ELISA analysis in R

OK, here’s a little taste of what I usually do, rather than some random ramblings… I have a PhD student who is running enzyme-linked immunosorbent assays, or “ELISAs” to the initiated. This is a standard technique for measuring (in a semi-quantitative way) the amount of a given substance in a sample. Basically (and this is a pretty basic description), you stick an antigen to a surface (like the bottom of a plastic tray) and then add an antibody that sticks to the antigen. The antibody has an enzyme stuck to it and when you add the substance of interest the enzyme catalyses a reaction that causes a change in the intensity of a colour. You can shine a light through the sample to see how much the colour has changed and that gives you an idea about the concentration of your sample.Read More »

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One quick trick to increase visibility and citations of research papers

digitization-of-library-3068971_640Since I’m “young” (whatever that means) I sometimes get asked to advise on how to disseminate research outputs through new-fangled doohickies like “the social media” (like writing click-baity headlines). This came up in a School Management Group meeting today, in the context of trying to increase visibility and citation rates for papers published by our faculty. It was something that I was quite interested in, so I spent about an hour doing some quick literature searches and then implementing some of what I found. Here’s the gist:Read More »

Tweeting over the Great Firewall

Wow, six months without a post is the longest I have neglected the blog for a while! I’ve got a couple of posts to write now that the summer is over, but I thought I would start with something that was a bit of a challenge for me over the summer. I spent a couple of weeks in Beijing in August, including five days attending the International Congress on Ecology (INTECOL). Usually, I like to try to promote the work that is going on at conferences and contribute to the general online science community by live-tweeting. The only trouble is that in China Twitter is banned… I came up with two solutions:

Solution 1: VPN

I used a virtual private network to bypass the firewall. That worked pretty well, and while VyperVPN cost about $12 for a month it gave me regular access to the web for the duration of my stay in China. Not bad value. However, part of my reason for going to China in the first place was to exchange ideas with Chinese researchers, and that’s tough if they can’t see what you are tweeting.

Solution 2: Weibo

My second solution, then, was to take to Chinese social media to try to communicate. There is a fair amount of guidance on Twitter and conferences, but I couldn’t find anything on Weibo and conferences. Also, Weibo is very much Chinese (as opposed to global) and so there wasn’t much hope of me communicating in the local language. Still, I tried my best and punted most of my first day of tweets (in English, unfortunately, and one as an experiment in Chinese via Google Translate) out through Weibo as well.

Screen Shot 2017-09-05 at 00.23.23

The results were not that surprising…  I got a bit of interest on the Twitter feed (interestingly, many many bot accounts, which has never happened before), but very little on the Weibo feed. In fact, I got absolutely no interaction whatsoever. The Twitter feed was completely out of sync with the rest of the planet (or so it seemed), but at least a few people both saw and understood them!

So, what I learned here is that social media is tough to crack in China, even when trying to use local tools. It’s also tough to sign up for Weibo because the authentication uses Chinese mobile phone numbers… Aside from that, the hashtags are a little different (note the “#” at the beginning as well as the end of the hashtag above) and I really never got to grips with finding profiles of people who might be interested and trying to add them to “Weibos”. Has anybody else had any success? Are there academics using both Weibo and Twitter in their social media arsenal?

PS: If you are interested, here’s a quick run down of the conference via my tweets and another from another attendee.

A hat-full of academic how-tos

Dipping in and out of the stream of tweets, there are always fascinating links to excellent resources for academics at all stages of their careers. I just spotted another, and thought it might be about time to aggregate some of these for posterity. Here’s the quick list (to which I will add if people suggest links), and details are below

  1. “How to find a postdoc”
  2. “How to get started with R”
  3. “How to use Github and RStudio”
  4. “How to use Github effectively”
  5. “How to respond to reviewers’ comments”
  6. “How to write a literature review”
  7. “How to help fight sexism in academia”
  8. “How to make your publications more accessible”
  9. “How to make your work reproducible”

Read More »

Why I am voting “Remain”

stronger-in-logoAs with a number of friends, I am growing increasingly concerned that the UK will vote for Brexit. My postal vote is already submitted, and I voted to remain. From our continued membership of the EU we gain human rights, environmental protection, workers’ rights, huge trade benefits, free movement, valuable immigration, a leading role in the governance of 500m people, and a place on the world stage. Specifically for my situation, I value the ability to work across borders as a researcher where I have the opportunity to learn from and work alongside academics across the continent. I am funded by an EU Fellowship which has brought cash back into the UK, am involved in EU grants which is bringing expertise and cash back into the UK, and am working to build international networks of researchers to solve major problems in sustainable urban development. Investors are pulling out of the UK for fear of Brexit, independent statistical bodies are advising of net loss if we leave, and thousands of valuable workers will be forced to go through long-winded (and currently unplanned) immigration processes to continue their contribution to our economy. Finally, this false notion of “taking back control” ignores the fact that one of our two legislative Houses is unelected, we remain an anachronistic constitutional monarchy, and only 25% of UK voters voted for the current Tory Government. To retain control, we need to stay a major player on the world stage and institute democratic reform within our borders. I’ve voted Remain, and I hope you will, too.

The Fishy Business of Brexit

fishing-boat-1281272_960_720Before you start to feel bad for the fishermen (fisherpeople?) on the Thames, here are some facts:

1) Quotas are important. If we fish all the fish, there are no more fish. The fishing industry has been utterly unable to regulate itself. EU quotas have led to the glacially slow recovery of managed stocks, because the quotas are higher than scientists advise. We need lower quotas combined with no-take zones, otherwise there will be no industry at all. Furthermore, UK quotas are divided among UK fishermen by the UK government so if one individual boat loses out it’s not necessarily the EU’s fault.

2) Three large companies own 61% of all fishing quotas. This isn’t about Michael Gove’s father alone on a tiny boat in a stormy sea. This is an industry monopolised by millionaires who are fighting regulation, just like all other industries. Viewed in that light it is completely unsurprising that “Big Fish” has joined Farage, alongside his banker allies.

3) Fishing rights to certain waters are set based on historic use. The fisheries industry does not want that to change because British boats are in loads of places that definitely aren’t British.

I know emotive stories about these poor Scots in their woolly jumpers and orange hats are relatable, but (as always) it is more complicated than that. It is completely understandable that they are unhappy: the history of their industry has generated a lot of jobs that simply cannot be supported through sustainable fisheries. It seems that the fishermen think Brexit would lead to higher quotas. Someday quotas might increase, but only if ecosystem-based management leads to increases in stocks that can support higher quotas, and that is the point of the EU Common Fisheries Policy.

Making my research more open using Kudos

I’ve always tried to make sure that my academic work wasn’t tucked away on a dusty shelf (or paywalled in an obscure academic journal, which is the equivalent in the digital age) and that has meant that my digital footprint is huge. I have accounts on ResearchGateTwitterSlideshareLinkedInFigshareGoogle ScholarAcademia.eduFlickr, and Google+ (as well as probably a few more that I’ve forgotten!). I don’t think I have lost anything by “scattering my wild oats” across a huge swathe of the internet, because I assume that it increases visibility. Indeed I get a few views across all platforms:

However, what I have been looking for is a service that allows me to aggregate all this content. Ideally it would have (i) a single page per publication, where I could bring together all the bits of information relating to that paper (data, preprints, press coverage, and a lay summary), and (ii) a personal profile page that brings all of those publication pages together under my profile. Well, I think I’ve found it!Read More »