Advancing computational biology and bioinformatics research through open innovation competitions.

Open data science and algorithm development competitions offer a unique avenue for rapid discovery of better computational strategies. We highlight three examples in computational biology and bioinformatics research in which the use of competitions has yielded significant performance gains over established algorithms. These include algorithms for antibody clustering, imputing gene expression data, and querying the Connectivity Map (CMap). Performance gains are evaluated quantitatively using realistic, albeit sanitized, data sets. The solutions produced through these competitions are then examined with respect to their utility and the prospects for implementation in the field. We present the decision process and competition design considerations that lead to these successful outcomes as a model for researchers who want to use competitions and non-domain crowds as collaborators to further their research.

Development of data acquisition components for simultaneous recording of 3D epicardial and surface ECG signals in the langendorff perfusion apparatus.

Sudden Cardiac Death (SCD) claims 7 million lives per year. The importance of myocardial electrogram (EGM) repolarization alternans and surface electrocardiogram (ECG) T-wave alternans is gaining traction for understanding the underlying SCD mechanisms. However, the relationship between the 3D spatial distribution of myocardial EGMs and surface ECG with respect to SCD has yet to be investigated. To make this happen, a modified data acquisition system has been developed and fabricated in conjunction with the Langendorff perfusion system to enable simultaneous recording and analysis of the 3D spatial distribution of myocardial EGMs and the surface ECG. Two devices have been fabricated: a basket catheter, which obtains 3D EGM data; and an ECG chamber, capable of keeping the constraints of the Langendorff system. Noise analysis confirmed, for all devices, a signal to noise ratio (SNR) of median (µ) >= 51.7dB and standard deviation (σ) <;= 2.1dB. A Langendorff rat heart experiment further confirmed successful recording of 3D EGM and surface ECG data with an acceptable SNR. The developed system can be used to study the relationship between 3D EGM and surface ECG data, which can be utilized to understand the mechanisms of SCD.