Toluu

What You're Doing Is Rather Desperate

Notes from the life of a bioinformatics researcher

A brief ecological interlude: iNaturalistAugust 27

Recently, I was toying with ideas for fun side projects involving web applications. “Here’s a good one”, I thought, “a place for amateur naturalists to record their observations.” They could upload photos, place items on a Google Map, tag items and all manner of web 2.0 stuff. Over time, with enough users, such a site might even become a valuable conservation resource, allowing data miners to see interesting changes over time.

Today, via FriendFeed, I discovered that someone else also likes the idea. I’m delighted, since I’ve long since abandoned all hope of even starting a fun side project; I lack both the requisite skills and the time to learn them. If these ideas appeal to you, please visit iNaturalist. Better still, post some feedback at their Google Group.

It’s a site that will only succeed with users and for that, they need a slick interface that makes data entry simple, quick, fun and comprehensive. Not quite good enough to persuade me to enter observations just yet, but I’ll be following their progress with interest.

What if journal current contents were tag clouds?August 23

Would it tell us anything useful? Does it tell us anything useful about the current state of journal RSS feeds, or suggest areas for improvement?

Let’s find out. It’s as simple as locating the feed URL from your journal subscriptions, pasting it into Wordle and eyeballing the results. Here’s what came back for the 25 journals in my current subscription list.

Biochemistry
Not especially successful. Items in the Biochemistry feed consist largely of dates/times, DOIs and author names, with no information regarding article content. Bioinformatics
Rather better. It’s obvious at a glance that protein kinases and phosphorylated substrates are topical in this issue. BMC Bioinformatics
Also very good. We would guess straight away that analysis of proteomic data is a hot topic in this issue.

Mysteries of CCP4August 18

Since moving to a structural biology group, I’ve had to become somewhat familiar with CCP4, a suite of programs that do all manner of things using structural data, typically PDB files.

Being a bioinformatician, I tend to ignore the GUI in favour of the input -> script -> output approach, as I’m mostly interested in batch processing. Documentation describing this operation for CCP4 programs is strangely lacking on the web. The best that I can find is the CCP4 wiki; if you know the package well, please contribute to it.

I eventually dug up what I was looking for in:

/opt/ccp4/ccp4-6.0.2/examples/unix/runnable/

or the equivalent on your system. Here, you’ll find a collection of shell scripts, confusingly named with the suffix “.exam”. As an example, here’s how you might run the program “contact”:

#!/bin/sh set -e contact XYZIN $1 << eof > $1.contact MODE ALL ATYPE ALL eof

You might run that on a bunch of files using e.g. “find ./ -name “*.pdb” -exec contact.sh {} \;”.

Other mysteries: many CCP4 programs are quite happy to take gzipped files as input (such as you might download from the PDB FTP archive), but may choke if unzipped filenames don’t contain “.ent” or “.pdb”.

Vindication for videoAugust 17

Announced first via FriendFeed (of course), Moshe from JoVE is circulating an email with exciting news. I can’t do better than to quote it here:

JoVE, the video-publication for biological research, was accepted for indexing in PubMed and MEDLINE.

JoVE is the first and only video-publication to be included in these databases maintained by the National Library of Medicine (NLM). The decision was made by the NLM advisory committee, Literature Selection Technical Review Committee, which is composed of the authorities in the field of biomedicine, such as researchers, physicians, editors, health science librarians and historians. This committee evaluates the scientific quality of publications and typically approves only 20-25% of the applications.

Inclusion in PubMed/MEDLINE is a big milestone for JoVE, and for the scientific publishing in general. It demonstrates the official acceptance of new approaches to science communication, such as video online, by the scientific community. Overall, it will increase the interest of the scientists to communicate their findings in video, making biological sciences more transparent and efficient.

Well done to the JoVE team.

BioBarCamp wrap-upAugust 8

The latest “unconference”, BioBarCamp, wrapped up today. Once again a FriendFeed room was used to great effect in providing coverage. I think it’s worth stressing that in addition to the “as it happens” aspect, FriendFeed provides a permanent, searchable archive that you can revisit to revise your notes and refresh your memory.

Further information is at the BioBarCamp wiki and Deepak has a nice summary of the back-channels and other, similar events.

Congratulations to all involved - sounded like an excellent event.