Thesis writing, Typesetting, Latex tricks, Reference Managing

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Thesis and paper writing

Well what you really want to do is desktop publishing or to express it right choose how things are formated.

In general Office applications have some abilities here but you need to know a lot of tricks how to make it work and there are simply better tools:

A very powerfull and "mousepusher" tools is  Scribus.  A Opensource Desktop publishing program (like InDesign). Made for setting thesis and other Pages to be published (even presentations) It is powerful but needs some time to get a feeling. Here you choose where is text where are pictures and how things are set.   http://www.scribus.net/   Disadvantage here, while most reference programs work together with both office suites and Open/libre office even brings its own reference manager with it scribus is needs some external plugins to manage references

For a scientist on the long run Latex is the better choice for long documents. The new suites make using latex easy and fast. Some advices here:
For windows Miktex is a nice and full package it can be installed or run as a binary (external drive) (http://miktex.org/)

Even so you can use every text editor i would recommend to use a specialized tool to write tex. They offer not only source code and fancy preview features but also take parts of the awkwardness of tex. With the right tool writing tex is writing like in Word. Tools Like "LYX" promise even life capabilities so "what you see is what you get" with TEX but I favor a more simplistic solution.
At the moment I would recommend TEXSTUDIO that is a branch from TEXMAKER. The first has a few nice features more then TEXMAKER but is just a question of taste TEXSTUDIO offers SVN integration and with this an automatic versioning system   http://texstudio.sourceforge.net/    http://www.xm1math.net/texmaker/
Texniccenter is also nice and has more functions but more is not always better http://www.texniccenter.org/

Both have an inbuild BIBTEX editor (how to manage references). However sometimes it is just nice to do this externally with jabref (see section refmanager)

A few handy tools:

This is a online equation editor similar to word. At the end it gives you the latex syntax, but while you generate it you see what happens:http://www.codecogs.com/latex/eqneditor.php
This is another equation editor:  https://viereck.ch/latex-to-svg/
If you need to count words there is a webinterface that does this for you: http://app.uio.no/ifi/texcount/online.php
This is a nice tool making citations from books. Simply use the ISBN and the program looks up the book and generates the bibtex code:http://www.ottobib.com/
All the editors mentioned above have a table generator but sometimes you want to make it externally this webpage might help:http://truben.no/latex/table/
Hint it works also nice if you export your code from Python or Matlab already with the right separators
One very hand tool is this difference manager, it highlights differences in the TEX code like word review http://www.peteryu.ca/tutorials/publishing/latexdiff
Real time cooperative working with latex (cloud):  https://www.overleaf.com/
this page has a nice overview over word/writer/pc to latex converters http://www.tug.org/utilities/texconv/pc2txtbl.html

Many cooperators still like to use word to write papers, to oblige them you don't need to convert the original Latex into word but you can convert the final pdf including the formatting.
This script worked for me very well: https://github.com/dothinking/pdf2docx
At Lund university we have a cite license to PDF-X. See https://program.ldc.lu.se/Download

If you need your custom bibtex format try to run "latex makebst" in any command line. If custom-bib package is installed (and in the standard miktex installation it would be reloaded if not) this will generate your style sheet after a few questions how it should look like
there are several solutions for multiple bibliographies in a single document, find instructions here http://www.tex.ac.uk/cgi-bin/texfaq2html?label=multbib
A multitude of templates can be found here http://www.latextemplates.com/

Writing a book:

Well that is a long story, in general you could use a wordprocessor like "Microsoft Word" or the opensourceversion "writer" from Libreoffice. However these are not really made for long texts and there are a lot of different little helpers missing.
The next question is what kind of book. If it is science, Latex, since you need plenty of cross-references, formulas and similar things.
If it is something with pictures like a magazin and you want to place them by mouse, Scribus, since it is Desktop-publishing you want.
For pure stories there are nice tools that help to develop characters and storylines. One tool i particularly like is the yWriter:  http://www.spacejock.com/yWriter5.html
Just remember, after the first version you need a good versioning system. Especially if there are several authors or editors. Additionally, some people swear on mind mapping to organise their mind for papers

Reference managing

Reference managers can do much more then just make the reference list in the document. They can collect your PDF and keep them sorted and even more, you can write notes in them, comments to the paper.

Jabref and docear have the advantages that they are based on a singe file and can put the file links relative to this file. That means you can have your whole database on cloud services or a usb stick and are independent.
https://www.jabref.org

https://docear.org

Build into many of the tools are the automatic extraction of bibliographic informations from e.g. the DOI or the ISBN There are however specialized tools available that perform these tasks too.
This webpage creates a citation from the ISBN http://www.ottobib.com/
This webpage creates a citation from the DOI https://www.doi2bib.org

Mendeley has a need import feature. It reads in the PDF’s and analysis them.  It’s free in its basic functionality, if you store files in it (which you want) than it will cost you at some time. A need function is the sharing with other people. I was acquired by elsevier. It works in  Microsoft and Openoffice/Libreoffice and synchronizes to bibtex http://www.mendeley.com/   I found the exporting function to be  bit buggy, but in general a nice program

For bibtex files, there is a nice free java based reference manager called Jabref. https://www.jabref.org There is a new plugin for Word available that offers similar features to Endnote and the other mentioned (see below). It now has automatic import features from ISBN or DOI. I usually get a citation with DOI into the program. Important you can link all your PDF (an rename them) and give a relative path to the bibtex file. So I use Dropbox and synchronize all my files with it.  It has a neat group function that allows for sorting of references into groups and then you can choose multiple groups to limit your vast library. My go to program.
The word citation tool now works very nicely. Find an instruction here: http://www.ee.ic.ac.uk/hp/staff/dmb/perl/index.html

We (Lund University)  have Endnote and an old version of Reference manager in the department for free.
Openoffice/Libreoffice has it’s own reference manager.

If you write with LATEX, you could of course write the references in the file by hand and use a formatting tool. The better choice however is to collect the references in a so-called bibtex file
a need thing for bibtex is this cleanup tool:   http://bib-it.sourceforge.net/
just stumbled over this useful tool. It extracts a library from a word document and makes a new file out of it. highly recommendable https://rintze.zelle.me/ref-extractor/