FriendFeed Life Scientists: 14-day summary

Since I haven’t posted for 14 days, what better (and lazier) way to post something than to surf over to a 14-day summary from the Life Scientists Group and link to the top ten items!

  1. Review process files in the EMBO Journal – but why only for “the majority of papers”?
  2. How XML threatens Big Data. Or not. How JSON might be an alternative – or not.
  3. Solve any computer problem – with this classic XKCD flowchart.
  4. Science reviews the revolution in ‘strategic scientific reading’ – are they way behind the curve, or providing a useful summary for the uninitiated?
  5. Best practice in microbial genome annotation – spirited discussion on the nature of best bioinformatics practice.
  6. FriendFeed Life Scientists user survey – no further word on whether this will happen.
  7. 50 Years of Structure – link to a JMB review on the early days of structural biology.
  8. Reflections on Science Online London 2009
  9. Workflow tools that speak SOAP?
  10. Advice on cleaning up a protein sample – a nice example of useful discussion from the group.

Who knows, this could become a semi-regular feature.

Improvements to the reference management workflow

I use Google Reader to subscribe to the RSS feeds from journals that interest me (see my public page). I’m also a big fan of CiteULike as a reference management system.

For a long time I’ve thought: it would be great if GReader handled journal articles more efficiently. Rather than going from link in GReader -> article at journal -> CiteULike bookmark -> back to GReader, how about “post directly from GReader?”

With Google Reader’s new send-to feature, you can do just that. See this forum post for the details. Also, take a look at this how-to for a quick way to post to CiteULike by entering a PubMed PMID, DOI or ISBN identifier in the address bar.

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.

Share at PLoS

PLoS get it. As you'd expect.

BMC get it too.

BMC get it too.

Even ACS kind of get it.

Even ACS kind of get it.

OUP get the serious options

OUP get it to a degree.

Someone doesn't get it.

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?”

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…

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. Read the rest…

It’s true: you can’t believe everything that you read on the Web

An oft-repeated cliché is that “you can’t believe what you read on the Web.” Of course, you can’t believe what you read anywhere: it’s up to individuals to assess the quality and reliability of information, regardless of the source. That said, it can be alarming to sit back and watch the speed with which errors propagate in cyberspace. Yesterday, I watched this unfold in a few short hours:

  1. I (and others) bookmark a link to a project called gpeerreview, hosted at Google Code
  2. A blog post (since corrected) states that the search giant has been working on a peer review tool
  3. My bookmark appears at FriendFeed, where we discuss the incorrect attribution of the project to Google
  4. Another blog post on Google Peer Review appears
  5. Links and comments about gpeerreview start popping up all over FriendFeed, some of which suggest it is a Google project

The great thing about the Web though, is that it corrects itself just as rapidly. With a few well-placed comments, some discussion at FriendFeed and the best solution – an email enquiry to the project developer (well done Richard!), the phrase “Google Peer Review” was consigned to the error basket.

I’m not pointing the finger or criticising anyone here. Unless you develop software, you’re unlikely to be aware of Google Code and the URL/site design do make it look like a “content owned by Google website”. Just be aware: when writing, to be sure of your facts and when reading, to critically assess and not blindly accept.