Tag Archives: researchblogging

Tip of the week: ResearchBlogging and PubGet

A couple of years back the OpenHelix team attended the first ScienceOnline science blogging conference (and the subsequent ones too).  The repercussions of this continue to affect what we do today. We got tips on effective blogging, we got leads on great tools, and we became part of the science blogging community–a chatty and helpful network of people who really want to communicate science more broadly and effectively.

One of the tools we learned about back then we continue to use regularly is ResearchBlogging.  I thought today I’d introduce this utility because we’ve found ourselves in conversations with people who would like to have some kind of mechanism to discuss research in their fields, but weren’t aware of this opportunity.

The short story: ResearchBlogging is a blog post aggregator (and more). If you blog on peer-reviewed research papers, you can obtain a little bit of code from the ResearchBlogging citation generator.  You register your blog, and use this code, the RSS feed sweep from ResearchBlogging detects your post and brings it over to the main site.  It also distributes it to other sites that host the widget with recent posts.  If you hang out at ScienceBlogs you’ve probably seen the widget on the right when reading blogs over there.  ResearchBlogging also automatically tweets your entry via Twitter.  Every time we use this, we see increased traffic from both the main site, from the widget, and from Twitter.

The longer story: ResearchBlogging is a community of science communicators.  Some of them are in your field, some are in far dispersed fields.  But they want to talk science.  They offer substantive discussion on papers they’ve read. Sometimes this is praise for the work, sometimes not.  Sometimes it opens the discussion to new ideas. Sometimes it is a launching point for further discussion in other directions.  The posts vary, of course.  Sometimes they are like having a discussion around the water cooler about some paper a colleague read.  Other times they are more like a journal club.  There are guidelines that describe the goals in more detail, and there is a community forum for discussions about it.  There’s also an editor’s selection: if your post is selected by the editors for the quality, even more people will see your work.  They also recently held a competition for quality in science blogging, and recognized many science bloggers who are taking science out of the journals and on to the web.

We use this often to discuss new software papers we’ve seen.  As great as papers are, especially for software we find we want to give a bit of a movie about the software and how it is used–so for us the paper is usually a launching point for a software tip.

Recently ResearchBlogging has also teamed with the PubGet folks.  PubGet is a cool type of literature search that can be integrated into your local journal subscription set, and it’s a speedy way to get access to PDFs you might want.  But the bonus piece is that if a paper in PubGet has been blogged in the ResearchBlogging system, a little icon indicates this.  So you can go look at what the science blogger had to say about that paper as well.

So for this week’s tip of the week I demonstrate the mechanics of how to get that bit of code from ResearchBlogging, using the DOI or digital object identifier, where to put it back on your blog, and then show how PubGet can lead you to cool discussions of papers that you might be interested in.

For more details:

ResearchBlogging help: http://researchblogging.org/static/index/page/help

ResearchBlogging guidelines: http://researchblogging.org/news/?p=53

PubGet: http://pubget.com/

OpenHelix page of stuff we’ve done with ResearchBlogging: http://researchblogging.org/blog/home/id/154

Impact Factor

I remember considering the “Impact Factor” of journals when submitting research papers, and wondering what the impact factor of a specific paper I published might be out of curiosity. Not particularly seriously, my field was narrow enough in my Ph.D. research that there were just a few journals to even consider, so it was usually pretty simple choosing. And for individual articles, I am pretty sure I knew the 4 people in the world outside my lab that were interested in my research (I jest, a little). During my postdoc, my PI was pretty good and choosing journals based on the article, the journal’s audience… and impact factor.

But impact factor measuring has it’s issues (Article-Level Metrics and the Evolution of Scientific Impact, Neylon and Wu. PLoS Biol 7: e1000242), and there is always a search to measure the impact of journals and individual articles better, or at least differently. Well, one of my favorite science sites and one of my favorite journal publishers ResearchBlogging.org and PLoS, have worked together to measure the impact of journal articles. PLoS has a lot of metrics to see what the ‘impact’ of an article might be, and now they’ve added a metric to see how many times it’s been written about on blogs using blog aggregators like Postgenomic, Blog Lines and Nature Blogs, and now ResearchBlogging.

I like the partnership with ResearchBlogging specifically because whereas the other blog aggregators are not necessarily picking up articles that discuss the science of the article (Postgenomic) or aggregate only a subset of science blogs out there (Nature Blogs), ResearchBlogging is specifically blogs posts discussing the research of  peer-reviewed articles.

Of course I don’t find this particularly useful to compare one article against another (the best articles aren’t always written about, and those that are might not be in the blog aggregators), but I do think this will be great way to carry on the conversation and dig deeper into the research topic.

You can view that metric at PLoS of any article, for example the one I link to above, click on the “metric” tab, scroll down a bit until you see the heading “Blog Coverage.” For that article, you’ll see two ResearchBlogging posts (as of this writing), a metric for this paper about metrics :).

Science blogger challenge: classic paper blogging

By way of Coturnix at A Blog Around the Clock, I learned of this challenge from skullsinthestars:

A fun challenge for science bloggers

One of the things that I still find incredibly fun about being a scientist is the ability to “touch” history, in the form of the original publication of now famous scientific results….

I agree on this. Some of the old papers are remarkable to read. Although they can feel sort of sepia-toned because of the structure and the language, sometimes the insights are stunning–especially considering the state of the field at that time.

There is a paper that I read in grad school that I have never been able to shake out of my head. So I leaped at this challenge to re-read and analyze this paper. I’m not saying yet what it is–you’ll have to come back and see. I was stunned to find the PDF available (for just $10). Last time I read it I don’t know if they had PDFs….However, it doesn’t have a DOI. I’ll have to create a reference myself for Researchblogging.

The challenge was informal at first, and skullsinthestars completed the personal challenge already with this post:

Classic Science Paper: Otto Wiener’s experiment (1890)

Although not my field, I love the presentation of this. And I’m impressed with the reach back in time and across the language! I would love to see people’s take on classic papers on other areas as well.

The challenge has picked up some steam and interested other science bloggers. The basic idea is this:

My “challenge”, for those sciencebloggers who choose to accept it, is this: read and research an old, classic scientific paper and write a blog post about it. I recommend choosing something pre- World War II, as that was the era of hand-crafted, “in your basement”-style science. There’s a lot to learn not only about the ingenuity of researchers in an era when materials were not readily available, but also about the problems and concerns of scientists of that era, often things we take for granted now!

A companion paper to the one I want to highlight actually refers to the basement. I LOLed when I read that.

I asked for a deadline (because I work a little bit better that way :) ). It is the end of May. If you can get the paper and post on it, email skullsinthestars, it will be collected on a permanent page. Also–the date may vary by field. The paper I’m choosing is mid-war, actually. But others may even be more recent, I would think, in molecular biology.

C’mon–touch the past. Join us with a post.

Increased atmospheric CO2 levels: an itchy situation?

When I get time, I like to garden. I mentioned to my aunt, who is a master gardener in my area, how much trouble I had with poison ivy last year. She responded that she wasn’t surprised because many master gardeners had noticed that poison ivy was on the rise. Being the curious biologist-type, with limitless research resources at the tip of my fingers, I of course searched PubMed for ‘poisin ivy’. And guess what I found – a report on a six-year study indicating that increased carbon dioxide levels resulted in healthier, more prolific poison ivy that ALSO has increased ability to irritate our skin. If you need yet another data point to inspire you to go green, check out the interesting (scary?) original research, which I’ve cited here.
ResearchBlogging.orgMohan, J.E. (2006). Biomass and toxicity responses of poison ivy (Toxicodendron radicans) to elevated atmospheric CO2. Proceedings of the National Academy of Sciences, 103(24), 9086-9089. DOI: 10.1073/pnas.0602392103

TE insertions in genomes

transposon graphicIn the recent database issue of NAR, there are two reports of transposable element (TE) databases. I already discussed one in an earlier post. That one is a database that includes Gypsy elements (non-LTR retroposons) and retroviruses and aims to be a database “devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements.” Hopefully to develop into a database of all TE’s. The other paper, by Levy et al. (“TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates“)1, I’ll discus briefly here introduces a somewhat different database of transposable elements.

ResearchBlogging.orgAs the paper discusses, TE’s have been implicated in a large number of effects on the vertebrate genome: affecting expression and “contributing to genetic diversity, genomic expansion, genomic content and genomic rearrangements.” Whether these immense changes are the raison d’être for transposable elements or the byproduct of a parasitic DNA element, I’ll leave for discussion (though I would side with the latter), but they are unarguably major factors in genome evolution and don’t fit the definition of “junk DNA.” :D.

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Research Blogging and CrossRef

At the Science Blogging Conference we were introduced to researchblogging.org. I made mention of this earlier and have we have been using it since. It’s a great service and I’ve been reading many of the blog posts. One of the other things they announced at that same session (and in a previous newsletter) was a WordPress plugin from CrossRef. This would allow you to look up (by title, author) a reference and get the DOI citation to put into your blog post. It was supposed to come out that week, but I hadn’t seen it (and asked, they said “soon”). Well, I found it today ;) (update at end)

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