May 2015

Data security

David Bernick addressed the part of the PIC-SURE API that is going to depend on a variety of state-of-the-art authentication protocols. This should be of considerable utility for many of us in the BD2K community. Paul Avillach then illustrated the use case across three hospitals already with IRB approval.

PIC-SURE

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May 22nd Core meeting

Nathan Palmer provided a masterful review of database optimizations (a Stonbreakerian view) over the last 40 years and what’s real in the current arguments (e.g. main-memory oriented vs. disk oriented, logging vs no-logging, dynamic locking vs multithreading, Hadoops vs SQL). Definitely at the heart of core scaling issues of big data. Also nice review of how mainstream row-level database systems are getting on the OLTP bandwagon.

Shawn Murphy, Tianxi Cai and Griffin Weber described several additional approaches to probabilistic patient matching and the experiments under way.

Aim 3 Social Web subaim May 7, 2015

Jared Hawkins discussed the experience mining 5.5 billion tweets (1/2 of all geotagged tweets) and how we are going to approach integration within the PICI API of PIC-SURE. He discussed the curation challenges (using known humans in Boston and unknown humans in Amazon’s Mechanical Turk). He also highlighted patient features that this data source can obtain on patients that are otherwise not obtainable.

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5-1-15 PIC-SURE meeting

Aim 3 report came in from Peter Tonellato. Brownstein et al., working on the social web data, Chirag et al. on environmental data and the MT/HMS group evaluating different pipeline approaches (including the use of infrastructure tools such as Julia and SciDB)

David Bernick led a discussion of the extensive teams working on data linkage, API development, cloud hosting, meta-data index and how to use our shared resources.

John Brownstein gave a nice heads up on his PIC-SURE project on mining Twitter for health status on an hourly and diseases-specific basis: The Digital Phenotype...

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4-24-15 Weekly PIC-SURE meeting

Paul Avillach led with a discussion of IRB issues. Discussion of HMS level 3 restrictions and how this impacts cloud hosting of data. I am sure that parallel discussions are happening at many academic health centers. 

Shawn Murphy foreshadowed some issues that will be addressed in depth at the PIC-SURE Architecture breakout group later today. 

  • The metadata associated with each patient.
  • How to do probabilistic joint across databases, some with identified data and some with aggregate data.

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