Science Highlight

"The Center for Biomedical Informatics at the Children’s hospital of Philadelphia is the home for the development of innovative solutions to healthcare's immediate and long-term informatics needs. CBMi provides informatics-focused services, applications, and educational programs to Children's Hospital clinicians and researchers and seek to transform their craft with high-impact, low-cost solutions. One of the CBMi’s main areas of focus is genomics.

Pegasus Workflow Management System is our platform of choice for processing next-generation sequencing data including hundreds of whole-genome and whole-exome data sets. To implement clinical sequence analysis workflows, we needed a system that provides a reproducible, self-documented and well-logged solution and Pegasus addresses all of our concerns. Our Pegasus-based NGS sequence analysis workflows turn hundreds of gigabytes of raw sequencing data into manageable list of variants that can then be interpreted by scientists and geneticists.  We take ‘big data’ that even cutting edge compute systems struggle with, and turn it into tangible data formats, enabling physicians and investigators to answer questions otherwise too complicated to solve with other methods."  --- Mahdi Sarmady

As the second OWM (old world monkey) sequenced (the first is Rhesus macaque), vervets, unlike the great apes who are mostly in near-extinction status, are widely available for biomedical research. (Rhesus is widely available in India but the export restriction imposed by the Indian government makes it less ideal for biomedical research). Given the genetic proximity to human compared to other model organisms such as mouse, vervet is a great model to study high-level cognitive traits, such as novelty-seeking, ADHD (Attention deficit hyperactivity disorder), etc. and some primate-specific diseases, such as HIV. A large pedigree of vervet monkeys housed in VRC (Vervet Research Colony) at North Carolina offers a great genetic resource to study these various traits in a controlled environment. Our focus right now is to sequence a large number of VRC monkeys with well-characterized and highly heritable phenotypes. The purpose is to find the genetic loci underlying these phenotypes.

A collaboration with NASA/IPAC Infrared Science Archive (http://irsa.ipac.caltech.edu). The imaging capabilities of the Spitzer Space Telescope have enabled for the first time surveys of the plane of our Galaxy across the infrared spectrum. When taken together with images from existing all sky surveys, these new image surveys contain over 18 million images and reveal in unprecedented detail the structure of the Galactic plane in the infrared between wavelengths of 1 µm to 70 µm. The images provide for the first time a global view of the absorption of light in the near-infrared by the interstellar medium and dense molecular clouds and its subsequent re-emission at longer wavelengths. Investigations of the details of this act of absorption and re-emission over the infrared spectrum and on a global scale is the key to making progress in important questions such as: measuring the total star formation rate of the Galaxy; assessing the supernova rate of the Galaxy; and determining whether coagulation or fragmentation governs the formation of massive stars.