Category Archives: Digital Researcher

Find Article PDFs easily with Lazy Scholar

Looking to speed up your research? The Lazy Scholar extension for Google Chrome is now even more helpful.

Lazy Scholar Extension Page

I’ve mentioned Lazy Scholar before, but it’s worth mentioning again as it’s had an update. It’s an extension for Google Chrome that looks for PDFs of articles when you’re browsing abstracts. It also has some other nifty features.

You can search for papers by typing into your address bar, then your search. With Lazy Scholar you can shorten this by typing ls search term which works as a direct search on Google Scholar for whatever you’re searching for.

The recent updates are easy paper sharing links and something else that looks useful: Lazy Scholar now checks Beall’s list of Predatory Journals. These are open access journals that will accept more or less anything, so long as you hand over the money. I have seen one or two good authors publish papers in predatory journals, but Lazy Scholar now adds a warning to let you know that what you’re looking at is a questionable journal.

If you use Chrome during your research then it’s well worth downloading Lazy Scholar from the Chrome Web Store (for free).

A new website introducing genetic engineering

The Journey of a Gene is a new website at UNL-Nebraska that teaches the basics of genetic engineering. There’s a combination of videos, some from YouTube and some specifically made as well as some interactive sections.

The video above, explaining what a gene is, is an example of what they’re bringing in. Later they explain the role of promoters and coding and you get elements like the video below explaining how to use the interactive elements.

I tend to be wary of websites a teaching tools by themselves. There are very few good ones. However, I don’t know if they have some sort of special unit at UNL, but this is the second time I’ve found useful interactive animations produced there. They also do some handy astronomy tools. As one of AoB Blog’s non-botanists, I found the videos genuinely helpful in explaining some of the genetic engineering process.

It’s hard to say why some sites work and some don’t. If it was easy to spot why something was rubbish, then it’d be easy to fix. In this case, I think building it around one specific problem, Soybean Sudden Death Syndrome, means that you have an idea of what the context is. It’s not just random information; there’s actually a point to it. That kind of narrative structure means that the sections follow on from each other in a sensible way.

If you’re a new student and want a little extra help getting your head around what a gene is, and how DNA inheritance works when you start crossing and backcrossing plants, then you should definitely give the site a go. I can’t guarantee you’ll be genetic engineering your own plants by the end of the course, but you might at least have a better understanding of how it happens.

A tip o’ the hat to Agriview for pointing me at this.

Floating Forests brings Plant Science to YOU this summer

Do you fancy doing plant science off the shores of Tasmania, around the Antarctic, or even Hawaii? Then the Zooniverse has the project for you. Floating Forests is a website to study the growth or decline of giant kelp, Macrocystis around the world.

Floating Forests

Giant kelp is pretty well named. It can grow to sixty metres in length and it is found around the world. The undersea forests they make are vital habitat for many other species. So tracking growth or decline would be a good thing. The difficulty is that you simply cannot dive everywhere to examine the forests up close – and this is where the Zooniverse comes in.

The Zooniverse site was set up to have the public classify galaxies at a site called GalaxyZoo. Astronomers knew humans were much better at recognising what sort of galaxies they were looking at than computers. The average member of the public wouldn’t be as good as a professional astronomer, but ask enough and you can average out all the errors and get a result better than one professional classifying galaxies. They also found you got results faster, because there’s plenty of people willing to help with primary science.

Floating Forests works in a similar way, but instead of looking out from Earth to space, the Floating Forests images are taken from orbit looking at Earth.

To take part you first sign up. Then you can see a tutorial on how to mark up images, but it’s basically drawing loops around what you think is kelp.

Your eyes might be better than mine, and you might see more kelp in the images. Or maybe I was trigger happy and marked too much. Averaging will help factor out mistakes similar to the concept of The Wisdom of Crowds.

The images are from Landsat. It means the any individual image could be lousy. There are corrupted images, some which are just land or sea and plenty that are clouded out. They have tools for working round this. The upside of using Landsat data is that there’s an archive going back thirty years, so while a place might be clouded out one month, it’s not likely to be covered all the time. It opens the potential for detailed analysis by season and over time.

The project is a collaboration between the Zooniverse and the Kelp Ecosystem Ecology Network, and they’re running a blog to keep people up to date with what they’re finding. The Zooniverse has been terrific in getting people engaged with astronomy. With luck, KEEN can do the same for marine ecology.

Increase the Impact of Your Research Paper in One Step

Annals of Botany had an editorial meeting recently one of the topics that came up was how can authors increase the readership of their paper? One place that can have a surprisingly large impact is the abstract.

If you’ve spent an age trying to get all the details of your research right, it can be painful reducing everything to a couple of hundred words. However an abstract isn’t a mini-version of your paper, it’s a tool to get people to read your paper, and that means making it as easy as possible for people to see why they should care. There’s the full slidedeck up at Haiku Deck or press play above.

Gingko, a writing tool that will help you organise your text

There seem to be plenty of writing apps launching on the web at the moment. Most seem to be a replacement for Notepad or similar, with a little extra formatting. A few have unique selling points. Hemingway for example will test your text for readability. ZenPen is a distraction free editor and StackEdit is a markdown editor that can sync with Dropbox, so your work is accessible from multiple computers.

Enter Gingko, whose selling point is not so much the editor as the organisation of the edited files. All the other editors deal with single blocks of text. Gingko organises text into trees. It’s not simply for writing text, but also for organising a plan of what you’re going to write and ordering sections of what you write.

The basis for Gingko is the tree. You have a base column, and you can add cards to this. Each card can take as much or as little text as you like. You enter the text, click to save it, and then you can drag and drop the cards to order or re-order them as you like.

An example of a tree in Gingko

An example of a tree in Gingko.

Continue reading

Find scientific papers the easy way

Kitteh on the computer

Kitteh on the computer. Photo: William J Sisti / Flickr

Not all scientific papers are easily accessed. If you want to blog about an AoB PLANTS paper, they’re all Open Access and Annals of Botany papers are free access a year after publication, if you’re patient. If you’re not that patient you’re welcome to contact us and we can pass along the paper to you. But you have other options.

The Open Access Button wants to map access to papers, or rather lack of access. Every time you hit a paywall you can click this button to fill out a brief message about what someone has stopped you doing. Normally when people hit a paywall there’s no sound. If there’s more of a noise then scientists might see publishing in some venues means a large chunk of the potential audience doesn’t get to read the research.

That might vent a little frustration but, if you use the Chrome browser, there’s something else you can do.

The Lazy Scholar extension adds a button to the right of the omnibox. When you hit a paywall you can click the button and LazyScholar will use Google Scholar Search to see if it can find a full text version of the article for you. The search is over the whole web, so it stands a good chance of finding it if it’s in an institutional repository, a personal repository or a file that someone has craftily stored somewhere. As far as getting a paper goes, it can be a lot quicker than #icanhazpdf.

The only drawback I’ve found with Lazy Scholar is you forget other people don’t have it and you start getting messages asking “Where did you find…?”


Kitteh on the computer by William J Sisti / Flickr. This image licensed under a Creative Commons by-sa licence.

Plant Central

Twitter Eggs

Photo: Garrett Heath / Flickr

Another experiment we’re working on is how we aggregate posts from the blogs we follow. We were talking about this in June, and Jeremy, of the Agricultural Biodiversity Weblog, had what was the best solution. We’re using Yahoo! Pipes to track blogs. The (currently) twelve pipes get read by IFTTT and anything now gets pushed to our Delicious account.

From Delicious it gets pushed out to a twitter account @PlantCentral, and I can follow that on Flipboard to browse the feeds. I also use the Leaf RSS reader.

I’m not sure yet how it’s going to turn out. So far the performance has been patchy, but it’s also near zero-maintenance so if you want to have a look, it’ll be around for a while.


Twitter Eggs at OSCON by Garrett Heath / Flickr. This image licensed under a Creative Commons by licence.

Altmetrics beyond the numbers

There’s an interesting post up on Gaming Altmetrics at We’re looking seriously at improving how our papers are presented for altmetric services like and ImpactStory.

What interests me is that there is a qualitative aspect to the coverage. Take for instance this entry on a recent paper:

Altmetrics for a recent paper.

Altmetrics for a recent paper.

If you have the bookmarklet you can track down who is saying what. That’s much more value than a number because it shows where the debate around a paper is going. I think this is why directly gaming altmetrics will be difficult. Easy solutions will add little value. For example, I could go to and pay $5 for someone to retweet links to our papers. However I don’t see what bland links from accounts with no followers will add qualitatively to the conversation around a paper, and I think it would show up pretty easily in the altmetrics.

I’m looking improving how we link to papers, our own and others, for a few months. Today, I’ve released a prototype plugin today for WordPress blogs (not blogs, sorry) that handles linking to DOIs, figshare, arXiv and ISBNs. It produces a citation that I hope will be able to read and a META tag to help sites like If you want to try the beta, you can pop across to my personal site and download the plugin to test yourself. Once I’m happy it’s not going to accidentally destroy anyone’s site it’ll be released with a GPL, so anyone can use or re-write it for free.

The target is to produce something that adds value by making connections that are already there easier to spot, and not creating spurious mentions. Of course, I might have a lower standard for value than you.’s post is a helpful starting point in working out what we should be tracking.

A cautious welcome for Digg Reader

There are problems with Digg Reader, but maybe the biggest is that there’s a big demand for a reliable Google Reader substitute and very little time to make one. Digg Reader is now live and working, but it’s a bit Spartan. Despite that it might be a shot in the arm for Digg.

Digg Reader screenshot

Digg Reader has an uncluttered design.

Digg was for a while the top social sharing site on the internet. People would submit stories and vote them up or down and stories making the front page would be wildly popular. It’s since been eclipsed by other sites for various reasons and now while Digg isn’t actually rubbish, there’s not a compelling reason to visit there instead of any other social news site. Digg Reader could be that reason.
Continue reading

Social media and Google Analytics – who’s interested in botany?

We’re coming round to our annual assessment here at AoBBlog. Spurred by JSTOR Plants and their blog post on Social Media we’re sharing our thoughts. And if you have better thoughts we’d welcome them as a comment on this post.

In our case we have three social networks we target: Facebook, Twitter and Google+. Facebook and Twitter are easy to populate, we have auto-posting from the weblog to Facebook and Twitter so you don’t have to keep visiting here to see what’s new. Google+ has to be posted to manually. We’ve also played with Reddit, Stumbleupon and Pinterest over the past year. If you’d like to see what referrals we’ve had to this site from social media, here’s an animation of the past year:

Note that it’s a logarithmic scale horizontal scale for the number of visitors. This is because there was such a spike from Reddit that, if we had a linear scale, everything would appear to be stuck on the zero visitors axis, except for a quick flurry from Reddit in March. In fact you can see our year on Reddit below:
Continue reading