$1.7 million to open science’s Friend

Two honors this summer have burnished the reputation of Seattle scientist Stephen Friend for his pursuit of what is called open science.  On top of White House honors in June, he received a grant last week that adds to his credibility as someone trying to change the culture. The phrase “open science” has dozens of meanings, but in Friend’s case it is primarily about opening up data that medical researchers once kept hidden from each other. He calls it a “geek sandbox.”

Just a few days ago, he won a $1.7 million grant from the Robert Wood Johnson Foundation.  The money goes to a project called Bridge, more about that later.

Friend has spent decades being an academic (at Fred Hutchinson Cancer Research Center) and working at the giant pharmaceutical company, Merck, but now he’s director of his own pioneering effort called Sage Bionetworks.

When he explains this passion for open science, he talks from his experience. He talks about trying to make data work for patients and not just to help scientists with tenure and startup companies.  He titled one of his speeches: “Dreaming of tenure and IPOs while patients die,” at a conference in 2012.

He speaks critically of the “medical industrial complex” getting in the way of helping patients. He’s building tools that are designed to let researchers share and network with patients to try to help solve some puzzles about chronic diseases. Already, they’ve had some success with modeling which women with breast cancer might respond best to certain medicines.

Friend was honored at the White House Office of Science and Technology in June as one of the leaders in open science. He announced new projects on Alzheimer’s disease and rheumatoid arthritis that may help predict which patients will respond to certain medications. Sage Bio’s work on modeling risk for breast-cancer patients was called a “geek sandbox” by one writer, who said the results (a new model) are less important than the building of a system where researchers collaborate and compete at the same time.

Friend’s particular passion is also a place where two Seattle strengths overlap, like Venn diagrams. Seattle is strong in software, everybody takes that for granted. Besides the behemoth of Microsoft, Seattle has hundreds of other companies exploring how to use algorithms to uncover signal patterns in the noise of data.  Among the newest of those companies are Socrata and Tableau Software.  Seattle is also strong in genomics and proteomics, and the study of diseases as complex systems that require millions and millions of data points to begin to understand. Software development is ahead of medicine in seeing the wisdom of open source design, he points out.

Friend believes that allowing medical researchers to see each other’s terabytes of data will allow patterns to emerge that spell answers for some diseases. In fact, he believes the institutions and the foundations that donate money must adhere to five concepts – including sharing with patients – or they will fail at finding answers for chronic diseases.

In a video discussion with the patient-advocacy group, Faster Cures, he listed these five rules for success.

1. Make use of massive genomics, proteomics and other “omics” data

2. Put that in the cloud so thousands can access it from anywhere and doesn’t use your server space.

3. Use network modeling of disease.

4. Give patients the ability to send you data (for example, measuring their health using a cell phone)

5. Use open social media to involve patients and share with other researchers instantly.

Friend’s colleague, Thea Norman, talked to us about coming to Seattle to join him and how she will help leverage the RWJF money to make patients bigger partners in research. Bridge is designed to help groups of patients donate their own medical data in a way that provides a basis for discovery for researchers. For example, melanoma patients have already donated photographs of their own skin abnormalities to help build a database that scientists can scan.

“He’s visionary and inspiring,” she explained, of her decision to leave a job in San Diego and move to Seattle to work with Friend. Her title is director of strategic development.

“We get the cream of the crop of software engineers,” she explained of the special strengths that Seattle brings to the open science work. Some of what Bridge will do is build the web-based platform where patients can volunteer their data, or read and download consent information. (John Wilbanks, also at Sage, is one of the designers of what is called Portable Legal Consent.)

The next blog in this series will explore some of the patient advocacy that is driving open science. As Friend says, patients are the key to the enormous energy needed for change.

 

Open science: sharing salmon counts

Imagine for a moment a seagrass meadow in the mouth of a river as it rolls out to the Pacific. We have these meadows here in the Pacific Northwest, and I’ve walked in their murky shallows.

They are rich places, in the sense of full of critters. They mix different ecosystems when salty sea water backs up at high tide into the fresh river water dumping out by the gallons. They are messy places, and frequently don’t charm tourists the way beaches and waves might. But many species of fish find these waters the ideal place for babies to hide out and grow. They are dynamic nurseries.

In a similar way, the movement known as open science is an argument for a rich and messy public place where ideas mix like salt and fresh water, mixing the scientific equivalent of separate ecosystems in a way that brings fresh fertile new ideas. New ideas get nourished there, in the space between disciplines. Open science means a lot of different things. It’s too big for one story, but I want to share one fishy example of how the state of Washington is sharing science data directly with you, or anybody else.

Open science can mean helping scientists to communicate faster with each other about discoveries that have synergies. But it can also mean opening data to public scrutiny and helping policy makers to visualize complicated trends and patterns in data more easily.

Jennifer Johnson, who works for the Governor’s Salmon Recovery Office, helped create a website portal that lets you see the counts of fish from any stream or lake or river where the state does this math. Sharing data directly with the public is one element of open science – literally opening up Excel spreadsheets in ways that let the public and other scientists peer inside.

People are so excited about this, she told an audience during the Seattle Science Festival. Measuring the fish is just one part of trying to understand ecosystems. By sharing the counts, there could be discoveries about regional trends that happen faster.

Just to give an example, you can click through the stateofsalmon.wa.gov and find “adult abundance” and read how many summer steelhead have been counted in Toppenish Creek. Before this data was open and online, it was dated material printed on paper in a report issued every two years. As Johnson explained in an archived panel discussion, her team took a 150+ page report and turned it into an active portal that the public, including other scientists and elected officials, can use to get updated information and make decisions.

But just like the salt and fresh water of our seagrass meadow, Johnson sees the portal as interactive and an exchange between many communities. It doesn’t just save money for taxpayers in printing and publishing hassle of mailing paper reports.  It allows state collaborators from Snohomish to Walla Walla to send information back to the portal, and “see” the data locally or regionally any time they wish. The fish are counted by many different agencies, from tribes to state biologists. In the past, those agencies had to send their data to a central state office where this was uploaded to software. Now, qualified members of the collaboration can send their new counts directly into the portal.

“We collaborate with tribes and salmon recovery efforts all over this state…This portal allows them to contribute to the data directly and shows them all the data they might need about local areas and regions,” Johnson said.

Opening up the data has led to other collaborators “racing me to see who can get their data up first,” Johnson said. “That’s fantastic. That’s exactly what we need in salmon recovery.”

More information at this video with a panel discussion of the portal.

Next blog in series on “open science” will be profile of Seattle scientist given honor by the White House in his bid to speed medical research by throwing open data.