The problem of keeping up with scientic literature is not new. In 1986, information scientist, Don R. Swanson, published an article about mining the wealth of knowledge buried in academic literature. In his article, “Undiscovered public knowledge”, Swanson investigated information that was not readily available simply because individual biomedical research papers were (and in many ways still are today) created “to some degree independently of one another.” By investigating literature that was “logically connected”, but was otherwise “non-interactive”, Swanson teased out a hypothesis essentially joining two small fields of research.
Since then, researchers are still trying to develop methods to wade through this ever-growing body of literature, only now there are about one million new biomedical research articles being published per year compared to the roughly 350 thousand published in 1986.
Compound this issue with the growing amount of information that is now contained within biomedical research literature, but is not readily accessible due to lack of appropriate annotations.
As hilarious as the image is, it draws attention to several important issues in research. First, is the excessive attention paid to indices such as Impact Factor, or citation-based indices. How often are highly cited articles cited without being read simply because they’re locked behind pay-walls? Why should the merits of a researcher judged primarily on their publications in highly cited, pay-walled journals? Let’s not even touch on how tweeting may impact the perceived respectability of a scientist by his or her peers.
If getting people to read the research article is of genuine interest, then open-access takes the cake. Citations may serve as a proxy for the number of people who read an article and found it valuable, if they actually had access to read the article. Otherwise, it’s just another number.
The Research Information Network (RIN) conducted an analysis of the articles published in Nature Communications and found that OA articles are cited more than subscription articles and attracted three times as many views as those only available to subscribers. More about this study here, see the report here or the full data set here because it’s open access, SO YOU CAN!
Of course, these issues may not be as important as getting and keeping a job. Unless academic institutions consider other metrics in their hiring practices, less established researchers may face considerable pressures against publishing in OA journals.
As one keen PhD candidate put it,
“Scientists applying for funding and positions are judged not only according to the quality of their work, but also where it is published. Having a single paper published in any of these high-profile journals can have a transformative effect on a career. If publication requires flashy work in fashionable fields then, so the argument goes, this offers the most reliable path to funding and permanent positions.”
And more recently, Erin McKiernan, an early career researcher, posted a compelling call for researchers to stand up for and publish in OA journals.
At any stage of your career, you have the right to stand up for what you believe in. If you believe in openness, stand up for it. Access to information is a human right, but it is often treated as a privilege. This has to change. And it will take all of us to make it happen.
If these were not reasons enough, then consider the public good. How can grant-funded researchers expect the public to fund science (ie- grants), and not be able to see the results of their investments? One woman went to extreme lengths in order to gain access to research articles about the her children’s genetic disease.
“We spent hours copying articles from bound journals. But fees gate the research libraries of private medical schools. These fees became too costly for us to manage, and we needed to gain access to the material without paying for entry into the library each time. We learned that by volunteering at a hospital associated with a research library, we could enter the library for free. After several months of this, policies changed and we resorted to masking our outdated volunteer badge and following a legitimate student (who would distract the guard) into the library.”
As mentioned on Monday, the researchers at the Su lab have been working diligently on a paper to introduce their new computational framework for reproducible multi-omics data analysis. Advancements in sequencing technologies have made sequencing cheaper and more efficient, but this means that researchers need a way to handle all that data. Different groups have generated a variety of tools for analyzing disparate datasets, but pipelines that integrate these different tools can be daunting to use without a computational background, or may be unaffordable due to commercial licensing fees.
And that’s where Omics Pipe comes in. Its framework is modular and open source so its functionality can be extended by the research community; it already supports several pipelines; it has built in version control; and best of all, it’s free!
They’re staples for a reason, they fill you quickly and are readily affordable. I’m talking about staples that people have eaten for ages now… noodles, rice, oatmeal, potatoes, and beans. I probably missed some fancier ones, because this is all about eating on the cheap. We’ll devote a post to each staple, starting with noodles. I briefly mentioned pasta/ramen noodles before because noodles are a very cost-effective way (and easy because who has time) for turning a side dish into the main meal.
Any cream-based soup can become a great pasta sauce. Add noodles into broth-based soups for a filling meal. Toss pasta noodles with olive oil, a can of tuna, and some veggies for an instant pasta salad. If you must eat out, don’t get pasta because it’s too damn cheap/easy to make. Cooking pasta is fast and easy, but if you really can’t spare the 15-20 minutes to do it when you’re hungry, make it ahead of time, and throw it in the freezer. That’s what you buy when you get those frozen pasta entrées anyway. When making pasta, the noodles will cost you less than a dollar a pound, so it’s almost like paying $5-$9 for sauce when you buy a pasta entrée. You can do this when your income is higher, but if you’re living off a stipend, save your money and make your own darned pasta.
Here’s a ridiculously easy-to-make pasta recipe, courtesy of Campbell’s soups:
1 can (10 3/4 ounces) Campbell’s Condensed Cream of Chicken and Mushroom Soup (50 cents a can on sale)
1/2 cup milk
2 cups cubed cooked chicken (Hello Costco $5 chicken!)
3 cups medium egg noodles, cooked and drained
Chopped fresh parsley (you can get bunches of these for less than 20 cents on sale at the international markets)
+Whatever random seasonings you like
It’s supposed to make four servings, but I’ve personally found the recipe to be too salty as is, so usually I just use 1 pound (uncooked dry weight) of cooked pasta, which means a lot of frozen pasta entrées afterwards. For variety, you can substitute the cream of chicken with clam chowder and the cubed chicken with canned tuna.
The hardworking researchers at the Su Lab have been working diligently to get this paper out about Omics Pipe, a computational platform that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud.
The new genius who was here before, but not was not mentioned when I first joined the lab because this genius was not (as far as I knew) actually a part of the lab…yet. Sure, his name floated around in the Su Lab chat channels, but he was not physcially present presumably because he was in another lab. I also saw him during some of the Su Lab meetings, but then again, there are also other labs which show up during these meetings, so his status was still unclear to me. What is clear is that the new genius who was here before, but not is a genius. Not only did he give a fascinating presentation on one of his research projects, he also has an MHS in Public Health AND an MD, which makes the new genius who was here before, but not the perfect person to conduct research on developing open source translational bioinformatics methods to advance personalized medicine.
Specifically, Erick’s research projects include:
Developing statistical methods for adaptive enrichment in clinical trials with extensions to post-hoc subgroup analyses.
But issues with crowdsourcing are not limited to just information platforms like wikipedia. Crowdsourcing competitions in order to foster participation and innovation have also been hijacked as covered in a recent (and very interesting) post on Science2.0.
According to the original post found at The Conversation about a new study: “The research, published today in the Journal of the Royal Society Interface, found the openness of crowdsourced competitions, particularly those with a “winner takes all” prize, made them vulnerable to attack.
The researchers used game theory to analyse the trade-off between the potential for increased productivity from crowdsourcing a project, and the possibility of it being set back by malicious behaviour. They cited the DARPA Network Challenge as an example of a hijacked crowdsourcing competition, in which the organisers were left to sort through many fake submissions, including fabricated pictures of people impersonating DARPA officials….continue to the original post