Using the internet for open science
A few days ago, PLoS hosted a talk by Michael Nielsen at their San Francisco offices. Nielsen, author of the book “Reinventing discovery”, due late this year from Princeton Press, is a strong-voiced proponent of the need for a change in the way we share data.
The Polymath project, his opening story, is one of the best examples of how and why open science works. Tim Gowers, a Fields medalist, posted a famous mathematical problem on his blog, an open invitation to anyone interested to try their hand at solving it. For the first 70 hours, nothing happened. Then a math professor left a comment, quickly followed by a high school teacher, another Fields medalist and so on. In the span of 37 days, over 800 comments collectively solved the problem. How many conferences and scientific papers, peer reviews boards and editorial revisions would it have taken to even get these diverse minds thinking together in the same space? Nielsen describes it as the difference between “driving and pushing your car”.
If you’ve looked at our NextBio Publications page lately, you’ve probably noticed that the list of publications from authors who have used NextBio to make novel connections is growing at a steady pace. To this, we add a publication from the Scientific and Computational Biology group at NextBio itself:
Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data
Ilya Kupershmidt, Qiaojuan Jane Su, Anoop Grewal, Suman Sundaresh, Inbal Halperin, James Flynn, Mamatha Shekar, Helen Wang, Jenny Park, Wenwu Cui, Gregory D. Wall, Robert Wisotzkey, Satnam Alag, Saeid Akhtari, Mostafa Ronaghi
PLoS ONE 5(9): e13066. doi:10.1371/journal.pone.0013066
In this article, we explain our processes for data curation and the computational methods by which signatures are compared in NextBio to yield novel findings. We also include four use cases that illustrate how this all comes together for the purpose of investigating brown preadipocytes and brown fat lineage. We hope you find the paper illustrative of how you can apply NextBio’s platform to discovery in your area of research. And don’t forget to include this publication in your citation when you make novel discoveries using NextBio.