Write A Manuscript

This page is a little unusual, but we are constantly pressured to publish - thankfully not as much as in the academic world where the 'publish - or - perish' phenomenon has been elevated to the status of a sociological principle called "the Matthew principle".

But none the less even though it is possible to go through long period where you don't publish, I don't think that this is a good habit to be in - being lazy can be described as a habit, can't it? Or are habits things you have to work at? Specialist radiation oncologists have brains and they need to be exercised at something more than reading papers and seeing patients. Besides the research is fun when you don't have a course or deadline to meet!

I want to address the issue of writing a manuscript, in particular the infrastructure with respect to computing assistance. Now it is very tempting to say "it's only a small article and I'll just do it by hand", but believe me, this is not helpful in the short or medium or long term. This is a skill which is EXCEPTIONALLY useful and time saving. Learn it early!


What you want to write is one of these - an article! But to do this, you actually have to read what other people have written before you (basically you can't just have a brilliant idea, you have to show that this brilliant idea has not been thought of before and already been written about, and since few ideas are genuinely without previous basis in recorded literature, you have to show the logical progression and explain yourself). So when you want to write an article refuting this article here as 'absolute bollocks' (fortunately the editors will make you write something much more presentable as 'the author fails to consider even the obvious ramifications of his suppositions'!), you will either have to say the name of the article over and over, OR use a BIBLIOGRAPHIC REFERENCING SYSTEM!

What will appear at the bottom of the article will be a section titled "BIBLIOGRAPHY" or "REFERENCES" or such, and then a list of what are called 'citations' - you will not be surprised to see a wikipedia article on this and it is worth a short browse at it explains some things about formats that are relevant later. I would like you to concentrate of the second listed reference by Delaney et al.

… in Reference List … in the body of the article
Delaney, G., Jacob, S., Featherstone, C. and Barton, M. (2005). The role of radiotherapy in cancer treatment: estimating optimal utilization from a review of evidence-based clinical guidelines. Cancer 104(6): 1129-1137. ..; indeed, service planning is often based on this estimate (Delaney et al. 2005).

This will be a little unfamiliar to you because the journals that you read more frequently tend to use the Vancouver system of referencing. This is the style that has the reference signified with a numeral, usually based on the order of appearance, but could be alphabetical order also. In addition, the wording of the citation in the reference section is also different.

… in Reference List … in the body of the article
Delaney, G, Jacob S, Featherstone C, Barton M.
The role of radiotherapy in cancer treatment: estimating optimal utilization from a review of evidence-based clinical guidelines.
Cancer 2005 104(6): 1129-1137.
..; indeed, service planning is often based on this estimate 1.

So far so good, and not too difficult if you look up the required formatting of the manuscript before you start writing, AND you keep it firmly in mind the whole way through your writing - yah, right!! OR, you could use the easy way! Use some software. Yes, I'm sorry people, but it is the TWENTY-FIRST CENTURY, and you do have computers and you do use email, etc, etc, etc, so just get on with it.

What do you need? Well this depends if you have money and a computer you carry everywhere, and what operating system you use, and whether the machine is yours.

Before you get into using the software, you should understand what you are going to do. You will start with nothing (!) and at the end of the first part of the exercise you will end up with a 'library' of citations. Whether you have the PDFs at this point is immaterial, although I advise that you do. (We might keep that for an advanced level though!). Once you have your library then you will insert the appropriate citation into the appropriate place in your writing.

What you will NOT do is to worry about the appearance of the referencing in the manuscript or what is in the Reference section at the bottom of your manuscript.

Using Windows

The CHEAP and EASY way to do the first step (got your attention?), follow the instructions:

  • firefox_words.png

    download and install PortableFirefox. This is an open source browser will much better compliance, security and features than any IE made to date.

    • you might think about installing this on a USB thumb drive (make it bigger than 512MB you cheapskate!), as then you will be able to plug it in to any Windows computer and use it. The software gets around the Administrator issue by loading no DLLs to the Windows operating system but rather having all the special ones held in the local directories, so Windows is none the wiser! It will automatically update when you have a functioning internet connection also. [While there, you might also like to look at all the other free software available for use from a USB drive.]
  • start up PortableFirefox (wherever you have stored it! No, I don't know where that is, you should have taken note of that when you did the installing onto the thumb drive, but at a guess, open Computer and then open the USB drive and look at the folder called PortableFirefox and inside will be a file called firefox.exe - that's the one you want!)
  • now that you have Firefox open, you need to get an add-on called **Zotero**. Install it.
  • when done you should now see the zotero name in the bottom right-hand corner of the browser window. Click on it.
    • now like all really useful software, Zotero comes with some documentation. So all you males can now ignore it, start clicking in the program, get lost and then return to read it in 2-3 weeks (or you could break the pattern!). And all you females can open it, say "I don't understand", and close it, exit the program and then return in 2-3 weeks because what you are doing is really repetitive and time consuming (as a rule, if you are doing something repetitive in a computer, there will be tool to help you!). What I am saying is READ AND UNDERSTAND THE INSTRUCTIONS!!!!
  • zotero.gif

    Zotero has three panels.

      • The library on the left (I suggest having a general library to hold all the unused stuff, and individual libraries for your unfinished projects)
      • The current citations list in the middle
      • The citation details on the right. You will see that you can annotate the citation with several things like an Info (this is the basic downloaded information that you can peruse and modify if needed, doing such things as adding the Abstract, putting in a URL or ISSN or ISBN), Notes (intiially there are none, but here you can enter your own notes (in academia this is called your annotations), or the entire text of the article if you wish), Attachments (good place to save the PDF if you get it), Tags (these are like topic or search terms which for this article would include "Radiation oncology; informatics; epidemiology; database management system" and any other words you might find useful to group on), and finally Related (allows you to group articles into those used for a particular article or such like)
    • But we still haven't any articles in there! So ….. in the left panel, right click on My Library and select New Collection and call it something like Rubbish (because you will want to discard it after!). Leave Zotero open.
    • click in the browser address window and go to Google Scholar. This is a most invaluable resource! When it opens, select the link to Scholar Preferences and look for Bibliography Manager and where it says 'Show links to import citations into' select the EndNote option. Click Save Preferences. Now put your name into the Google Scholar search window and press enter. Look at the found citations and you should see two things. Firstly the last line should have a link option saying "Import into EndNote" - this is good. Secondly the end of the title line might include text saying something like : "all 139 versions ยป". If you want this citation then click on this text and then select one of the 139 entries that come up to Import into EndNote. Now I know you don't have EndNote, but that is bye-the-bye! Why? …. Because you have Zotero! Sounds like Zorro's second son doesn't it?
    • and VOILA! you should see a message telling you Saving Item… Name follows and then you should see the selected reference appear in the middle panel of Zotero. Look in the right panel to check that all the right detail is there.
    • variations of the theme? Lets get the Delaney articles! You can search on Google Scholar but eventually you will end up with this address for the publisher website. So just go there now. On this page you will see a link titled Download Citation, select this and then select EndNote and Abstract and Citation and PC and finally Go. And VOILA! The citation appears in Zotero. Now you will note that this is not fool-proof because 2 of the authors have been dropped off, now you go into the right hand panel and edit the authors. "Geoff Delaney" needs to go to Delaney, G and Featherstone and Barton need to be added (use the '+' sign).
  • So STEP 1 is now complete. When you do your research, you keep doing the same thing.

Now the second part!

Before we can demonstrate, there is some configuring to do (yes….always!). On the Zotero page is a little cog, if you click on it you will see a Documentation option. When selected it will open a page in the browser window and one of the options says "Word Processor Integration" and there you will see several options for integration with your word processor :

The web page gives you all the details, follow them. Once all of this has been configured, open your word processor with a new document and type any old rubbish. Put your cursor where you want the reference number to reside and make the selection from the menu. You should see a marker placed in your document. When you select the option to construct the bibliography, you will see all your references appear at the bottom of the document (if that is the way it is configured!). Now the really amazing part. If you want to change the citation format, make the appropriate select and VOILA! The formats are changed everywhere.

So you see, no keeping orders and lists. Just Cite While You Write (CWYW - like WYSIWYG for citations!) and let the software do the hard work.

So, the equations look like this:

  • $WORK_{WordProcessor} > WORK_{Zotero} + WORK_{WordProcessor}$


  • $Cost ($) = Cost_{OpenOffice} + Cost_{Firefox} +Cost_{Zotero} = 0$

What else can you do that might fit your circumstance?

If you want to carry the repository separate to the browser, there is an option to save the repository to another site. The repository is a SQLITE database file. You just need to remember that if you want to use it, you have to point Zotero to its position whenever you want to use it.

What about if you use Linux as your operating system?

Well, there is even better and worse news! Firstly, setting up a portable app type situation is not as easy, BUT all reports say that you can easily run portable apps under WINE. Secondly, if you are carrying the zotero repository, using it with Firefox on a Linux OS is the same as under Windows. Thirdly, AND THIS IS A BIG DIFFERENCE, if you save the PDFs within the Zotero repository, you can install and use the xpdf libraries to search inside the PDF [this functionality is not available for Windows users].

Satisfied? No!

What other options do you have?

If you still wish to keep your money ….

  • find Bibus, an open source bibliographic program which does easy searches within PubMed.
    • It will integrate with OpenOffice and MS Word.
    • It is available in Windows and Linux versions
  • use Mendeley, an open source bibliograhic program built on Web 2.0 technology.
    • It is similar to Zotero and integrates with it.
    • it integrates with MS Word and OpenOffice similarly to Zotero
    • It cannot search inside PDFs.
    • It is much more of a single machine solution, as opposed to the portability of Zotero with Firefox.

If you have more money than sense ….

  • Use Windows, MS Word (both of which you will have legal copies) and then buy EndNote (which incidentally doesn't have the same functionality as Zotero)
    • It will integrate with MS Word, but not OpenOffice
    • It is only available in Windows version, but you can run it under WINE, but then you would also need to be using MS Word under WINE also, so why bother?
    • It will cost you an unnecessary $200 approximately - yah, it's only money!
Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License