initial goal and history LaTeX provides an aesthetic mathematical formula typesetting in the context of technical texts (and it still is a leading player in this market ): From G. Grätzer: Math into LaTeX Many extensions were added over the years from other fields of science: Physics (Feynman graphs), chemistry (chemical structures),...

8 TeX Installation First, install the TeX system (i.e. compiler, libraries, packages, and typographic infrastructure) Examples of TeX-systems for different operating systems Microsoft : MikTeX, protext Linux : TeXLive Apple : MacTeX ipad : TeXWriter / Texpad

9 Type Up a TeX File Input file: Artikel.tex \documentclass{article} Preamble part: Specify the necessary packages \begin{document} \titel{ein Artikel} \author{h. Harzenmoser} \maketitle \section{einleitung} Text... \cite{harzipigs04} \section{methoden} Text... \subsection{habe gemessen} Text... \subsubsection{... und \emph{gemessen}} Text... \section{resultate} Text... \bibliographystyle{plain} \bibliography{meineliteratur} \end{document} Result Ein Artikel H. Harzenmoser 1. Einleitung Text Methoden Text... Harzenmoser (2004) 2.1. Habe gemessen Text und gemessen Text Resultate Text... Referenzen. Harzenmoser, E. 2004, Pigs and Porcu Hugentobler, H. 1962, Braunvieh Inter

10 La/TeX IDEs For Microsoft systems: TeXnicCenter WinShell WinEdt and the WYSIWYG-ly LyX

11 LaTeX IDEs on Linux distributions Kile and again the WYSIWYG -like LyX

12 LaTeX IDEs Texmaker runs under Windows/OS X/Linux

13 pdflatex pdflatex the modern alternative to classic LaTeX: Source: agodemar on Tex.stackexchange.com 18. Jan N.B. Since TeXLive 2010 pdflatex accepts not only.eps figures but most bitmap/vector graphics formats:.pdf,.jpg,.png,.tiff,

14 The LaTeX Bib(La)Tex Connection How to typeset references in LaTeX documents

15 Bibtex vs. Biblatex \usepackage{natbib} \bibliographystyle{<uvw>} %.bst file \begin{document} \usepackage[]{biblatex} \bibliography{mylib} \begin{document} %.bib file Let's cite! Einstein's journal paper \citep{einstein} and the book of \citet{dirac} are physics related items. Let's cite! The Einstein's journal paper \citep{einstein} and the Dirac's book \citet{dirac} are physics related items. \bibliography{<mylib>} \end{document} %.bib file \printbibliography \end{document}

16 The Inner Workings of the BibTeX Application MeineLiteratur.bib Artikel.bbl Artikel.tex BibTeX Artikel.aux BibTex application.aux files list the bibliographic requirements (from the \cite-like references) as extracted from the source file (Artikel.tex). The BibTeX program loads to corresponding BibTeX data (from say MeineLiteratur.bib) and generates the reference section (Artikel.bbl) which belongs to Artikel.tex. A new compilation of the LaTeX-file, Artikel.tex, molds together text and references into a coherent whole.

17 BibTeX Format BibTeX (Oren Patashnik, 1986) is a data format as well as an application to store and work on bibliographic data which is necessary to produce the bibliographies in LaTeX documents. Publication type BibTeX, the data format BibTeX key Tags

18 JabRef: BibTeX s Good Soul Graphically oriented bibliographic information manager of BibTeX files. GUI for painless generation and maintenance of BibItems. JabRef MeineLiteratur.bib Artikel.b BibTeX JabRef is an OpenSource Java VM application. Advantage: Program runs platform-independent. Artikel.a

19 JabRef s Bibliography Viewer

20 Import to JabRef Direct filling of the JabRef GUI forms Import ASCII data file with BibTeX-formated bibliographic information Import of proprietary data formats from: Inspec (engineering-oriented literature) ISI (Web of Knowledge/Science database) Medline (US National Library of Medicine, bibl. database) Ovid (Platform for STM information) Scifinder ( Chemistry-specific database for literature & substances) EndNote.

21 Working with References using LaTex & JabRef

22 Literature/Reference Management: Zotero Finally, use Zotero as the frontend tool to acquire, manage and deploy the bibliographic Information necessary for scientific writing. Register for free at with free 300 MB cloud storage space.

23 A Most Versatile Web Picker Book This applies to Firefox! Picker uses (Context Objects in Spans) COinS: Zotero tries to sense the content type in web browser. If successful: add information to personal library with a single click. Zotero supports thousands of sites from book stores, to newspapers, to academic journals and repositories. Correctly identifies Table of Contents as a folder with a set of single entities For other browsers (IE, Safari, Opera, ),.js Bookmarklet solutions available

24 More than just Reference Collection Bibliographic information

25 Group Libraries to collaborate For collaborative working: Group Libraries Zotero groups can be private or public, open or closed. For example, you and a few colleagues might initially work on a research project in private. After publication, why not share your research notes and library with the world? Administration: Through setup process at zotero.org by the group-library owner Number of group libraries and number of participants: unlimited

26 Export Zotero entries to BibTeX Output Options:

27 Synchronized across the Universe In preferences: Zotero automatically synchronizes data across as many devices as you choose. Add to your research library on your work PC, and organize your collections on your home laptop. All of your notes, files, and bibliographic data remain seamlessly and silently up to date. Returning from field work? Your data will be waiting for you when you get home.

28 The Good and the Bad Excellent web-picker + - Synchronization across all popular platforms - MS/Mac/Linux. Standalones (Desktop versions) for Linux/MS/Mac. A viewer exist on ipad (ZotPad) Firefox optimized (however, there exist Bookmarklets as web-picker for IE, Safari & Chrome) Bulk transfers are done as website- «scrapes» using COinS. Integration in word processors (MS- & Libre-Office) Bibliographic data download can be coupled with PDF grabbing

29 Exercise 1 1. Collect at least 5 references on the web using Firefox and the Zotero plugin. 2. Select a few or all of the new references, export them in BibTex form to the local desktop. Import the Bibtex file to the existing MyBib.bib BibTeX data collection using JabRef. N.B. All files connected with LaTeX/BibTex are kept in the folder \LaTeX_Artikel on the USB stick.

30 Exercise 2 1. Add new citations to the LaTeX File Zrad.tex using texmaker. 2. Process (pdftex) the wrapper files WrapperSimple.tex and WrapperStylish.tex to obtain two different forms of the same article. 3. Change the bibliographystyle to say (plain, nature, abbrvnat, unsrtnat) and reprocess the article.

31 Alfred Gautschy, Fachreferat für Physik & Astronomie