Where to share?

A brief and unscientific survey of social bookmarking buttons provided by journal websites. Take with pinch of salt and/or tongue in cheek.

PLoS get it. As you'd expect.	BMC get it too.	Even ACS kind of get it.
OUP get it to a degree.	Someone doesn't get it.

I know, all bookmarking services provide their own tools, such as bookmarklets. However, I suspect that a button is more convenient for many people: it’s a courtesy and an advertisement for social bookmarking and online reference management tools.

So NPG: is it “we promote sharing” or “we promote sharing so long as you use our service?”

Great work, ISMB microblogging team

Another year, another ISMB/ECCB meeting and – another great blogging effort.

It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too.

Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up.

How-to: search across linked tables using acts_as_ferret

I’m in the process of adding search to a Rails application, using acts_as_ferret and ran into this issue. How to search a table using a field from another table, supplied by a foreign key?

At a complete (Rails) loss

I’ve been banging my head against the wall for almost a week with a Rails application. This post is not a plea for help – I’d use a forum for that – just a record of the problem. That said, feel free to comment, especially if you have a similar problem.

This is all using Rails 2.3.2, Mongrel 1.1.5, installed as gems on Ubuntu 9.04.

The basic issue: 2 models, 2 controllers, 2 sets of views. Identical in almost every respect, little more than basic CRUD (index, create, update, destroy). (1) works, (2) does not.

Update – thanks for your comments, here and elsewhere. In the end I rebuilt from scratch with scaffolding and it’s all good so far. Guess there was something rogue in my hand-crafted code.

Querying NCBI Entrez database fields using Ruby

Here’s a problem. You’d like to construct a complex query at NCBI Entrez using various fields. Example:

“9606″[Taxonomy ID]

to limit your search to Homo sapiens. Except – you don’t know which fields are available for the database that you want to query.

Baby steps with RSRuby in Rails

Plotting and charting libraries for Ruby (on Rails) abound. However, few are sophisticated enough for scientists and many are not actively maintained. Plotting in R, on the other hand, is about as sophisticated as it comes.

Can we bridge Ruby and R? Yes we can, thanks to Alex Gutteridge’s RSRuby. The next logical question: how to plot data using RSRuby in your shiny new Rails application?

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!

Brief words on the FriendFeed beta

The best place for discussion about the latest FriendFeed beta is at FriendFeed, of course. However, it would be amiss of me not to record a couple of thoughts.

On the whole, there’s little about which I feel strongly for better or worse – which rather suggests that the current design is just fine. With three major exceptions:

Slideshare FAIL

I enjoy a good joke. I’m not so politically-correct that I won’t laugh at the expense of others – remember I grew up in the UK, where bullying was part of the culture ;-), nor so po-faced that I can’t laugh at my own expense.

I do not enjoy April Fools. Jokes on this day are rarely, if ever, good jokes. Perhaps they were more fun when humans lived in small, isolated communities with little knowledge of the outside world and so could be fooled en masse by spaghetti trees. However, this is the 21st century, the age of information. We should be harder to fool, because we know more about the world.

Paradoxically, it’s the information age that enables the flood of tedious, blatantly false, time-wasting stories in our inboxes and feed readers every April 1st. You might even say that everyday is April 1st, somewhere on the Web. The elements of surprise and ignorance are gone. Perhaps it’s time to abandon this quaint custom.

Which brings me to Slideshare, who decided that it would be tremendously funny to (1) inflate users’ slide views by adding two zeroes and (2) inform their users by email.

everyONE…

…is the new community blog from PLoS ONE. They write:

This blog is for authors who have published with us and for users who haven’t and it contains something for everyone.

You’ll need a WordPress.com account to contribute; it’s a quick, unobtrusive sign-up and why not start a blog there too, if you haven’t already done so.
Bora writes:

and spread the word, outside of just twitter and friendfeed ;-)