There are many reference managers out there to use for organizing the myriad of references and papers one acquires during their career.  One that I found recently is Zotero which is a javascript add-on for Firefox.   I won’t go through all the interesting features here, but basically, it is extremely easy to save information you find on the Web.  Not only web pages, but also journal article references (and PDFs) are easily saved. Another feature is one can sync the references to a database on their server and can be shared with groups of people.

Obviously a reference manager isn’t that useful if the information can’t be written into articles.  So, the Zotero people have included mechanisms to pull references from their database and put it into documents being written in both Microsoft Word and OpenOffice.  I have used it for one paper already and it worked out reasonably well.

So, how much does all this cost? Nothing, it is free.  Try it out.

When I first started in Science I can’t say anyone every sat down with me and told me how to write a paper. In reading papers, obviously something reasonably linear is easier. If one knows the background well, one can skip the Introduction and go right to the results. In writing a paper, I find it easier to think of it a little different. To that end I wrote up a template to help me order my thoughts and ideas. I will not say this it the only way to do it, nor the best. I find this way simple for me.

Below is the text. Attached here is a paper_outline one can print out.

---

The primary objective of this template is to help you organize your thoughts on the contents of a scientific paper. The standard format of a scientific paper is: Introduction, Methods, Results, Discussion and Conclusions. There are many modifications to this (e.g. inculde a Theory section or combine the Results and Discussion sections). Below is the likely order that one should work through to organize your paper, which can then be translated into the standard format (order). Try to move through each section in order, one follows naturally from the previous. Typically, each bullet point that you write below one of the sections is going to be a paragraph (though maybe not).

1      Primary Objectives

List the primary objective(s) of the work. Probably one primary objective and several secondary objectives.

2      Results to Fulfill Objectives

List the primary results that will fulfill the objectives. Will the results be shown by a figure, table or in the
text?

3      Discussion – Anomolies

List each discussion item. For each result, was there an anomoly about the result that needed to be described
further? Outliner in the data? Simple re-analysis with different starting conditions (e.g. curve fitting)?

4     Discussion – Pertaining to Previous Work

List each discussion item. For each result, how does it pertain to previous work? Are your results better? If
not, why?

5     Discussion – Future Work

List each extension to this work. How can the work be extended?

6     Describe the Methods

List each method that needs to be described. A method could be apparatus setup. Data analysis (and statistical tests). Participants (entry criterion, exclusion criterion). You will likely have several points here, again, each point will likely end up being a paragraph.

7    List the areas to Introduce

Given the results and discussion, what are the main areas that need to be introduced?

7.1   Motivation

7.2   Previous Work

7.3   Restate objectives

It can be an onerous task to keep track of all the research that gets published these days. I can’t say that I am great at it either, but there are some reasonably standard Google tools that I have found useful.  Back when I first started in MRI research, my supervisor had a lab meeting in which one person’s job (rotating, thankfully) was to go to the library and photocopy the Table of Contents of all the relevant journals, go through looking for relevant or interesting articles and present to the group.  Those were the days.

Google Reader is an RSS feed aggregator which basically means you can subscribe to RSS feeds and it gives an interface to be able to see them. Sites like PubMed are great for searching for journal articles (PubMed for the medical arena). Their site has changed a lot over the past 10 years. Recently, on the search results page there is an RSS feed symbol (orange symbol in the graphic above) that one can click. In most browsers this will bring up a window in which you can select how to watch the feed. There are lots of offline readers, but I like Google Reader.  Many journals also have RSS feeds of the articles that come out.

Another Google tool that works well is Google Docs. It is a good place to writeup documents that need to be shared with others and it keeps revisions of the documents. I can’t say I have used it for writing a paper, yet, but it is getting very close. The one thing that I haven’t worked out is how to put references in a Google Doc though I am sure there is a way.