The recent attention to the challenges of reproducibility is new, but the problem itself is as old as science. Fortunately, over the past decade, a range of tools and resources have been created to help scientists communicate more easily and clearly, helping to make our work easier to build on, for ourselves and other researchers.
This workshop will highlight some of the resources available to help share code, data, reagents, and methods. Speakers from Addgene, Code Ocean, and Protocols.io will discuss a variety of reproducibility tools and then will be available during a hands-on section to work with students directly.
Join us on January 25th to:
Food will be provided at 12pm. We recommend you bring your laptops for the hands-on, one-on-one portion starting at 1pm.
Caroline leads the Outreach & Marketing Team at Addgene, the nonprofit plasmid repository. Her mission is to make it easier for scientists to find and share high-quality reagents, learn about the latest molecular biology tools, and communicate their research to others. Caroline received her PhD in Biomedical Engineering from Boston University, where she learned both valuable bench techniques and science communication skills. You can follow Caroline on Twitter @CarolineBME.
As Developer Advocate, Seth is the liaison between scientists (Code Ocean’s developers) and the product/team; he helps authors get their code up and running on the platform and also tries to represent their interests in internal discussions. He did undergrad at Swarthmore and a few years of a Ph.D. program at Columbia, which he left with a masters degree in 2015.
Lenny has over a decade of computational and experimental biology experience. He did his graduate studies at UC Berkeley and finished his postdoctoral research at MIT. For three years, prior to switching from math and computer science to molecular biology, he was a database developer. Lenny brings to protocols.io a strong passion for sharing science and improving research efficiency through technology.
Addgene is a nonprofit plasmid repository whose mission is to accelerate research and discovery by improving access to useful research materials and information. Addgene is a huge proponent of open reagent sharing and primarily distributes, stores, and curates plasmids for use in academic research. Through its viral vector service, Addgene also produces ready-to-use viral vectors from a select subset of plasmids in the repository. Finally, Addgene develops science education content including webpages, blog posts, eBooks, protocol videos, and a podcast. You can follow @Addgene on Twitter and Facebook.
Code Ocean is an open, computational reproducibility platform enabling researchers to run, share, discover code in an executable, cloud-based environment. Researchers, engineers, developers and scientists can link executable code and data to articles published in academic journals and conference proceedings, while retaining copyright. Code Ocean assigns Digital Object Identifiers (DOIs) to support citable attribution and partners with publishers to add working code to the research outputs readily available from research articles. Code Ocean was founded in 2015 with the goal of saving researchers’ time and advancing science by making the world's scientific code more reusable, executable and reproducible.
Protocols.io is an open access online platform for sharing, discovering, and discussing research methods. It allows scientists to describe the details of protocols upon publication of results and provides a way to correct and optimize these protocols in a collaborative fashion after the paper is published. Similarly to GitHub for software developers, protocols.io supports versioning, forking, and discussion of public and privately-shared protocols.