[1st to 8th of August 2013] Open Science in Seattle : Big Data, Complex Systems and Open Data

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After California, the last step on the West Coast led me to Seattle. During this week, I was fortunate to have an outstanding guide Brian Glanz, co-founder of the Open Science Federation. In Seattle, I was able to explore a facet of the Open Science different from San Francisco. In fact, the directions taken by big software and services companies, such as Microsoft or Amazon, strongly oriented themes treated in Open Science. Open Data, administration and management of Big Data in Life Sciences, were the recurring themes of the various meetings and interviews.

If San Francisco has been an immersion in the world of startups and hackerspaces, Seattle instead was diving in the world of innovative academic. I had 9 meetings, 13 interviews and one event. The week was busy with Brian Glanz, who planned the entire program and took the time to accompany me to every meeting. Brian Glanz is one of the busiest people I know in the community of Open Science. He is the co-founder of the Open Science Federation (@openscience on Twitter), organizer of ScienceOnline à Seattle, founder of the chapter OKFNUS. He is also very active in civic activities (open government, open food…) and wants to see research more involved in each of his actions.

The University of Washington: a wealth of actors and projects for the Open Science

 First day in Seattle, I discovered the School of aquatic and fishering sciences  which is part of the College For Environment. This is a classic laboratory in appearance, but with innovative research practices. We meet Steven Roberts, who manages one of the research laboratories. Behind his computer, he begins to explain to us how he manages his research notebook: he shares all his data and the progress of his work on Ipy. Student involvement contributes for many to the dynamic image of the laboratory: they communicate on the progress of their work on social media but also on a Wiki. Steven Roberts is an « openscientist » in the soul; for him it’s quite normal to implement these practices, and try, and test these new tools like Github ( a collaborative platform for writing code, increasingly used in research).

A few yards away, we have an appointment at the Research Commons space, tables and walls in whiteboard, open 7/7… Everything is done to facilitate the emergence of new ideas. The administrators of the center are also interested in the training of researchers in data management. How to organize and label them? How to standardize them? They recently organized a workshop on the reproducibility of data in research. The University of Washington evolves in data culture. This can be explained by the particular structure of companies and research institutes in Seattle area. This old library has been completely restored to foster creativity and collaboration between researchers and students.

 

Steven Robert

Steven Robert : Open Scientist en action..

research commons osf

Research commons by OpenScienceFederation

A strong OpenData culture in Seattle

Indeed in Seattle, I noticed a strong orientation of Open Science issues around Open Data. The background, made of big software and services companies like Microsoft or Amazon, play a major role.

I discussed it with Sally James, scientific journalist in Seattle. She gives some explanations in this interview:

“There is an interesting mix in Seattle. Many people look at the signal/noise ratio. Some build applications for mobile, others observe how proteins are expressed in cell. This city is a place where different domains overlap.”

These ideas are contained in a book published by Microsoft, The Fourth Paradigm: Data-Intensive Scientific Discovery. This book states that we are entering in a new era of research: At experimental, theoretical, and computational studies are added the fourth key concept of data mining.

It strongly inspires Eugene Kolker Co-founder of DELSA. DELSA project – Data Enabled Life Science – seeks to place the question of data, their analysis, sharing and reproducibility at the heart of research in Life Science.

The huge amount of data generated – what is called Big Data – by the study of increasing complex system in Science, certainly brings a new era for research, but accelerates thereby the development of news practices.

Big Data and Open Data: a need for an approach of complexity in Science

Many research groups in Seattle, including those related to Life or Environmental Sciences, adopt a multi-disciplinary and multi-scale approach. The ISB « Institute for Systems Biology » is one of these organizations. Created 13 years ago, it is one of the first to study Life Science as a complex system. There, they try to understand how different parts of an organism, a cell and a gene interact with each other. Researchers are studying the emergence of new properties in these systems, depending on the context. The ISB has a longstanding Open Science policy; it publishes all the articles in Open Access, shares data and also the code source of software.

The Open Science seems fundamental to analyze Big Data especially in the context of complex approach of the living. Indeed, such research objectives require the collaboration of large number of researchers from different fields. Such collaboration is permitted by models of Open Publications and Open Science approach type…

Thirteen years ago, the IBS was one of the few such institutes. Today, hundreds of organizations are created on the same principle. Their use of Open Science is certainly ahead of our time, but is nevertheless one of the most appropriate responses to the challenges of Life Science and Health.

Laboratoire de l'ISB

Institute for Systems Biology laboratories

Departure from the West Coast: “Bidouille Ton Doc” in Montreal

After a busy week in Seattle, the « redeye flight » took me to Montreal for a few days. The expression describes well the passengers of these flights, arriving with 3 hours of confiscated sleep by the time zone difference. HackYourPhD became “Bidouille Ton Doc” for a few days.

For more pictures and interviews, here is the story of the week in Seattle.

Thanks to Rodrigue Asseu for the english translation from french.

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