Category Archives: this blog

A minor update to my “apply functions” post

One of my more popular posts is A brief introduction to “apply” in R. Come August, it will be four years old. Technology moves on, old blog posts do not.

So: thanks to BioStar user zx8754 for pointing me to this Stack Overflow post, in which someone complains that the code in the post does not work as described. The by example is now fixed.

Side note: I often find “contact the author” is the most direct approach to solving this kind of problem ;) always happy to be contacted.

This blog in 2013

In something of an end-of-year tradition, WordPress provides users with an effort-free blog post in the form of an annual report. Here is mine.

My ambitious plan at the start of 2013 was to aim for 4 posts a month. I managed 28 and I’m happy with that; about one every two weeks.

Looking forward to a new year of blogging. All the best to you and yours for 2014.

This blog: 2012 in review

Thankfully, WordPress.com have established an end-of-year tradition whereby you get a blog post for no effort, in the form of an annual report. Here it is.

Frankly, I’m amazed that I managed even 22 posts – hey, that’s almost 1 every 2 weeks! As for 2013…no promises. However, I’m looking forward to sharing at least a few useful snippets with you. All the best to you and yours for the coming year.

Draft post cull

Work and life are currently impacting the frequency of my blogging. I’m falling back on the old trick of clearing out draft posts and explaining briefly why they never saw the light of day.

1. How to launch a website (January 18, 2012)
Anyone can publish a website. Is this a good thing? In one sense yes, of course – empowerment and democratization of information are important. However, I’m increasingly of the opinion that scientific websites should meet some minimum standards and that those who create them have an appropriate level of programming competency. Having an idea is great but if it’s poorly-implemented, tools will break, whither and die, creating a Web of broken links and non-functional resources.

So the title of this post was supposed to be ironic and it went on to list a series of steps which described (wittily I hoped) how not to launch a website. Unfortunately, when I read over the post, it was not at all witty. In fact, it was just a thinly-veiled attack on a recently launched aggregator.

I think some of the points in the post do need to be made, but not in their current form and perhaps not by me.

2. Google Plus: what’s in it for the online scientist? (July 1, 2011)
I started to write this one when Google+ first launched. There were more than enough posts which reviewed its features so, as the title suggests, I was trying to come up with a different angle: how useful might G+ be for scientists?

In the end, I simply could not come up with anything interesting to say. I know that other scientists use G+ and find it very useful. I’m not one of them – in fact, I don’t use it at all. What’s more, I can’t even explain why. It’s not that I have strong feelings one way or the other about G+; for some reason, it just doesn’t register on my “must investigate” radar.

Still to come (hopefully)

1. Sequencing for relics from the Sanger era part 2: FASTQ manipulation and sequence quality
There are supposed to be 4 posts in my NGS series and this one looks at tools for manipulation and QC of FASTQ sequence files. My NGS self-education is a side-project and “real work” takes precedence just now, so no timeline promises for this one. Soon, I hope.

2. My day out at #osddmalaria
I’ve been meaning to write a summary of my day at the Open Source Drug Discovery Malaria meeting, back in February. Here’s a brief one: it was really interesting and I enjoyed it. More than that to follow at some point.

Syntax highlighting of R code at WordPress.com

If your WordPress blog is hosted at WordPress.com (like this one), you may know that source code in posts is formatted and highlighted using a shortcode, as explained here.

Until recently, R was not on the list of supported languages (neither was Perl), but I noticed today that both of them are now supported. This may have happened months ago and I just wasn’t aware of it. I spent a merry hour or so updating my old posts in the R category, so the code should now feature pretty colours. Let me know if you spot any errors that I may have introduced inadvertently.

I guess this is in some sense recognition that R is now used quite widely and that usage is growing.

The laziest blog post ever: 2010 here, in review

Over the holiday, I received an email from WordPress, containing a brief statistical summary of activity at this blog in 2010. Their automated procedures aren’t quite infallible: busiest day was 3 016 views, not 3, but they’ve done a reasonable job.

Even better, they’ve compiled the results into a draft blog post, ready for publishing. So here it is! Thanks, WordPress.

Normal service with original content will resume in due course.
Read the rest…

Where next for this blog?

It’s apparent that my activity at this blog has been on a downward-slope for some time. I currently post about once a month and when I do, it’s more likely to be a rant about some social network/web2.0 application than about bioinformatics.

So the question is what to do about it.
Update: thanks for the many, rapid and helpful responses. The unanimous view was – stay here, keep blogging. So that’s what it will be!
Read the rest…