Open research and collaborations

A few days ago, I posted this tweet:

The response has been amazing. People have sent me links to all kinds of interesting projects: open collaborative transcription and editing of humanities texts; biomedical research made possible by publicly available data; projects creating open source tools that can be used by all and continue to be improved by online communities;  and personal stories about how they got PhDs, jobs, and authorships through open science. I’ve collected some of the examples sent to me below, and hope to keep adding to this list. These examples illustrate why open science/open research is so important and how we can advance both our careers and our fields when we share.


1. Zebrapedia

“To open and elucidate the terra incognita of Philip K Dick’s Exegesis, using collaborative scholarship and 21st century networking tools to explore this mammoth digital text…”

2. Pupil Labs

“Pupil is an open source mobile eye tracking product, in active community driven development.”

3. Radiopaedia

“…a rapidly growing open-edit educational radiology resource which has been primarily compiled by radiology residents/registrars/fellows and consultants from across the world. The site’s collective aim is to create the best available radiology reference, and to make it available to you as well as your colleagues to use for free and forever and for all.”

4. OpenWorm

“OpenWorm is an open source project dedicated to creating a virtual C. elegans nematode in a computer.”

5. GRID – Geographic & Reporting Information Database

“GRID is built on open source platforms, including PostGIS, Django, Geoserver and OpenLayers (and a few others).  The underlying GRID codebase is not yet open source, but it is freely available…, under the proviso that any general changes are submitted back to the central code base for all to benefit from.”

6. An open manuscript about open data

Moving toward a sustainable ecological science: don’t let data go to waste!

7. Collaborative project in public health using open data

Estimation of MERS-coronavirus Reproductive Number and Case Fatality Rate for the Spring 2014 Saudi Arabia Outbreak: Insights from Publicly Available Data

8. GIBBON: The Geometry and Image-based Bioengineering Add-on for MATLAB

“GIBBON is an open-source MATLAB toolbox…and includes an array of image and geometry visualization and processing tools and is interfaced with free open source software…”

9. ICGC Cancer Genome Projects

“The primary goals of the ICGC are to generate comprehensive catalogues of genomic abnormalities…in tumors from 50 different cancer types and/or subtypes which are of clinical and societal importance across the globe and make the data available to the entire research community as rapidly as possible, and with minimal restrictions, to accelerate research into the causes and control of cancer.”

10. Global Alliance for Genomics and Health

“The Global Alliance for Genomics and Health (Global Alliance) is an international coalition, dedicated to improving human health by maximizing the potential of genomic medicine through effective and responsible data sharing.”

11. Global Collaboration to Fight Malaria

“[Matthew] Todd turned publicly available data into a global effort to help identify new anti-malaria drugs.  He did this by creating an open-source collaborative involving scientists, college students and others from around the world. They use open online laboratory notebooks in which their experimental data is posted each day, enabling instant sharing and the ability to build on others’ findings in almost real time.”

12. The E-coli “tweenome”

“By releasing the first genomic data before it had even finished uploading to NCBI via twitter, and promoting its use and releasing subsequent improved assemblies this way, a huge community of microbial genomicists around the world took up the challenge to study the organism collaboratively…”

13. Biomedical research using publicly available data.

Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.

“…we applied a computational approach to discover new drug therapies for IBD in silico, using publicly available molecular data…”

14. Population Genetics in R Hackathon

“…allowed a diverse group of population genetics researchers, method developers, and people with other relevant areas of expertise to collaborate on code, documentation, use-cases, and other resources that will aid their communities.”

15. Open data and open source helping students 

16. Sharing revives a project and leads to publication

So I emailed…and she had an excellent example (described with her permission). In 2011, after not finding a journal home for her manuscript on electroencephalographic methods, Bishop posted the full article to her blog. This led to correspondence with researcher Maximilien Chaumon from the Berlin School of Mind and Brain, who expanded on Bishop’s methods and developed a plug-in. Chaumon drafted a manuscript on the work, to which Bishop contributed, and they now have a paper in press.


Thanks to everyone who responded to my query! Please keep the examples coming…

6 thoughts on “Open research and collaborations

Add yours

  1. Figshare made it possible to finally publish results of a research project aborted 46 years ago. April 7 was the first anniversary of the third of 3 papers going online and I’m still waiting for the global peer review.
    Google: Neuromuscular Endplate Exocytosis 888504

    1. Thanks for your comment! I’m so glad figshare provided the platform for you to finally be able to share your work. I’ve been going through your documents and images with interest. For any readers who would like to do the same, you can find the project here.

  2. You might be interested also on our Open Collaboration project to understand lipid molecule structures running at (and of course also on the Polymath project which was our main inspiration).

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