Reflections on developing a research methods course outline

I write this blog post as I write and reframe the course I offer at the University of Canterbury, I think I am going to do some more innovative stuff this time.

I have been using the Essentials of Research Design and Methodology, a text by DeMatteo and Marczyk for some time now. It's a very informative text written at the right pitch for students who are about entering the subject area of conducting a research work or a research project.

Traditionally, I have used lectures and class discussions as my teaching methods. This year, I plan to organize the class entirely around problem solving and focusing on problem-based learning or principles of inquiry guided learning.

How to use conkeror and Mendeley to organize information ((tags: Mendeley, conkeror, productivity))

I recently started using conkeror -- the keyboard-centric emacs like implementation of firefox browser for surfing the web. It's a simple, blazingfly fast browser that helps you to focus and cut out the information clutter in a number of ways that one may not think important till one actually starts using it: (1) focus on the screen and use the keybord entirely for writing and surfing the web, and (2) organize information collection. I use Mendeley for organizing  my PDFs and general reading materials. In this post, I'd like to share how I use Conkeror and Mendeley to quickly sort, track, and archive information.

First, for those of you who are not familiar with Conkeror, let me write a few goog things about Conkeror. I was not aware of this new way of browsing the web enitrely using keystrokes till recently. Conkeror is a very small sized but very efficient little browser based on xulrunner (more about xulrunner here

https://developer.mozilla.org/en/XULRunner

and Mozilla that lets you browse the web very efficiently.

You can download more information about Conkeror here

http://www.conkeror.org.

The software is available for windows, macs, and linux; configuration is very easy (there is really nothing to do other than unzipping a few filles and writing a few lines in the shortcut windows, see "installation" for windows. For linux, the process is even simpler. I am not familiar with Mac, therefore cannot comment on this, but I guess the process cannot be too dififcult either.

Essentially, conkeror has an emacs like feel and functionality. Which makes it very efficient to use for browsing for information almost totally clutter-free. I like the feature that I can extend the browser using javascripting. My use of mouse is minimum; almost everything can be accessed using keywords that you define upfront even if I never programmed anything at all. it has an innovative bookmarking system titled "webjump"; There is a learning curve though. However, the results of time invested in learning the system is worth it in the end. If you haven't tried it yet, I'd encourage you to give it a shot. .

Anyway, conkeror needs configuration to get it to work, and you need to use keyboard and need to learn a little about combining keystrokes to really play with it well. People have written several different "commands" to interact with it in different ways and here is a list of collection of these commands and webjumps

http://conkeror.org/Webjumps

A feature that I wanted was a quick linking to Mendeley because I wanted to combine the simplicity of conkeror and power of Mendeley for organizing information. Conkeror works very well with citeulike and delicious bookmarking services, so one of the ways to use conkeror with Mendeley could be to use citeulike and then use the link between citeulike and Mendeley to collect PDFs and organize references. However, although a reasonable workaround, the process was slow. To speed up the process, I wrote a small javascript code to import references directly to Mendeley (basically to use the web importer). Here is the code:

---- Code for conkeror adoption of Mendeley web importer begins ---

function send_mend(i){
check_buffer(i.buffer, content_buffer);
i.buffer.document.getElementsByTagName('body')[0].appendChild(i.buffer.document.createElement('script')).setAttribute.('src', 'http://www.mendeley.com/min.php/bookmarklet');
}

interactive("mendeley-post","post the page to Mendeley", send_mend);

--- End of the lines of code ----

By default, conkeror blocks pop ups. To enable popups for Mendeley web importer to work, you can use the following (I have used it by changing the about:config part) thus:

dom.disable_open_during_load set to "false"


I  think a combination of the simplicity and distraction free surfing of conkeror with the power of Mendeley can really speed up work and help to stay focused. I think the simplicity and the ability to focus on the screen, reading and reflecting while being less bothered about simultaneously shifting attention between the mouse and the keyboard is helpful. Add to this the simplicity provided by Mendeley to keep PDFs organized in watched folders and automatically scrape references and add PDFs.

It's a great combination of simplicity of a web browser to cut the clutter of information and power of Mendeley to organize them, both for free. Useful stuff.

How to write a literature review using only the web

This morning we were discussing cloud computing and the next big thing where everything gets done in the so called cloud. In the "cloud", data are hosted in servers elsewhere, available all the time for downloading to machines or downloading may not be necessary as all software and software implementations to handle data will be readily available and one can work as often as one wishes, wherever, whenver, whatever. That discussion brought into mind if we can conduct a systematic review of literature entirely on the web using say only Google Docs, some online reference management website, and pretty much that.

Why is that a desirable thing to do?
For one, if a framework of conducting simple evidence based reviews can be developed that can be done entirely off the cloud or let's say off the web, that frees up resources that are entirely local on someone's computer. Besides, developing systematic reviews is entirely a team work, so more distributed work essentially means faster turnover. That said, I wanted to give it a shot.

The plan is this.

In one hour, I am going to run a simple review by framing a research question, running a search, gathering essential studies, summarizing the key points and writing up the review with nothing other than an online word processor such as Google Docs.

The question:
Is there any association between low birth weight (birth weight less than 2500 grams) and adult heart attacks (acute myocardial infarction)?

OK, it's a random question, but at least a question that has two simplicities:
a) A fairly well defined "exposure" variable if you will
b) And a fairly straightforward health outcomes that we are going to consider

The challenge is to answer this question with a write up or review within a limited time. The tools that we are going to use:
1) Google Docs (Google document or word processor; indeed any other online word processor would do)
2) Google Spreadsheets (or any other online spreadsheet application)
3) Mendeley reference manager (reference management could also have been conducted by Zotero, and more about that later)
4) Pubmed Central (because pubmed central allows free access to full text articles. If there are other implementations, they can be used as well). We add to that Google Scholar

Other than these four fully integrated online services nothing else will be used to develop an answer to the above question.

To test the feasibility, we start the review process thus:

Research question:
Is there a valid association between low birth weight and acute myocardial infarction in adults?

Search terms:
"low birth weight"
"pre terms"
"lbw"
"premature infant"
"AMI"
"acute myocardial infarction"
"heart attack"
"myocardial infarct"
Restrict the search terms to:
English language
all articles that got published within the last five years
all totally freely available articles
We are also not going to include studies that are case studies or case series
We are going to present the results in the following hierarchy:
Systematic review
Randomized trial if any
Cohort studies
Case control studies
Cross sectional survey
Case series

We are not going to conduct a formal meta analysis but just narrative analysis

Let's get going. The plan will be something like this.

1) Set up a document in Google Docs (* more comments about this later)
2) Set up a spreadsheet
3) Set up a data abstraction form in Google Spreadsheets
4) Create a collection in Citeulike
5) Create a collection in Mendeley
6) Run a search in Scholar Google, and pubmed
7) Export the results to Mendeley
8) Get the PDFs after discarding the excludable articles
9) Summarize and annotate the PDFs
10) Write the results

Ten tasks, let's say two hours. Can this be done? Can this task be distributed among a number of participants?

If this is a model and if this works, then this process can be used to speed up the process of evidence generation remarkably fast and perhaps develop a plan for analysis of high throughput literature database.