Research tools

Whilst I have not been at this research malarkey very long, several people have made suggestions for useful software, in addition to my own past experience. I have put some notes/links below on various tools that should help towards the process of research. Hopefully this might be of interest to others, and feel free to add your suggestions below.

Organising papers/references

I am using Mendeley to organise my ever growing library of literature. I also looked at and tried a few others, including Qiqqa, but they didn’t really seem to work for me.

Having used it for several months, I can’t imagine trying to organise and then reference several hundred papers and texts without some sort of tool. I remember the pain of manually trying to keep track of and insert references in Word97 during my undergraduate thesis.

Mendeley comes with a powerful “cite-o-matic” plugin for Word, that inserts nicely numbered and formatted references. These can be added either by a searching for the author/title, or by selecting the open file in the main Mendeley interface, both of which I use as I’m not sure which is faster.

There is also a plugin for browsers –actually a bookmarklet– that lets you save the results of a web search directly to your Mendeley library. This works well with Google Scholar, on sites like Science Direct, as well as some journal sites but not all. Presumably it needs specific code for it to work, but not sure if this is a limitation of the Mendeley script or the particular website.

Mendeley is tied in with as online account, which synchronises onto the different computers you have. There are also phone/tablet apps, which are handy when in the library looking for a book.

There are a number of useful features, that probably apply to most reference managers, but they certainly make my life much easier.

  • Being able to do a full text search of everything in my library is incredibly powerful.
  • The ability to highlight and add comments (which are also searchable) and then later edit these. As they are stored within Mendeley, they synchronise between devices. But it is also possible to quickly open the original PDF file if you want a clean print.
  • Automatically renaming the files from the garbled reference ID that the journal uses into a much more human friendly “Author (year) Title”.

It would be great to have freeform comments/markup and multiple highlight colours, but I suppose every piece of software is a compromise between features and bloat.

Organising notes and thoughts

A month or so ago, I started using OneNote to try and collect my thoughts. I have found it to be very useful, and fits in well with my way of thinking, although there are a few annoying limitations.

The basic interface has a hierarchy of notebooks, sections, and pages (which can be indented to form another level of hierarchy), see screenshot below. Each of these pages is a freeform area where you can type, paste images/screenshots, and links to documents/spreadsheets. It is also possible to insert hyperlinks to other pages within OneNote.

Screenshot of OneNote software

The text input has the usual rich formatting (headings, bulleted lists, bold/italic/strikethrough, etc.) although it is more limited in terms of style than Word. It is also possible to add todo checkboxes, and reminders that synchronise with Outlook. The Equation Editor is also built in, so you can type fancy equations (plus copy them from/to Word) relatively easily.

Reordering text is simple, as each paragraph has a handle in the left margin to drag it up/down the page, or to change the indent level right/left. This also applies to images.

That said, there are a few things that I think could do with improvement.

  • It is not possible to crop images within the program. As a workaround, it is possible to copy into Word, crop, then copy back — but a bit of a PITA.
  • It is also not possible to group items, so if you try and use the highlighter over an image or add text as an annotation, then insert text above, things have a tendency to become misaligned. There is an ‘insert space’ tool, which seems to work, but is not as natural to me.
  • It would also be great if the Mendeley cite-o-matic tool worked in OneNote, but it isn’t too much bother to just copy in a formatted citation, so that is what I have been doing.

Finally, it is possible to synchronise using Microsoft’s version of DropBox — OneDrive — and then edit on my phone/tablet using the free app. While I don’t want to make a habit of this, it is useful to be able to jot down something as it occurs to me, and have it in the same location as all my other notes, rather than on a tatty scrap of paper which I will almost certainly loose.

Writing up

While I am a long way off writing things up, I wanted to think about this and try to avoid abortive work. I plan to write up my final thesis using LaTeX , as I can see that it offers a lot of control as well as looking very professional. It is also well suited to large scientific documents, with equations and figures throughout.

However, to start writing up bits of text, I would prefer to use something  bit more user-friendly and that I am used to. For all it’s sins, Microsoft Word is still a useful piece of software, and I find that I can easily express and structure my writing using that, without having to spend time thinking about or looking up the correct markup syntax.

This then leads to a dilemma, as I want the best of both worlds. I want the convenience of writing in Word, with the power and quality of LaTeX, and hopefully without too much extra bother.

Searching for convertors, I found that there is an excellent one freely available for LibreOffice called writer2latex. I was pleasantly surprised how straightforward it was to open a .docx file in LibreOffice Writer, and export this via the plugin to a .tex file. While there were a few minor glitches, almost everything in a reasonably complex document rendered as expected. This included formulae written in MS Equation Editor, which were converted to proper LaTeX input.

With the settings I used (below) the structure of the document (headings, lists etc.) is kept intact, but most of the other formatting is stripped, which is fine as I will be using LaTeX to format everything anyway.

  • Export to Latex 2e (tex) format
  • Configuration: default.xml
  • Encoding: UTF-8
  • Untick ‘enable multi-lingual support’ but tick ‘use greek letters as symbols’, this saves greek symbols in the text as inline math[2]For me Greek letters will almost always be mathematical symbols, as I don’t plan to write many Greek words

This means I can write things up in either Word or LibreOffice, then transfer them to LaTeX without too much work in re-typing things. Although I am sure there will be more than a few drafts towards my final thesis.