Intervene: A tool for intersection and visualization of multiple gene or genomic region sets

Posted on June 6, 2017 By John Jones Journal articles

As Khan and Mathelier note in their abstract, one of the more common tasks of a bioinformatician is to take lists of genomes or genomic regions from high-throughput sequencing and compare them visually. Noting the lack of a comprehensive tool to visualize such complex datasets, the authors developed Intervene, a tool for computing intersections of multiple genomic and list sets. They conclude that "Intervene is the first tool to provide three types of visualization approaches for multiple sets of gene or genomic intervals," and they have made the the source code, web app, and documentation freely available to the public.

Users’ perspectives on a picture archiving and communication system (PACS): An in-depth study in a teaching hospital in Kuwait

Posted on May 31, 2017 By John Jones Journal articles

The picture archiving and communication system (PACS) is an increasingly important information management component of hospitals and medical centers, allowing for the digital acquisition, archiving, communication, retrieval, processing, distribution, and display of medical images. But do staff members using it find that a PACS makes their job easier and more effective? This journal article by Buabbas et al. represents another attempt by medical researchers to quantify and qualify the impact of the PACS on radiologists and technologists using the system. In their case, the authors concluded that "[d]espite some of the technical limitations of the infrastructure, most of the respondents rated the system positively and as user-friendly" but, like any information system, there are still a few areas of improvement that need attention.

Effective information extraction framework for heterogeneous clinical reports using online machine learning and controlled vocabularies

Posted on May 23, 2017 By John Jones Journal articles

Even in the digital realm (think electronic medical records), extracting usable information from narrated medical reports can be a challenge given heterogeneous data structures and vocabularies. While many systems have been created over the years to tackle this task, researchers from Emory and Stony Brook University have taken a different approach: online learning. Here Zheng et al. present their methodology and findings associated with their Information and Data Extraction using Adaptive Online Learning (IDEAL-X) system, concluding that "the online learning–based method combined with controlled vocabularies for data extraction from reports with various structural patterns ... is highly effective."

Selecting a laboratory information management system for biorepositories in low- and middle-income countries: The H3Africa experience and lessons learned

Posted on May 15, 2017 By John Jones Journal articles

What's important for a biorepository laboratory information management system (LIMS), and what options are out there? What unique constraints in Africa make that selection more difficult? This brief 2017 paper from the Human Heredity and Health in Africa (H3Africa) Consortium outlines their take on finding the right LIMS solution for three of their regional biorepositories in Africa. The group emphasizes in the end that "[c]hoosing a LIMS in low- and middle-income countries requires careful consideration of the various factors that could affect its successful and sustainable deployment and use."

Baobab Laboratory Information Management System: Development of an open-source laboratory information management system for biobanking

Posted on May 10, 2017 By John Jones Journal articles

This journal article, published in Biopreservation and Biobanking in early 2017, presents the development philosophy and implementation of a custom-modified version of Bika LIMS called Baobab LIMS, designed for biobank clients and researchers. Bendou et al., who enlisted customization help directly from Bika Lab System, describe how "[t]he need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for biobanking." The group concludes that while the open-source LIMS is quite usable as is, it will require further development of more "generic and configurable workflows." Despite this, the authors anticipate the software to be useful to the biobanking community.