Postgraduate Research - Tips for Postgrads

Rick Shine on Writing Papers

  • The relevance of my experience is research and publishing, not teaching and not grant applications. I have done it the old fashioned way through ARC and Discovery grants so I don’t have a lot of advice for getting funding. The way I got grants and continued to get grants was through publishing lots of papers
  • A third of all papers published in biology each year are my papers and this equates to 40-50 papers per year. I was either going to be a crime fiction writer or a scientist. Either way, I have always liked to write and I write all the time.
  • Writing papers is the same as writing anything. You need to attract attention so make it interesting and entertaining. Make it clear where you work fits into the conceptual understanding that already exists. Exploit ruthlessly the uniqueness of an organism and the fact that it’s Australian. Think of it like story telling and start with a simple cute question to intrigue the reader.
  • When putting a paper together get al the information from the research you have done and bring it down to a statement or generality. The final step is to discuss what the generality means, where does it fit, and what does it tell us.
  • Above all the story needs to be simple with clarity of thought. Work out what the simple story is and how you can tell it.
  • Red Thread concept for writing papers – from Bill Magnison:
    The Red Thread is a single conceptual theme. A single long argument that goes the entire way through the paper. Bill’s advice is to write the paper in reverse;
    - What is the story? (Discussion)
    - What bits of the results do I need?
    - Sift the methods
    - The intro then basically writes itself
  • Think about the paper while you are doing the work. Once the research is done. Put the tables and figures together and study the stats and then make sure they match.
  • Keep it short.
  • 1st person (I did this). Active voice. Short sentences.
  • Never make the author the subject eg. Use "Roos jump high (Smith etal)" instead of "Smith et al found roos jump high".
  • Accept that everything you ever publish will one day be wrong. The only thing you can do is be scrupulously honest with what you did.

Tips for PC Users

Movies for presentations

If you take movies of ".MOV" format using a digital camera (e.g. Nikon Coolpix) and want to insert them into powerpoint so you can run them during presentations, here's what to do:

  1. Powerpoint uses MediaPlayer not QuickTime to run movies, so will probably not recognize the ".MOV" extension. You need to convert your ".MOV" files into ".AVI" files using some freeware called "Rad Video Tools".
  2. Go to the web site:
  3. Download and install the "Rad Video Tools" software.
  4. Go to your "Programs" folder then the "RadVideo" Folder in which the stuff has been installed.
  5. Ignore things called "Bink" and "Smack" (!) and open the "RadVideo" icon (or drag it onto your desktop and create a shortcut). This is the thing which converts your movies to ".AVI".
  6. Select the file you want to convert, make sure it is set to convert to AVI, then hit the convert button. It does not overwrite, so you still have your original .MOV version too.
  7. In Powerpoint, go to "Insert", then"Movies and Sounds" then "Movie from file" and select your movie (AVI version).
  8. Make sure you copy the AVI movie files onto your CD or harddrive when you run your presentation because powerpoint does not actually embed the movie, it just creates a link to it.

Scanning text and having the computer recognise it as text

Recently I had over 70 pages of printed data that I needed to get into a spreadsheet. Do I spend 2 weeks entering it, threatening my sanity and risking RSI. No, this would be silly. I want technology to help out. The plan - scan or photograph the pages and then have some program turn the images into text.

Sounds simple enough but first, you need the appropriate term -
"Optical Character Recognition". Names are power and Google is the conduit for that power. You will find a bunch of freeware or demo versions of OCR software on the web. As usual there is a bunch of freeware for PCs but nothing for Macs. I managed to find one demo version for macs - a program called Readiris (which is very good and if anyone is thinking of buying software, I recommend this). After that, it was a simple matter of taking a photograph of every page, downloading them, running them through OCR and checking the output (these programs do make mistakes). It took me half a day to enter >10 000 data points.

Scanners are readily available and first year biology in Carslaw may have a scanner with OCR software - which may save you the hassle of finding your own.

Modifying output styles in EndNote

One of the most common issues identified by users of EndNote is the range of styles required for publishing. This often results in the need to edit an output style in order to meet the criteria set out by individual journals.

The EndNote program comes complete with a large number of commonly used styles, eg Harvard, APA 6th and MLA, as well as a number of individual journal styles. Additional styles are available on the EndNote website. If the required style is not available, either in the EndNote library or on the EndNote website, it may be necessary to edit an existing style.. Here are some instructions for carrying out some commonly required changes.

Select the style you're going to edit using the Output Styles Menu on the EndNote Library Window toolbar (if the style isn't already in your pre-selected list use the "select another style" option to open the full list of styles available.

Go to Edit > Output Styles > Edit "style name".

Save the style with a new name to ensure the settings of the original style are kept. For example, an edited version of Harvard might be saved as "Harvard Edited Copy".

Changing the punctuation used to separate multiple in-text citations

Some styles, eg Harvard, separate multiple in-text citations with a comma, while others use a semicolon (i.e. Brown et al., 2000; Martin, 2003; Francis and Grant, 2003). To change the punctuation: click the 'Templates' option under 'Citations'. Enter the required punctuation in the 'Multiple citation separator' box that appears at the bottom of the Citations window. Save changes.

Some styles will require a different approach

Some journals have very specific formatting requirements. For example, the journal Copeia requires the use of double-dashes (–) between page numbers. There is no simple way of editing an output style to incorporate this as the information used in the formatting is drawn directly from the reference template. The easiest way to fix the problem is to save the final draft of the document then remove the field codes using the 'Convert Citations and Bibliography' > 'Convert to plain text' commands on the EndNote X6 toolbar of word. Then work through the document replacing - with –.

Creating bibliographies with journal abbreviations

This is a two-step process. First, change the preferences in Endnote so that the abbreviated journal title is selected in preference to the full journal title when formatting the bibliography.

  1. Use the command above to open the ‘edit output style’ feature.
  2. From the list of options at the left of the Style Editor window, click Journal Names.
  3. Select the required option, eg Abbreviaton 1
  4. Close and save the style. Now when you format a paper or look at the Preview panel, all of the journal names should be replaced with the appropriate abbreviation.

Note: If a reference does not have the selected abbreviation entered in the Journals term list, the journal name appears in the bibliography exactly as it is entered in the Reference window.

The second step is to load one of the supplied journal title lists to use for data entry. These lists also contain journal abbreviations for alternate output, and are used by certain output styles. The lists are supplied as plain text files in the EndNote X6\Terms Lists folder.

To replace the existing Journals list with one of the supplied journal abbreviation lists:

  1. In EndNote go to Tools > Open Term Lists > Journals Term List.
  2. Highlight and delete all existing terms from the list
  3. Still in the Terms list dialog box, click the Lists tab and ensure the Journals option is highlighted
  4. Click Import List
  5. In the File dialog, navigate to the EndNote X6\Terms Lists folder (located in the Program Files), select the list you want to use, and click Open to import the journal names and abbreviations from the file into the Journals term list.

For more tips on getting the best out of EndNote see the Library’s EndNote Subject Guide.