Thesis toolkit

Here I will mostly gather the info about useful software during a PhD thesis.

I: Word processor

To write your thesis and eventualy put it together, you will need some Word processor. Notepad could do a good job if you want to, but to have a decent layout and some pictures in it plus the references, something more advanced should be used.

Main possible options:

  1. MS Word;
  2. OpenOffice;
  3. LibreOffice;
  4. LaTeX; (my chosen option)

I.* Simple text editor

For simple and fast plain text documents (data, notes, or even simpla script viewing) some simple yet powerful text editor is needed. Somtimes- just to take of the effects added to the text- paste the text in text editor, copy it out and here you go- text without any formatting in seconds. My choise: Notepad ++. Yet in my mind there exist a difference between text editor and word processor- one is more simple and only for text based operations while other takes care of the layout, pretty looks etc.

Notepad++ text editor

Notepad++ text editor

II: Reference manager

Not to get lost in your pile or read papers and cited ones. Grouping the paper versions can become quite a pain…

Possible solutions are many, here I will show the ones I have tried:

  1. JabRef  (GPL) (suggested by Radu)
  2. Mendeley (Proprietary) (Suggested by Gundars, Janis and Karlis)

While JabRef is more like advanced .bib file manager, it includes procedures such as:

  • Grouping files (and logical operations between groups);
  • Quick search in info from .bib file;
  • Quick reference copy to clipboard;
  • Linking to files (file must have bibkey in the name to autoconnect).
JabRef

JabRef user interface

Mendely is more advanced software, having features such as:

  • extracting meta data from PDF;
  • connections to Journal database sites (citation import from site etc);
  • dropbox-type behaviour (for the journals) (1GB free for personal use, 100 MB free to share with colaborators).
  • linking to files;
  • searches also in the PDF’s themselves
Mendeley

Mendeley user interface

For the time being I don’t have much experience with Mendeley and I hope I will be able to provide good feedback. I have used JabRef for approximately one year and it has been helpful, trusty tool. Definitely better than changing your .bib file by hand.

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