Friday, February 25, 2011

Geekfest - Android help needed

Matts Magic Googlebeans For the first time since this term began, I've managed to find a few hours this week to do some development stuff. Not getting back to the new R-based statistics course for next year yet (hopefully today), but I have completed a substantial refurbishment of the MicrobiologyBytes Video Library as part of the OeRBITAL project I'm participating in.

One change is that the materials are now all available under a CC licence (CC BY-SA 3.0). I've changed the video hosting from Revver (which died) to YouTube. And the package is no longer available as a physical product, only online. This has negative consequences for developing countries with poor internet access, but I've never had many requests from there anyway and I'm no longer in a position to be able to offer to ship a physical product.

Under the hood, there's been a technical change which caused me a bit of a headache. I've done away with Flash embeds and tried to future-proof the site by opting for the HTML5 iframe embed code. This looks great on all the tests I've run so far (IE, Chrome, Safari, iOS), but I haven't been able to test it with Android yet, so I need your help with that - comments below please!

The difficulty with this decision comes from the fact that Mozilla presently refuses to sanction the h.264 codec used by YouTube for their HTML5 video player. This means the videos do not play in some versions of Firefox (although they do in others - initially I had big problems with Firefox, but after I ate one of Matt's Magic Googlebeans, they went away - go figure). Whatever the rights and wrongs of this, it means that Mozilla has placed itself in an isolated position, and I can't see how they're going to win this one. Compromise is in the air however and I'm confident this will be sorted out before long.

Right, now to try and get my (student)head around R again...

Tuesday, February 22, 2011

Me, a right wing reactionary?

Cock I'm shocked by how much I look forward to reading The Economist each week. It has something to do with the fact that this is one of the few print editions I still have contact with, in both my professional and personal life. But it has far more to do with occasional gems like this one.

Monday, February 21, 2011

My social media education policy

Acoustic chamber There's an interesting article in The Economist (How firms should fight rumours, 10 February 2011) which discusses the work of Rucker, Dubois and Tormala, and which suggests that formally denying a rumour is more likely to perpetuate than to stifle it, so the best policy in the face of misinformation may be to remain silent rather than to enagage.

I've been thinking about this recently, since Aleks Krotoski's talk at The Digital Researcher 2011 in which she touched on the social media echo chamber, and closer to home, in watching dissent spread as students get themselves worked up on social networks.

So far, my reluctant social media policy has been to enforce use of social tools though assessment. I have done this with a range of social tools over the last few years. Done well, you can expect 10% long term take up rate (some months post-assessment), as opposed to essentially zero without any compulsion to engage. 

But should I continue to push this approach?  Would it be better instead to offer my time to a minority coalition of the willing?  I've never managed to build a convincing extra credit model within our assessment schemes, but delayed gratification remains a tough sell in education.

These decisions are crucial in the ongoing struggle against over-assessment, but I remain uncertain of the best course to follow.


Thursday, February 17, 2011

A BLAST from the past

colony hybridization In 1979 a young researcher blundered into a laboratory and began working towards a PhD. Four years later, he emerged blinking into the sunlight and headed off to California for a while. This is the story of those years, which has lain buried under a layer of dust ever since until it was recently published online. Along the way, we had some laughs. For example, this may amuse some people:
Data Handling
Nucleotide sequence data was entered and analysed on a PDP 11/4 computer using a package of programs obtained from R. Staden, MRC Laboratory of Molecular Biology, Cambridge, UK (Staden, 1980).

At any rate, the truth can now be told:

Title: Studies on the Genome Structure of Neurovirulent and Attenuated Polioviruses
Author: Cann, Alan James
Date: 1984
Publisher: University of Leicester
Description: Thesis submitted for the degree of Doctor of Philosophy at the University of Leicester, 1984.

And if you want to read the full thing, here it is.

Abstract: The RNA genomes of neurovirulent and attenuated type 3 polioviruses have been cloned in E. coli using an efficient RNA.cDNA hybrid technique. The complete nucleotide sequence of the vaccine-associated neurovirulent revertant P3/119 and, in collaboration with others, the attenuated vaccine strain P3/Leon 12 a1b, have been determined. These have been compared with that of the neurovirulent parent strain P3/Leon/37. Ten nucleotide sequence differences were observed between the parent P3/Leon/37 and the vaccine P3/Leon 12 a1b, three of which resulted in amino acid substitutions. Between the vaccine and the revertant P3/119, seven nucleotide sequence differences were observed. Three of these resulted in amino acid substitutions. The possible significance of individual nucleotide sequence differences to the attenuation of and reversion to neurovirulence in poliovirus type 3 is discussed. The nucleotide sequence of P3/Leon 12 a1b was the first to be determined for a type 3 poliovirus. Comparison of this sequence with published type 1 sequences has demonstrated the extent of the molecular homology between them.

The major objective of this study was to identify the nucleotide sequence differences which account for the neurovirulent or attenuated phenotype of three closely related strains of poliovirus type 3. To achieve this, an efficient RNA.cDNA hybrid cloning method was devised. Although this was not the first report of hybrid cloning, previous unfavourable comments on its efficiency (Wood and Lee, 1976; Zain et al., 1979) and suggestions that the method given rise to cloning artefacts (Okayama and Berg, 1982) have almost certainly discouraged widespread use. Thorough investigation of each of the manipulative steps involved has shown that these problems can be overcome (Cann et al, 1983). Comparable in efficiency to the more used double-stranded cDNA cloning technique, the hybrid method has the advantages of experimental simplicity and that cDNA clones corresponding to entire virus genome can be obtained from a single experiment. The method has proved to be ideally suited to the molecular cloning of picornavirus genomes. It is possible that the transformation efficiency of RNA.cDNA hybrids could be further increased by treatment with E. coli DNA ligase and DNA polymerase I before ligation, thus carrying out repair of the hybrid molecule in vitro, as in the method of Okayama and Berg (1982). This modification has not yet been tested.
Together with the work of Dr G. Stanway on the neurovirulent strains P3/Leon/37 and P3/119, hundreds of cDNA clones were examined and more than 22 kbp of nucleotide sequence determined. These experiments resulted in the identification of a mall number of mutations in the genomes of the strains studied which must be responsible for their differences in neurovirulence. However, it has not yet been possible to identify the individual mutations involved in attenuation and reversion and further experiments are currently in progress. These experiments represent a number of different approaches. Firstly, the sequence of other neurovirulent vaccine revertants are being determined, to ascertain whether the mutations observed in P3/119 are shared by other strains. Secondly, the work of Racaniello and Baltimore (1981a) has demonstrated that the construction of recombinant virus genomes in vitro, at the level of cloned cDNA, is possible. Transfection of susceptible cells with these recombinant genomes gives rise to new, viable viruses with a defined set of mutations which can then be examined phenotypically. Initial experiments with recombinants between the neurovirulent strain P3/Leon/37 and the vaccine strain P3/Leon 12 a1b and also between the vaccine strain and the neurovirulent revertant P3/119 are in progress. Final proof that the mutations involved in attenuation and reversion have been accurately identified could be provided by the construction of an attenuated strain by recombination between P3/Leon/37 and P3/119. Parallel studies on neurovirulent and attenuated type 1 strains should help to explain the different stabilities of the type 1 and type 3 vaccines and may suggest how the type 3 vaccine can be modified to improve Stability. Finally, it is hoped to use site-directed mutagenesis of cloned virus genomes ln vitro to produce strains with specific biological properties.
Although the main aim of the work presented here has been the investigation of the molecular basis of attenuation in poliovirus, the information obtained has wider significance. The complete nucleotide sequence of P3/Leon 12 a1b was the first to be determined from a type 3 poliovirus. This has been compares with that of type 1 and the extent of the molecular homology between the demonstrated (Stanway et al, 1983a). As part of a larger study based on the analysis of monoclonal antibody resistant mutants, the major neutralizing antibody binding site of poliovirus type 3 has been identified (Minor et al, 1983). The nucleotide sequence information obtained is also being used currently in the design of synthetic antigenic peptides, a development which may hold many advantages for the prevention and perhaps treatment of poliomyelitis and other related picornaviral infections. At the outset of the work described in this dissertation, it was difficult to envisage that improved alternative to the Sabin vaccines would ever be a realistic proposition. It now seems that the immediate future holds just such a prospect.

Tuesday, February 15, 2011

Let me be the first #dr11

One of the most enjoyable things about yesterday's Digital Researcher meeting was that I didn't see a single Wordle. So let me be the first ...

Monday, February 14, 2011

Today's the day #dr11

Vitae Today is the The Digital Researcher 2011 meeting in London. The program for the event is here.

This year, we're hoping that as many people as possible will join us online, so we're planning to provide as much online content as possible and we encourage you to interact with the participants at the event (virtual attendance, Twitter: #dr11).

Hope to talk to you today, one way or the other.

Friday, February 11, 2011

Social media: A guide for researchers #dr11

Social media - A guide for researchers Last year, the Research Information Network (RIN) sponsored a report into the use of Web 2.0 tools by researchers (If you build it, will they come? How researchers perceive and use web 2.0). As many of us who work in this area know, the substantive conclusion of this work was, no - they won't. Which is a shame, as many researchers still don't know what they're missing. Over a slice of cake one day, Tris Hooley and I decided that it would be a good idea if someone told them. The nice folks a RIN thought so to, and kindly commissioned us to write a follow up pointing out the perils of not using social media (as well as some of the problems). So we're happy to announce the publication of:

Whether or not you're coming to the Digital Researcher meeting on Monday (in person or participating online), Social media: A guide for researchers is for you. More importantly, since you're already reading this online, download a copy and give it to someone you work with who hasn't figured it out yet. My thanks to everyone who has contributed to this report and helped with publication.

Citation: Cann, A., K. Dimitriou, and T. Hooley. (2011). Social media: A guide for researchers. Research Information Network.

Social media: A guide for researchers

Wednesday, February 09, 2011

It's all about activity streams stupid, part 472


"Tweetdeck now with huh? Let's test it: Dave Winer on Monday, January 31, 2011 at 6:47 PM: "Tweetdeck has announced something called, which promises to let you tweet in more than 140 characters, something I welcome. [I don't AJC] Beyond that the website is pure confusion." Source:"

Where do comments appear? On, or on Twitter? Or both?
OK, just on That's bad. I won't be using as it breaks the Twitter activity stream.

Tuesday, February 08, 2011

Dave White on the problem of Openness

Dave White Dave O. White nails it again:
Natives/immigrants was the tricky issue of the Naughties. Going in to the Tenties, the concept of ‘Openness’ is what we’re going to have trouble with. It’s crept up on us.
.. technically, he knew you could Google his Tweets. Was in the back of his mind, wasn’t going to Tweet anything outrageous, about 1000 people follow him, including funders. His mum rang him up about 20 minutes after Tweeting telling him he’d spelt ‘whisky’ wrong, the American way. She’s started Googling him. Technologically, he knew that functionality was there, but it wasn’t until he knew his mum was reading his Tweets that he had to redraw the map of his online digital identity. That knocked down a wall in the space, a social threshold had been crossed. It was the social dimension that made him rethink, moved Twitter use to being more residential than visitor.

Thanks to Doug Clow for blogging the session.

REF discriminates against the young, women and the disabled

Hefce - Analysis of data from the pilot exercise to develop bibliometric indicators for the REF

Hefce - Analysis of data from the pilot exercise to develop bibliometric indicators for the REF

Nice :-(

Friday, February 04, 2011

This isn't peer review

The End Of The Pier Show: "I reject at least four in every five manuscripts straight off the bat"

Nature's credibility now in tatters. Same editorial policy as the Daily Mail?

Thursday, February 03, 2011

Concept map? Don't talk to me about concept maps

Recall It's not often these days you hear people talking about under-assessment, but a paper this week in Science has stirred people up (NYT writeup here):

Jeffrey D. Karpicke and Janell R. Blunt. Retrieval Practice Produces More Learning than Elaborative Studying with Concept Mapping. Science 20 January 2011 DOI: 10.1126/science.1199327
Educators rely heavily on learning activities that encourage elaborative studying, while activities that require students to practice retrieving and reconstructing knowledge are used less frequently. Here, we show that practicing retrieval produces greater gains in meaningful learning than elaborative studying with concept mapping. The advantage of retrieval practice generalized across texts identical to those commonly found in science education. The advantage of retrieval practice was observed with test questions that assessed comprehension and required students to make inferences. The advantage of retrieval practice occurred even when the criterial test involved creating concept maps. Our findings support the theory that retrieval practice enhances learning by retrieval-specific mechanisms rather than by elaborative study processes. Retrieval practice is an effective tool to promote conceptual learning about science.

Most of the secondary reports of this paper I have read have implied that increased testing is the most efficient way of imparting knowledge, but that's not what the paper says. Concept mapping scored badly, as did reading though the material to be tested once, but the top scores came from old fashioned swotting followed by students actively rehashing what they could remember of the material ("free recall tests").

It's an interesting finding, especially for someone like me who abhors mindmaps. The question is, how widely applicable are these results (the paper doesn't actually describe the content the students studied, unhelpfully referring to it as "science"), and should what emphasis should be placed on this study? What do you think?

Tuesday, February 01, 2011

Quite interesting - #altc2011

ALT-C 2011 I'm always up for a bit of dissemination. Some days, it's all I do.

So the new ePoster format at ALT-C 2011 sounded interesting.

What would I do with my 6 minutes of microfame? What can you do to achieve lasting impact in 6 minutes?

Apart from the obvious.