MOTIVATION: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA. RESULTS: We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline. AVAILABILITY AND IMPLEMENTATION: The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Robotic vehicles have become a critical tool for studying the under-sampled coastal ocean. This has led to new paradigms in scientific discovery. The combination of agility, reactivity, and persistent presence makes autonomous robots ideal for targeted sampling of elusive, episodic events such as algal blooms. In order to achieve this goal, they need to be deployed at the right place and time. To that end, we have designed and will soon deploy a shore-based event recognition technology to continuously monitor remote sensing imagery for algal blooms as targets for robotic field experiments. A Support Vector Machine underlies a field-tested decision support system which scientists will consult prior to deploying robots in the coastal ocean. Our aim is to target oceanographic field experiments for evaluation and verification.

Iteration is often sufficient for a simple hand to accomplish complex tasks, at the cost of an increase in the expected time to completion. In this paper, we minimize that overhead time by allowing a simple hand to abort early and retry as soon as it realizes that the task is likely to fail. We present two key contributions. First, we learn a probabilistic model of the relationship between the likelihood of success of a grasp and its grasp signature—the trace of the state of the hand along the entire grasp motion. Second, we model the iterative process of early abort and retry as a Markov chain and optimize the expected time to completion of the grasping task by effectively thresholding the likelihood of success. Experiments with our simple hand prototype tasked with grasping and singulating parts from a bin show that early abort and retry significantly increases efficiency.