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LaTeX and other programs for making documents

LaTeX

LaTeX is a document preparation system. In practice, it means that you can add special tags to a plain text document to specify document structure and formatting. LaTeX is the standard in scientific publishing, because it allows you to concentrate on the content, instead of wasting time with the formatting, and it anyway produces the highest quality printouts, especially for mathematical formulas.

There is a LaTeX WikiBook to help you learn to use LaTeX. If you know it already, instead, why don't you contribute to it? :-)

overleaf.com is an online collaborative latex editing site. CERN users have premium account features and can host larger projects for others to collaborate on. There is also git synchronization to be able to keep an work on an offline copy using the tools below.

latexmk is a widely available script that will take care of running all compilation steps needed to render a document. It can be run as e.g. latexmk -pdf document.tex.

rubber is an alternative LaTeX build tool.

LyX is for people that write and want their writing to look great, right out of the box. No more endless tinkering with formatting details, 'finger painting' font attributes or futzing around with page boundaries. You just write. In the background, Prof. Knuth's legendary TeX typesetting engine makes you look good.
Lyx is available in ScientificLinux, Os X and Windows.

Kile is a LaTeX source editor, TeX shell that simplifies the creation of LaTeX documents.

Dot2TeX might be interesting to generate drawings.

Installation

• Windows : use MiKTEX.
• Linux : use TeX Live.
• Mac : use Mac TeX.

Tutorials etc

• The Not So Short Introduction to LaTeX2E, local copy of the May 2006 version. Updates from Oetiker's web site.
• http://www.latex-project.org/

Thesis writing : Latex

• Download a framework for writing your thesis
  • Version from Mark Dalton - UJ Thesis Framework - MMD
  • Version from Martin Cook then Chris Lee - UJ Thesis Framework-MNC-CL
  • Modernised version on GitHub RC-physics/UJ-template and overleaf https://www.overleaf.com/read/gmvbgyxmcffw#af3bbe
  • Use these commands or run with latexmk or rubber.
    • Only Vector graphics (figures as eps files)
      • (latex <filename.tex> ; bibtex <filename> )_n ; dvips <filename.dvi> -o <filename.ps> ; ps2pdf <filename.ps>
    • All kinds of graphics ..... jpg, gif, png .... pdf .... (make ps --> pdf)
      • (pdflatex <filename.tex> ; bibtex <filename> )_n
  The (~)_n means repeat several times so all references are resolved.

BibTeX

Wikipedia:BibTeX is a file format for storing bibliographies that can be used from LaTeX or LyX, so that you don't have to copy all the bibliography in each article you write. Also, the specialized tools for BibTeX help you to check it and keep it in order and updated. See Literature for links and tools.

Images, Vector Drawing

• GIMP - for pixel images. Highly recommended ..... download here
  Does not support 16-bit color depth or CMYK color model for professional printing. Needs quite a lot of RAM.
• ImageJ Image analysis and processing in Java, supports 16-bit depth images.
  It seems a bit "heavy", eating up quite some RAM, but it feels quite fast, and it has a lot of useful tools (including all the colour mappings that you can imagine!).
• Dia - really good for diagrams.
• Xfig - From the dawn of Unix times... Anyway, it's installed.
• Inkscape Open source vector drawing. It's getting better and better!
• Xara Extreme Vector Drawing program, now Open Source on Linux and OsX; not open on Windows. The porting from Windows was not jet complete last time I checked.

Office Suites

If you desperately need a MSOffice-compatible program, there is OpenOffice. OpenOffice is OpenSource Software, so it's free as in beer, and free as in speech too. Even more importantly, OpenOffice 2 uses that ISO standard OpenDocument format; so you can be sure that your documents will be readable in the future. It also means that you are not forcing the people to whom you send your documents to buy Microsoft software, which is not compatible with many operating systems.
OpenOffice 1.1.2 is installed in ScientificLinux, and also OpenOffice 2.0 is availabe.
If you are on Mac OsX, you might want to try NeoOffice instead - it's OpenOffice with a more Mac-style interface.
OpenOffice is available for Windows, too.

Fixing things

• To find unicode characters in a file ... use the regular expression [^\x00-\x7F]

If you are away from your PC, you can use Portable OpenOffice, for example to make presentations. It is still recommended, anyway, that you also bring along a fully cross-platform form of it, like a PDF. Bring a copy of a recent Acrobat Reader, too.

Remember - Don't use Word DOC files.