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LaTeX and a biological thesis -- part 2

Posted by bob1, 16 May 2014 · 9,980 views

Latex reference managers editors
In this post I would like to talk about not just LaTeX but some of the software front-ends associated with it, specifically LaTeX editors and reference managers (note: these are all freeware).
For those not familiar with the terminology, front-ends are those bits of software that allow you to access a deeper level of software to do a purpose.  This is kind of similar to how a web browser uses the internet - the browser takes the information on the internet and converts it into usable information for us to read easily, so the web-browser is the front-end.
Now let me point out there are many many ways of doing pretty much anything in LaTeX, and writing it is no exception.  For example, if you wanted to you could just enter your bibliography entries in a simple text editor and label it as a .bib file and that would work fine, but would be a little cumbersome if you had more than 100 or so references, and so instead you can use a reference manager to take care of the files,
These are just some nice programs I have found that work for me.  Hopefully these will help you escape from the costly need for Word and Endnote (particularly Endnote - as you might have guessed, I'm not a fan).
For the first part I want to talk about reference managers:
In terms of reference managers I use JabRef.  Its a Java based program, so works on any operating system available so long as they have Java installed. The power of JabRef is that it is fast and simple, but has a very customizable interface, so you can see whatever you want to see on screen, with nothing interfering. 
Entry of things is simple, you can get latex output from Pubmed as a file (similar to that for endnote, etc.) or you can use the TeXMed interface and get the  BibTeX output directly.  You can also search a number of different databases, including Pubmed/Medline and google scholar directly from within the software itself.  Referencing something is simple - the bibtex key is just lead author and date (e.g. Weinberg1995 in my database would get you to Robert Weinberg's 1995 review on RB), so no need to remember strings of numbers. 
It has plugins for Word and Open Office/Libre Office, so if you want to continue using those it's fine too...You can also search your database from within Word etc.
Note: There are a bunch of different reference managers that can also produce Bibtex output, including Mendeley, Endnote, Papers and Zotero - see here
The best bit is the formatting references - formatting of references takes less than 2 seconds for 200+ references - try that with Endnote and Word.
For the second part of this I'll talk about LaTeX editors and the one I use.
LaTeX editors can be as simple as a text editor (notepad for Windows based, Textedit for Mac are the built in ones) or anything you can type into - if you wanted you could even use Word.  If you own a Mac and want a cute little text editor - open a terminal and type "Pico" (without the quotes) or "Nano" - two more built in ones you never knew about...there 'cause your Mac is running a version of Linux.
Over the years I have used 3 different genuine purpose built LaTeX editors, MacTeX for the short time that I was using a Mac at work, TeXWorks until recently and now TeXstudio.  MacTeX and TeXWorks are very similar as they are the ones that come supplied when you download a new installation of LaTeX, their beauty is the simplicity of the interface and ease of use if you just want to type away and occasionally compile your document.  There is pretty much nothing supplied with these other than some nice syntax editing, and line colouring and numbering features.  They will work with *any* version of LaTeX that I can think of, so are probably the most robust.  It has a bunch of built-in commands that can be tabbed through, which takes a bit of time, and the selection is somewhat limited, but still useful if you don't want to type commonly used commands all the time.  However...
I now use TeXstudio, this has an interface sort of like most programs - menu bars and short-cut buttons on display.  It also has the ability to do all the things I mentioned above, as well as guess which command you are entering and offer suggestions (rather than tabbing through).  It will also complete brackets automatically, build a tree of your document structure (i.e. show you  all sections, subsections etc. in a side window).  If you use LaTeX you'll know that building tables and figures can be laborious - TeXstudio will do it for you with their wizards (there are also online spreadsheet to LaTeX table converters such as this one).  It will allow you to preview figures (mouse hover on figure name) once the directory is inserted, so you can make sure that you used the right one
Two other very powerful features 1) difference comparisons - where you can take two documents and it will show you the differences, and 2)version control (via Subversion), which works by creating a new version automatically every time you save and allowing you to revert back to any version in the past.  Both very useful if multiple people are working on a document at one time (paper writing anyone?).  Don't worry - LaTeX documents are just text files - images etc are all saved as separate files so this won't fill your hard drive in no time - I have a 30+ page document (my intro) that's taking up a whole 60 kilobytes.
If you are interested in other types of typesetting - try Scribus (freeware version of Adobe's InDesign), which is fantastic and more intuitive for page layout.  Other freewares you might be interested in - Inkscape (=freeware Illustrator) and GIMP (=freeware Photoshop).

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