Sequencing, cloud computing, and analytics meet around genetics and pharma

Bio-IT World shows what is possible and what is being accomplished

If your data consists of one million samples, but only 100 have the characteristics you’re looking for, and if each of the million samples contains 250,000 attributes, each of which is built of thousands of basic elements, you have a big data problem. This is kind of challenge faced by the 2,700 Bio-IT World attendees, who discover genetic interactions and create drugs for the rest of us.

Often they are looking for rare (orphan) diseases, or for cohorts who share a rare combination of genetic factors that require a unique treatment. The data sets get huge, particularly when the researchers start studying proteomics (the proteins active in the patients’ bodies).

So last week I took the subway downtown and crossed the two wind- and rain-whipped bridges that the city of Boston built to connect to the World Trade Center. I mingled for a day with attendees and exhibitors to find what data-related challenges they’re facing and what the latest solutions are. Here are some of the major themes I turned up.

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Citizens as partners in the use of clinical data

A Knowledge Currency Exchange for health and wellness

This article was written together with Mike Kellen, Director of Technology at Sage Bionetworks, and Christine Suver, Senior Scientist at Sage Bionetworks.

The current push towards patient engagement, when clinical researchers trace the outcomes of using pharmaceuticals or other treatments, is a crucial first step towards rewiring the medical-industrial complex with the citizen at the center. For far too long, clinicians, investigators, the government, and private funders have been the key decision makers. The citizen has been at best a research “subject,”and far too often simply a resource from which data and samples can be extracted. The average participant in clinical study never receives the outcomes of the study, never has contact with those analyzing the data, never knows where her samples flow over time (witness the famous story of Henrietta Lacks), and until the past year didn’t even have access to the published research without paying a hefty rental fee.

This is changing. The recent grants by the Patient-Centered Outcomes Research Institute (PCORI) are the most visible evidence of change, but throughout the medical system one finds green shoots of direct patient engagement. Read more…

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Culture’s impact on social media adoption

Commerce and censorship in in cross-cultural social media.

By Lydia Laurenson

Culture has a huge impact on social media adoption and usage. In Measuring Culture, I talked about specific cultural traits and attitudes, and I described how those things are being measured on social media. For this article, I’ll outline broader patterns in cross-cultural social media, specifically regarding commerce and censorship.

Commerce finds a way

Commerce always finds a way. Whether restricted by red tape or blocked by citizens’ mutual distrust, money flows around obstacles. Most examples don’t have much cultural data-crunching associated with them yet, but there are intriguing gestures in that direction. For instance, a recent survey from the European Commission reported that 62% of European Internet users say they use non-native language sites to communicate with friends online, but only 18% would use a non-native language site to buy something. Read more…

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Network Science dashboards

Networks graphs can be used as primary visual objects with conventional charts used to supply detailed views

With Network Science well on its way to being an established academic discipline, we’re beginning to see tools that leverage it. Applications that draw heavily from this discipline make heavy use of visual representations and come with interfaces aimed at business users. For business analysts used to consuming bar and line charts, network visualizations take some getting used. But with enough practice, and for the right set of problems, they are an effective visualization model.

In many domains, networks graphs can be the primary visual objects with conventional charts used to supply detailed views. I recently got a preview of some dashboards built using Financial Network Analytics (FNA). Read more…

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Measuring culture

Digital media influences culture -- and it's influenced by culture in turn

By Lydia Laurenson

Digital media influences culture — and it’s influenced by culture in turn. Culture matters in business: Facebook just spent an astonishing $19 billion to acquire WhatsApp because of WhatsApp’s international presence. Culture also matters politically: Turkey’s leader recently made it the latest country to try blocking Twitter. How can we use data to understand culture’s impact on digital media adoption and usage? How can we even measure culture in the first place?

Dimensions of Culture, And How They’re Being Measured

Language

Some cross-cultural elements are easy to see. For example, when a brand or platform expands into a new country, their stuff should obviously be translated. Sometimes marketers use basic analytical tools to cut words that are controversial in a given culture, like the Chinese localization service Kawo, which screens English tweets for words that would be sensitive in China before any actual translation is done.

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Solving mysteries using predictive analytics

In-depth Strata community profile on Kira Radinsky

Kira Radinsky started coding at the age of four, when her mother and aunt encouraged her to excel at one of her favorite computer games by writing a few simple lines of code. Since then, she’s been a firecracker in the field of predictive analytics, building algorithms to improve business interactions, and create a data-driven economy, and in the past, building systems to detect outbreaks of disease and social unrest around the world. She also gave a predictive analytics talk at the last Strata.

I had a conversation with Kira last month about her entry into the field and her most exciting moments thus far.

When did you first become interested in science?

KiraRadinsky_fullqual

Photo provided courtesy of Kira Radinsky

Kira Radinsky: When I was four or five, my mom bought me a computer game. In order to go to the next level, you had solve simple math problems, which became increasingly harder with time. At one point I couldn’t solve one of the problems. Then I asked my aunt for help because she was a software engineer. She showed me how to write some very simple code in order to proceed to the next level in the game. This was my first time to actually code something.

In the army, I was a software engineer. I built big systems. I felt that I was contributing to my country and it was amazing for me. When I finished my service, I was accepted to the excellence program at the Technion [Israel Institute of Technology] because I had already started studying there when I was 15. I just continued on to a graduate degree.

I knew I wanted to do something in the field of artificial intelligence, because I really wanted to pursue the idea of using computers to make a global impact. I was really into that. I realized that the vast data amounts that we produce could be used to solve important problems.

In 2011, thousands of birds fell out of the sky on New Years Eve. People were writing “we don’t know what’s going on”. It was a conundrum. A few days later, a hundred thousand fish washed up dead on the shore. Many people were saying that it was the end of the world because it was the end of the Mayan calendar!

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