Assessment of and response to data needs of clinical and translational science researchers and beyond
Published in the Journal of eScience Librarianship, this 2016 article by Norton et al. looks at the topic of "big data" management in clinical and translational research from the university and library standpoint. As academic libraries are a major component of such research, Norton et al. reached out to the various medical colleges at the University of Florida and sought to clarify researcher needs. The group concludes that its research has led to "addressing common campus-wide concerns through data management training, collaboration with campus IT infrastructure and research units, and creating a Data Management Librarian position" to improve the library system's role with data management for clinical researchers.
From the desktop to the grid: Scalable bioinformatics via workflow conversion
This featured article from the journal BMC Bioinformaticsfalls on the heels of several years of discussion on the topic of reproducibility of a scientific experiment's end results. De la Garza et al. point to workflows and their repeatability as vital cogs in such efforts. "Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization," they state. The researchers developed their own set of free platform-independent tools for designing, executing, and sharing workflows. They conclude: "We are confident that our work presented in this document ... not only provides scientists a way to design and test workflows on their desktop computers, but also enables them to use powerful resources to execute their workflows, thus producing scientific results in a timely manner."
Cloud-Based Big Data Warehouses Deliver Unparalleled Benefits for Healthcare
Evaluating health information systems using ontologies
Evaluating health information systems/technology is no easy task. Eivazzadeh et al. recognize that, as well as the fact that developing evaluation frameworks presents its own set of challenges. Having looked at several different models, the researchers wished to develop their own evaluation method, one that taps into “evaluation aspects for a set of one or more health information systems — whether similar or heterogeneous — by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework.” As such, the group developed the UVON method, which they conclude can be used ” to create ontologies for evaluation” of health information systems as well as “to mix them with elements from other evaluation frameworks.”
SUSHI: An exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Many next-generation sequencing (NGS) data analysis frameworks exist, from Galaxy to bpipe. However, Hatakeyama et al. at the University of Zürich noted a distinct lack of a framework that 1. offers both web-based and scripting options and 2. "puts an emphasis on having a human-readable and portable file-based representation of the meta-information and associated data." In response, the researchers created SUSHI (Support Users for SHell-script Integration). They conclude that "[i]n one solution, SUSHI provides at the same time fully documented, high level NGS analysis tools to biologists and an easy to administer, reproducible approach for large and complicated NGS data to bioinformaticians."
SUSHI: An exquisite recipe for fully documented, reproducible and reusable NGS data analysis
How Much Does a LIMS Cost – Licensing and Beyond…
Open source data logger for low-cost environmental monitoring
Open source data logger for low-cost environmental monitoring
This 2014 paper by Ed Baker of London’s Natural History Museum outlines a methodology for combining open-source software such as Drupal with open hardware like Arduino to create a real-time environmental monitoring station that is low-power and low-cost. Baker outlines step by step his approach (he calls it a “how to guide”) to creating an open-source environmental data logger that incorporates a digital temperature and humidity sensor. Though he offers no formal conclusions, Baker states: “It is hoped that the publication of this device will encourage biodiversity scientists to collaborate outside of their discipline, whether it be with citizen engineers or professional academics.”
SUSHI: An exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Many next-generation sequencing (NGS) data analysis frameworks exist, from Galaxy to bpipe. However, Hatakeyama et al. at the University of Zürich noted a distinct lack of a framework that 1. offers both web-based and scripting options and 2. "puts an emphasis on having a human-readable and portable file-based representation of the meta-information and associated data." In response, the researchers created SUSHI (Support Users for SHell-script Integration). They conclude that "[i]n one solution, SUSHI provides at the same time fully documented, high level NGS analysis tools to biologists and an easy to administer, reproducible approach for large and complicated NGS data to bioinformaticians."
