Navigation Links
In the age of open science, repurposing and reproducing research pose their own challenges

DURHAM, N.C. Growing numbers of researchers are making the data and software underlying their publications freely available online, largely in response to data sharing policies at journals and funding agencies. But in the age of open science, improving access is one thing, repurposing and reproducing research is another. In a study in the Journal of Ecology, a team of researchers experienced this firsthand when they tried to answer a seemingly simple question: what percentage of plants in the world are woody?

They thought the answer would be easy to find. After all, scientists have been distinguishing between woody and herbaceous plants for over 2000 years, ever since Plato's student Theophrastus -- often considered the "father of botany" -- made the distinction in 300 BC. Researchers already know when the first woody plants came to be, how wood develops and decomposes, and that woody plants like trees and shrubs evolve slower than herbs.

"We thought that if we just dug through the literature enough we would find the answer," said co-author Will Cornwell of the University of New South Wales.

But online searches weren't much help. Google didn't have the answer. Bibliographic tools like Web of Science didn't offer any clues, either.

Expert opinion didn't get them any closer. An informal survey of nearly 300 researchers from 29 countries revealed little consensus even among trained scientists, with guesstimates ranging from 1% to 90%. "[Surprisingly] it didn't matter how much research experience they had, or how familiar they were with plants," said co-author Matt Pennell of the University of Idaho, who was a graduate fellow at NESCent at the time of the study.

Thankfully public data were available. Before they could turn to existing databases, however, they had to deal with an additional problem: Even the largest plant trait database to date -- a global woodiness database containing nearly 50,000 species -- contains less than 20% of the more than 300,000 plant species known to science. Simply calculating the fraction of species in the database that are woody gave misleading results, due to missing data and sampling bias towards economically important or temperate species.

By applying statistical tricks to account for sampling bias, the researchers were able to determine that between 45 - 48%, or just under half, of the world's plants are woody. "[The take home lesson is that] all big databases are biased, but by acknowledging that bias is universal and accounting for it we can make better use of them," said co-author Rich FitzJohn of Macquarie University

The researchers learned another lesson when they published their work. Their goal was to make enough information about their methods available such that other researchers could retrace their steps. Could someone -- using the same data and code, but a different computer -- get the same or similar results?

In an ideal word, reproducing the analyses should be as simple as installing the necessary software, downloading the data and hitting 'run.' But software changes from one version to the next. Analysis standards evolve. Analyses that run on one machine don't always work on another.

Making a study easily reproducible, they found, requires a significant amount of time and technical skill. They made sure that everything needed to download and manipulate the data and even create the figures, was written into the code, and explained the thinking behind each snippet of code. They also provided links to tools that would enable researchers to compare changes between different versions of software and restore and run previous versions if need be.

"Nobody denies that researchers should try to make their work reproducible so that others can check their results, but actually making that feasible is easier said than done," FitzJohn said.

Contact: Robin Ann Smith
National Evolutionary Synthesis Center (NESCent)

Related biology news :

1. Improved access to integrated biodiversity data for science, practice, and policy
2. Decline of natural history troubling for science, society
3. Stanford climate scientist to discuss state of climate science, coming risks
4. Genomes for science, genomes for life, and genomes for you and me
5. Science, Innovation, and Partnerships for Sustainability -- Symposium May 16-18
6. Drug Repurposing, Rescue, and Repositioning: A groundbreaking new journal from Mary Ann Liebert, Inc.
7. Penn research combines graphene and painkiller receptor into scalable chemical sensor
8. Research suggests human microbiome studies should include a wider diversity of populations
9. Conducting polymer films decorated with biomolecules for cell research use
10. Research indicates coyote predation on deer in East manageable
11. Researching an endangered relationship
Post Your Comments:
(Date:10/29/2015)... , Oct. 29, 2015  The J. Craig Venter ... titled, "DNA Synthesis and Biosecurity: Lessons Learned and Options ... of Health and Human Services guidance for synthetic biology ... --> --> ... has the potential to pose unique biosecurity threats. It ...
(Date:10/29/2015)... -- Connected health pioneer, Joseph C. Kvedar , MD, ... and wellness, and the business opportunities that arise from ... of Healthy Things . Long before health and ... Kvedar, vice president, Connected Health, Partners HealthCare, was creating ... from the hospital or doctor,s office into the day-to-day ...
(Date:10/27/2015)... -- In the present market scenario, security is one ... verticals such as banking, healthcare, defense, electronic gadgets, and ... secure & simplified access control and growing rate of ... bank accounts, misuse of users, , and so on. ... and smartphones are expected to provide potential opportunities for ...
Breaking Biology News(10 mins):
(Date:11/25/2015)... (PRWEB) , ... November 25, 2015 , ... ... and the Organization of Black Aerospace Professionals (OPBAP) has been formalized with the ... other AMA team leaders met with OPBAP leaders Capt. Karl Minter and Capt. ...
(Date:11/24/2015)... LUMPUR, Malaysia , Nov. 24, 2015 /PRNewswire/ ... global contract research organisation (CRO) market. The trend ... result in lower margins but higher volume share ... increased capacity and scale, however, margins in the ... Research Organisation (CRO) Market ( ), ...
(Date:11/24/2015)... /CNW/ - iCo Therapeutics ("iCo" or "the Company") (TSX-V: ... the quarter ended September 30, 2015. Amounts, unless ... presented under International Financial Reporting Standards ("IFRS"). ... Andrew Rae , President & CEO of ... only value enriching for this clinical program, but ...
(Date:11/24/2015)... -- Clintrax Global, Inc., a worldwide provider of clinical research services headquartered ... the company has set a new quarterly earnings record in Q3 ... posted for Q3 of 2014 to Q3 of 2015.   ... , with the establishment of an Asia-Pacific ... United Kingdom and Mexico , with ...
Breaking Biology Technology: