Category Archives: Digital Researcher

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.


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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…?”

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

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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.

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

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Altmetrics beyond the numbers

There’s an interesting post up on Gaming Altmetrics at altmetric.com. We’re looking seriously at improving how our papers are presented for altmetric services like altmetric.com 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 fiverr.com 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 wordpress.com blogs, sorry) that handles linking to DOIs, figshare, arXiv and ISBNs. It produces a citation that I hope ScienceSeeker.org will be able to read and a META tag to help sites like altmetric.com. 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. Altmetric.com’s post is a helpful starting point in working out what we should be tracking.

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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.
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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:
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Social media: A guide for researchers

Social media - A guide for researchers While it’s not strictly botany, since the purpose of this blog is to promote research in plant science through the use of social media, it seems appropriate for me to announce the publication of a new report by the Research Information Network:

Social media: A guide for researchers

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, why not download a copy and give it to someone you work with who hasn’t figured out what they’re missing yet.

Disclosure: I am one of the authors :-)

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. http://www.rin.ac.uk/our-work/communicating-and-disseminating-research/social-media-guide-researchers

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I’m stealing this presentation

The social web isn’t just limited to blogs, Facebook and Twitter. Slideshare is a great place to look for presentations on all sorts of things. I’ve been particularly impressed by this presentation about how to give a PowerPoint presentation.

STEAL THIS PRESENTATION!
View more presentations from @JESSEDEE.
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Are there online communities?

Like Peas in a Pod. Photo (cc) Phil Price.
Putting things in one place does not always make a community, as these members of the pea community demonstrate. Photo (cc) Phil Price.

There’s thoughtful post up at Civil War Memory by Kevin Levin, Can You Afford Not To Use Social Media? Some of his thoughts are similar to discussions we had about what would be possible with AoB Blog. Some less so.

Firstly Kevin Levin is very upfront about the importance of communication through social media. The interesting thing about the brief from the Annals of Botany company is that they have never specified that we have a blog. The target has been to give the journal a social media presence. Alan Cann and I agreed that a blog would be a useful engine to drive updates to Facebook and Twitter, but the blog drives the social media elsewhere, rather than using social media with the intent to pull people to the blog. It terms of the set-up of the software it makes no difference, but it means that the Annals of Botany is taking the approach of wanting the best tools for the job, rather than deciding from the start what the answer is. It means that if a ‘Facebook for Scientists’ does emerge we could well decide that that becomes the primary hub for our activities. It’s a flexible approach and it matters for the next more provocative point.

There are no Online communities; in fact, it demeans the very concept of community.

Another feature is that I don’t think we ever discussed setting up an AoB Community. I did briefly think we could host AoB Blogs. The exact thought process went:
“WordPress 3.0 now has multiple blogging built in. That means we could host other people’s blogs, and everything that goes wrong with them will be my fault.”

Given yesterday’s mess with the back ups I think avoiding hosting was a good idea. Another reason is that we’re working in an almost anti-community way. There was never a chance of there being an AoB Ning because we’re keenly aware we need to go where the researchers are. That means giving up ideas of building an ‘AoB Community’ because the kind of people we need to engage with are people who read many journals across many fields. So if an Online Community is one site then I agree with Kevin Levin.

On the other hand I think we’re participating in something. Is there such a thing as the Botanical community? Probably, but I’d bet that every botanist has a different idea about what that is. Alan Cann has talked about building personal networks. I think it’s a realistic goal to participate in something like that and, because I hope that AoB appeals to more than one reader, there should be overlaps in connections. Whether you want to call that a network, community or audience might depend on how you see your connections interacting. Everyone in the office works to make Annals of Botany an essential journal for plant sciences, but that means making sure papers in AoB get the attention they deserve. In our case we want people to interact away from our site. If that’s the goal then you have to give people the tools to do that, hence the links on the journal Mendeley and CiteULike.

That loss of control makes measuring success difficult, so I can see why the idea of owning a community is attractive for a commercial enterprise. Effectively you have a free workforce pushing your branding and an easy way to measure if it’s working. But that’s not the way science works. Very few people publish exclusively in one journal. Even if it were possible, I don’t think dominating a niche would be healthy for a journal. Still, I think the idea of a blog participating in a community works. I think the key point is you can’t have a community of one.

So while the American Civil War might not seem immediately relevant to Botany, it’s had an influence on how I think about what i do. As well as the original post, there’s useful discussion in the comments.

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New Annals of Botany Bibliographies

At the suggestion of Alan Cann and AoB’s managing editor David Frost I’ve been working on a new section for the website. Up on the menu bar above there should be a Bibliographies option. It’s part of our move into Mendeley.

Mendeley is a desktop application and website that helps with research support. On the desktop it can manage your PDF files and help as a citation manager. You also install a bookmarklet in your browser so that when you see a paper you like you can click Import into Mendeley and the paper is in your collection of references. It’s also possible for you to share collections of references, which is handy for collaborative work.

The change this week is that they’ve now released an API and that means data can be pulled out of the site. We’ve used a plugin written by Prof. Dr. Michael Koch. There are still some problems, but this is partly due to Mendeley having a low rate limit for queries while they develop the API. I’ll be trying to solve that with caching the results on the website.

At the moment all the papers come from one journal. In the longer term we intend to add papers from non-AoB journals as well to make the collections comprehensive starting point for research on topics. In the meantime you can download Mendeley for free and get organising your digital archive.

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