Open Access: sometimes all it takes is the right person
We can debate the economics, complexities, details, implementation… of open access publishing for as long as we like. However, the basic principle: that publicly-funded research should be publicly-accessible seems to me at least, very obviously correct and “the right thing to do”.
So this, from April 2012, was very depressing.
Open access not as simple as it sounds: outgoing ARC boss
For those outside Australia, the ARC is the Australian Research Council. Much debate ensues in which one contributor to the comment thread writes:
…it is particularly galling that Sheil is projecting her own simplisti...
Source: What You're Doing Is Rather Desperate - January 8, 2013 Category: Bioinformaticians Authors: nsaunders Tags: australia open access arc publishing Source Type: blogs
Open Access: sometimes all it takes is the right person
We can debate the economics, complexities, details, implementation… of open access publishing for as long as we like. However, the basic principle: that publicly-funded research should be publicly-accessible seems to me at least, very obviously correct and “the right thing to do”.
So this, from April 2012, was very depressing.
Open access not as simple as it sounds: outgoing ARC boss
For those outside Australia, the ARC is the Australian Research Council. Much debate ensued in which one contributor to the comment thread wrote:
…it is particularly galling that Sheil is projecting her own simplistic...
Source: What You're Doing Is Rather Desperate - January 8, 2013 Category: Bioinformaticians Authors: nsaunders Tags: australia open access arc publishing Source Type: blogs
Non-fiction Reading Highlights 2012
I jumped on the bandwagon that is John Jeremiah Sullivan’s “Pulphead”. These are rightly considered to be some f.ing great essays. I reread some of them recently and was struck by how clean the prose was. Nothing particularly fancy, but it is the authorial stance that is breath-taking. His approaches to his subjects come askance, exposing some unexpected facet of his own life, which oftentimes succeeds in illiminating a shared humanity. In one brilliant biographical essay, Sullivan was able to turn Axl Rose into a tragic figure. In another, he gazes straight into the maelstorm that is Michael Jackson, an...
Source: Trapped in the USA - January 7, 2013 Category: Bioinformaticians Authors: bosco Source Type: blogs
Notable Books I Read of a Scientific Nature in 2012
After a barren few years for popular science books, I stumbled onto several good ones this year.
I first encountered evolutionary psychology about a decade ago in its former incarnation as social biology but was rather put off by it then, when it was rather short on data and long on theorizing, inevitably becoming a mirror for the writer’s political ideology. The field of evolutionary psychology has since progressed in leaps and bounds, and one of the glittering lights of the field is Jonathan Haidt, who also happens to be a gifted writer. His “The Righteous Mind” outlines a persuasive case that there...
Source: Trapped in the USA - January 5, 2013 Category: Bioinformaticians Authors: bosco Source Type: blogs
My Fiction Picks of 2012
2012 restored my faith in fiction. I read so many brilliant novels, phatagasmorphic books that dissolves reality and makes one ache for the pain of living. There was Kate Grenville’s “A Secret River”, a book that digs into the collective consciousness of the Australian psyche. It’s a richly imagined period piece of a man straddling the squalor of Victorian England and the prison colony of early white Australia. It’s an unbelievably tense collision of worlds, English, colonial Australia, and the indigenous world, with a ferocious climax that shook me up something wicked.
A page-turning jugger...
Source: Trapped in the USA - January 4, 2013 Category: Bioinformaticians Authors: bosco Source Type: blogs
On the need for a canon of Australian literature
I never used to, but I now believe firmly in a canon – a bonafide list of Australian novels that everyone ought to read. My moment of conversion happened at, of all places, a literary event. It was an event organized by the literary magazine Meanjin to celebrate great women writers of Australia. A panel of writers and publishers was put together to discuss a list of novels written by Australian women, and to launch a literary American-Idol of said novels. Despite the overt nature of the event, I was originally skeptical of the idea of a canon. But during the event I was surprising converted to the necessity of embrac...
Source: Trapped in the USA - January 2, 2013 Category: Bioinformaticians Authors: bosco Source Type: blogs
Books 2012
[* highly recommended if you’re into it, but YMMV]
1. Judith Lasater, Ike Lasater, “What We Say Matters”
2. Cal Newport, “How to Become a Straight A Student”
3.* Kate Grenville, “A Secret River”
4.* Suzanne Collins, “The Hunger Games”
5. Roger Lowenstein, “Buffet”
6. Suzanne Collins, “Catching Fire”
7. Suzanne Collins, “Mockingjay”
8. Helen Garner, “Monkey Grip”
9. Raven, “Biology”
10. Haruki Murakami,“What I Talk About When I Talk About Running”
11. Don Riso & Russ Hudson, “Wisdom of th...
Source: Trapped in the USA - January 1, 2013 Category: Bioinformaticians Authors: bosco Source Type: blogs
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.
Filed under: this blog (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - January 1, 2013 Category: Bioinformaticians Authors: nsaunders Tags: this blog Source Type: blogs
My Californian Life
Warning: No science ahead
I am in Portugal for the holidays having just left San Francisco. It is a part of the academic life that we have to keep moving around with each new job and after Germany and the US (California) I am moving to the UK in a few days. Its not easy to keep rebuilding your roots in new places but it is certainly rewarding to experience new cultures. It has been great to spend almost 5 years in California and it was very (!) hard to leave. I decided to try to write down a few thoughts about life in the golden state. Maybe it will be useful for others considering moving there. I apologize in advance fo...
Source: Public Rambling - December 26, 2012 Category: Bioinformaticians Source Type: blogs
The Voyager Golden Record: why is cytosine “S”?
Long time, no blogging. Breaking the silence with something a bit different than my usual content – a molecular biology question for you.
So a colleague posted this link to Yammer; a collection of images selected for the Voyager Golden Record. The record was designed as a “time capsule” illustrating aspects of life on Earth and was launched on the Voyager spacecraft in 1977.
Chemical definitionsThree of the images are confusing me: chemical definitions (shown at right), DNA Structure and DNA Structure magnified, light hit.
You see why I’m confused, right? The symbol used for cytosine is “S...
Source: What You're Doing Is Rather Desperate - December 5, 2012 Category: Bioinformaticians Authors: nsaunders Tags: space science biochemistry cytosine molecular biology voyager Source Type: blogs
Scholarly metrics with a heart
I attended last week the PLOS workshop on Article Level Metrics (ALM). As a disclaimer, I am part of the PLOS ALM advisory Technical Working Group (not sure why :). Alternative article level metrics refer to any set of indicators that might be used to judge the value of a scientific work (or researcher or institution, etc). As a simple example, an article that is read more than average might correlate with scientific interest or popularity of the work. There are many interesting questions around ALMs, starting even with simplest - do we need any metrics ? The only clear observation ...
Source: Public Rambling - November 6, 2012 Category: Bioinformaticians Tags: metrics academia publishing Source Type: blogs
Gene name errors and Excel: lessons not learned
June 23, 2004. BMC Bioinformatics publishes “Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics”. We roll our eyes. Do people really do that? Is it really worthy of publication? However, we admit that if it happens then it’s good that people know about it.
October 17, 2012. A colleague on our internal Yammer network writes:
Sad but true. I keep finding newbie bioinformatics errors in the Cancer Genome Atlas project data. This time a text download of 450K methylation from the Cancer Genome Atlas project reveals that Excel has had its evil way with th...
Source: What You're Doing Is Rather Desperate - October 22, 2012 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics research diary cancer errors excel reproducibility spreadsheet tcga Source Type: blogs
Addendum to yesterday’s post on custom CSS and R Markdown
Updates from RStudio support:
(1) “Thanks for reporting and I was able to reproduce this as well. I’ve filed a bug and we’ll take a look.”
(2) Taking a further look, this is actually a bug in the Markdown package and we’ve asked the maintainer (Jeffrey Horner) to look into it.
As juejung points out in a comment on my previous post, applying custom CSS to R Markdown by sourcing the custom rendering function breaks the rendering of inline equations.
I’ve opened an issue with RStudio support and will update here with their response. In the meantime, one solution to this problem is:
Do not...
Source: What You're Doing Is Rather Desperate - August 27, 2012 Category: Bioinformaticians Authors: nsaunders Tags: programming research diary statistics markdown rstudio Source Type: blogs
Custom CSS for HTML generated using RStudio
People have been telling me for a while that the latest version of RStudio, the IDE for R, is a great way to generate reports. I finally got around to trying it out and for once, the hype is justified. Start with this excellent tutorial from Jeremy Anglim.
Briefly: the process is not so different to Sweave, except that (1) instead of embedding R code in LaTeX, we embed R code in a document written using R Markdown; (2) instead of Sweave, we use the knitr package; (3) the focus is on generating HTML documents for publishing to the Web (see e.g. RPubs), although knitr can also generate PDF documents, just like Sweave.
It too...
Source: What You're Doing Is Rather Desperate - August 27, 2012 Category: Bioinformaticians Authors: nsaunders Tags: programming research diary statistics css how to rstudio Source Type: blogs
