Many additional links can be found on these sites:
- ICERM workshop report
- Best Practices for Scientific Computing (2014) in PLOS Biology by Greg Wilson et al.
- “Where next for the reproducibility agenda in computational biology” (2016) by Joanna Lewis et al in BMC Systems Biology
- The Reproducibility Crisis in science and the prospects for R (2016) by Tal Galili
- Results from the Belmont Forum’s Open Data Survey
General open science resources
- Science 2.0; see also this article, “Science 2.0: Great New Tool, or Great Risk?” (2008) by Mitchell Waldrop in Scientific American.
- FOSTER: Facilitate Open Science for European Research
- The Open Source Science Project
- Mozilla Science Lab
- Crowdfunding of scientific research: Experiment.com, “Crowdfunding Propels Scientific Research” (2015) by Ariana Eunjung Cha in the Washington Post, “Crowdfunding Science” (2013) by Roxanne Palmer in the International Business Times
- Open scientific pre-print servers: ArXiv (background and origin), alternative to arXiv ViXra, Social Science Research Network and BioRxiv
- TeX: open source scientific typsetting
- Center for Open Science (related to the Open Science Framework) has a few notable projects: Reproducibility Project: Pyschology, Reproducibility Project: Cancer Biology, the Transparency and Openness Promotion Guidelines and Registered Reports which promotes a two-stage peer review process by adding a stage after experimental design and before data collection; here is their google discussion group.
- Science Exchange is a marketplace for paid research and lab services, they work with the Center for Open Science on the Reproducibility Project: Cancer Biology and have their own reproducibility projects page.
- Sunlight Foundation mostly for government data, including open data guidelines
- Open Knowledge International including the OpenEconomics Working Group and their Projects page
- Panton Principles
Notable massive open science projects
- The Human Genome Project
- OpenWorm which birthed the geppetto computational biology and computational neuroscience platform
- The Blue Obelisk for chemoinformatics
- Allen Brain Atlas by the Allen Institute for Brain Science
- The Encyclopedia of Life, note also the University of Washington project creating 3D CT scan images of fish and putting them (online here).
- Sloan Digital Sky Survey
- GalaxyZoo famous for producing results with distributed human data processing
- Open Energy Modelling Initiative
- The PolyMath Project and its wiki where large groups work on an open math problem
- NIST Materials Genome Initiative
Pitfalls of irreproducible research
- add some examples
- You don’t want to end up in the The Journal of Irreproducible Results or, more seriously, here: retractionwatch.com
- “The Corruption of Peer Review Is Harming Scientific Credibility”
- Why Most Published Research Findings Are False (2005) in PLOS Biology by John Ioannidis
- The Case for Open Research: reproducibility, retractions & retrospective hypotheses (2016) by Danny Kingsley, University of Cambridge
- “The Nine Circles of Scientific Hell” in Perspectives on Psychological Science (2012) by neuroskeptic (who blogs about pitfalls)
- “Reproducible Methods”(2013) by Robert Flight, with several useful examples of irreproducible science.
- “A Baltimore researcher shows that the longtime standard for body temperature is wrong.” (2005) by Michael Stroh in the Baltimore Sun, including several examples of specific pitfalls and an overall example of what happens when scientific studies are never reproduced (here is the reviewed article and in another location).