medicalnerds.com

It is often necessary to batch convert PDF documents and graphics into other formats. I explain how to do this using totally free software. Searching for PDF software using Google is fraught with difficulty — one ends up with endless links to commercial sites, who charge lots of money, mislead users into paying for software that is similar to, or even uses free software. Freely available PDF software includes xpdf and ghostscript, and source code is fully available under a GNU GPL open source license. [Read more →]

Running your own email server is great, but it must be secure against attacks from hackers and “script-kiddies”, idiots who scan networks looking for systems that advertise services and allow remote access. You can secure certain services on your linux-based machine, such as sshd and imapd using tcpd’s hosts.allow and hosts.deny functionality, to limit the number of hosts that can even get to a login prompt. [Read more →]

Before you start out with your research project you need to be equipped with the tools required to help you keep notes, write papers and produce professional looking documents. In this 2 part article I will describe 10 of my favourite applications, most of which are open source, all are free. [Read more →]

R (The R project for statistical computing) and Filemaker provide a compelling solution for the common problems involved in medical research, namely data entry, reporting and analysis. However, there are pecularities in this combination, particularly when running on Mac OS X and trying to use ODBC, that can cause difficulties. This article discusses some solutions to these problems. [Read more →]

If you use TextMate on Mac OS X (and if you don’t I would thoroughly recommend you try it: it is by far the best editor I have ever used) and maintain a blog, then it is possible to create blog entries using TextMate.
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Spell checking medical documents can be a real pain. My spelling at the best of times is atrocoius atrocious. Luckily most software, even browsers now support spell checking. The problem is now getting hold of a good medical dictionary to use with your application. Now e-medtools.com a site which specialises in medical spell checking, medical proformas and PDA software have made a 40 000 word dictionary available for free under the GPL licence. Up until their product for MS word was only available with a $10 single user licence. [Read more →]

Using subversion (or any other version-control system) to manage your working laboratory or research files is sensible. All changes can be tracked, and it is straightforward to review old versions of files. I store all work relating to research, including notes, papers, thesis chapters, statistical analyses and even data. If I were to make catastrophic changes (deliberately or non-deliberately) it is easy to roll-back changes. It’s like a “Track Changes” on steroids. [Read more →]

Q: What do we do with old Filemaker databases?

There were massive changes in the way Filemaker works between version 6 and 7 (all of them good). You’ve got a number of options, mainly determined by the size and complexity of your existing solution. The main two options are upgrade or rewrite. [Read more →]

LaTeX is a powerful document typesetting system that I recommend for any large technical or academic work. LaTeX does have a significant learning curve, and works in a very different way to the modern WYSIWYG word processor, but the investment in learning this excellent system will pay dividends again and again. There are numerous front-ends that make learning the system even easier. [Read more →]

Pedigrees are essential when documenting large complex families with inherited disease. I spend a lot of time looking after families with a variety of inherited neurological disease, and have spent a similar amount of time trying to find decent software to make this work easier!

I last did a systematic search for software last year. On Mac OS X, there appeared to be very little available, and what can be found is often not suitable for complex human relationships. [Read more →]