Biotechnology PhD Training Program



Reproducibility and Transparency


With supplemental NIGMS funding, we collaborated with the Center for Open Science (COS), a Charlottesville VA nonprofit whose mission is ‘to increase openness, integrity, and reproducibility of research’.  A key tool of COS is their free opens-source ‘Open Science Framework’, a cloud based data organization and sharing platform recognized by a growing number of journals including eLIFE, Springer Nature, Biomed Central and many others, as well as institutions, as a scholarly web tool that enhances transparency, fosters collaboration, and increases visibility of research outputs at the institutional level.  Our goals were to: (i) involved COS staff and UVa faculty in the restructuring of our core ‘Essentials of Translational  Science’ course and (ii) with student input to begin to help evolve the Open Science Framework as a graduate student friendly electronic notebook.

A committee of graduate students plus one senior technician and one postdoc met with COS in the Fall to provide an initial group of suggestions on evolving the Open Science Framework as a graduate student friendly electronic notebook.


The newly designed ‘Essentials of Translational Science’ course was taught for the first time from mid February through the end of March.  Below are course elements:

  1.     Research integrity/reproducibility (COS)

  2.     Research integrity/reproducibility (COS)

  3.     Strategies of Design Thinking in Science

  4.     Scientist as Entrepreneur

  5.     Intellectual Property

  6.     Intellectual Property

  7.     Commercialization and Entrepreneurship

  8.     Commercialization and Entrepreneurship

  9.     Regulatory Science and Engagement

  10.     Regulatory Science and Engagement

  11.     Translational Science on Grounds

2017 - present

The Center for Open Science continues to teach in the ‘Essentials of Translational Science’ course


On 11.14.19, the BTP hosted a Center for Open Science Workshop on use of the Open Science Framework as an Electronic Notebook.  This is the presentation.  All BTPer’s are required to plan and document experiments in the Open Science Framework.  Here is an example template, and YouTube demo, and guide.

Other examples of use of the Open Science Framework as an Electronic Notebook:

  1. Wiki for cataloguing all lab protocols

  2. Project structure to organize lab experiments, references, meetings

  3. Johns Hopkins, Carnegie Mellon, Cambridge, Hull lab examples

Other Resources

From the Journal of Biological Chemistry, check out: ‘How to best present a quantitative Western blot for publication’