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technology, stats and IT for medics


Custom LaTeX bibliography style files: Part 1/4

October 13th, 2007 by Mark · 10 Comments

As part of an ongoing series of articles on BibTeX, I will present examples of using BibTeX to generate and format custom bibliography style files to suit a wide range of biomedical journals.

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Tags: LaTeX · Research

TortoiseSVN and svn+ssh problems

May 15th, 2007 by Mark · 3 Comments

I’ve had problems with TortoiseSVN connecting to a subversion repository on Mac OS X where the connection would just hang when trying to browse or checkout a repository, or would fail with the error “Unable to write to standard output (stderr)”. I show you how to diagnose the problem, and solve it (in my case).

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Tags: Free · Software

Port forwarding with SSH/Putty

March 27th, 2007 by Mark · 13 Comments

I regularly exchange data between computers at University and home. To maintain security, I keep a firewall running on all machines, and “tunnel” through the firewall(s) using SSH – the secure shell. For example, I run a web server on my main machine for web application development, and do not wish this to be publicly […]

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Tags: Free · Open Source · Software

Batch converting PDF to JPG/JPEG using free software

March 21st, 2007 by Mark · 40 Comments

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 […]

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Tags: Free · Graphics · LaTeX · Open Source · Software

Dovecot IMAP server, Debian Linux and tcpd’s hosts.allow

March 17th, 2007 by Mark · No Comments

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 […]

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Tags: Free · Linux · Open Source · Software

10 pieces of free software every doctor should haveAn introduction to R

March 9th, 2007 by Mark · 2 Comments

If you have the credentials to view February’s 2007 issue of The Lancet, have a look at a published letter about the “ten pieces of free software every doctor should have”. If you don’t, then don’t worry too much – you’re not missing much with this article. I should have guessed that something wasn’t right […]

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Tags: Free · R statistical computing

R and Filemaker on Mac OS X

March 1st, 2007 by Mark · 4 Comments

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 […]

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Tags: Filemaker · ODBC · R statistical computing

Editing blog posts with TextMate

February 27th, 2007 by Mark · No Comments

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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Tags: Software

Subversion directory organisation

February 26th, 2007 by Mark · 4 Comments

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 […]

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Tags: Free · Open Source · Research · Software

Upgrading old Filemaker solutions

February 13th, 2007 by Mark · No Comments

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.

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Tags: Databases