Blogs

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Martin’s latest challenge—building the IT and informatics infrastructure at Complete Genomics (see, “Will the Gene Microscope Change the World,” Bio-IT World, May 2009) to build a human genome sequencing service capable of delivering 1 million genomes in five years—is a doozy! If he’s having sleepless nights, he doesn’t show it. “It’s about crafting the right team with the right mix of skills and knowledge, and trusting them.” Recruited by CEO Cliff Reid, Martin didn’t hesitate. “For about a decade, I’d wanted to find something with a stronger footprint in the sciences, but also where I could contribute. So it seemed like a perfect marriage.” Martin brought the expertise in software development and high-scale computing, and built a team of bioinformatics experts, experts in genomics, assembly, and large-scale scientific computing.
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 We’ll have very reliable, redundantly connected connectivity at hundreds of gigabits at a fraction of the equivalent Internet connection. As we grow, we will be able to scale into hundreds, or multiple hundreds of gigabits per second [gbps] in 2010. That’s a function of how much data the instruments generate. Our cost, scale and reliability analysis indicate that we are better off putting most of our compute offsite. These instruments throw off a lot of data! [...]

Empirical Study of Data Sharing by Authors Publishing in PLoS Journals

Caroline J. Savage, Andrew J. Vickers

Abstract

Background: Many journals now require authors share their data with other investigators, either by depositing the data in a public repository or making it freely available upon request. These policies are explicit, but remain largely untested. We sought to determine how well authors comply with such policies by requesting data from authors who had published in one of two journals with clear data sharing policies.

Methods and Findings: We requested data from ten investigators who had published in either PLoS Medicine or PLoS Clinical Trials. All responses were carefully documented. In the event that we were refused data, we reminded authors of the journal’s data sharing guidelines. If we did not receive a response to our initial request, a second request was made. Following the ten requests for raw data, three investigators did not respond, four authors responded and refused to share their data, two email addresses were no longer valid, and one author requested further details. A reminder of PLoS’s explicit requirement that authors share data did not change the reply from the four authors who initially refused. Only one author sent an original data set.

Conclusions: We received only one of ten raw data sets requested. This suggests that journal policies requiring data sharing do not lead to authors making their data sets available to independent investigators.