Monthly Archives: August 2008

A brief ecological interlude: iNaturalist

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?

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.
Read the rest…

Mysteries of CCP4

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 video

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-up

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.

Why you, young scientist, should have a web presence

Three good reasons why you should be writing something, somewhere on the Web:

  1. Egalitarianism
  2. I hadn’t thought much about this aspect until a conversation with Roland at ISMB. Put simply, the Web democratises the science career ladder. It doesn’t matter if you’re an Honours student or a tenured professor; if you have good ideas and can articulate them, you can bring them to the attention of others and build a community around them. Previously, you would have had to wait until the stage of your career where you’re invited to give keynote addresses – and who has the time for that, these days?

  3. Connecting with the right people
  4. Ideally, we would all work in dynamic, stimulating environments, surrounded by talented, like-minded individuals keen to bounce ideas off each other. In practice – well, you know. No matter, because the Web allows you to find people on your wavelength, with whom you can interact. Increasingly, we’re seeing great examples of scientific collaboration established in this way. The process isn’t limited to science of course; Goth kids in small country towns find a friendly support network in just the same way.

  5. The big picture
  6. It’s all too easy in research to become obsessed with the minutiae and the day-to-day trials. It’s also easy to avoid writing until the time comes to publish a paper or apply for a grant. Writing something regularly on the Web can maintain writing skills, force you to assess critically your goals and progress and provide timely reminders about “the big picture”.

Those are my top 3 reasons: add yours in the comments (here or at FriendFeed).

Anniversary #2

Managed to fly through my blog anniversary.

August 2 marks two years here at wordpress.com. Stats as of now: 677 posts, 10 pages, 49 categories, 255 tags, 1,128 approved comments and 67,184 spam comments (!).

Blogging has really dropped off in the past few months, but I have some ideas about that. Stay tuned, thanks for reading and commenting.