Note: As one of the speakers at this week's BiotechLikemind event, Elmar asked me to provide a short summary of our company, Diatom Software. We look forward to seeing you there! We'll be talking about using cloud computing to address the computationally challenging problem of designing multiplex PCR assays for applications in next-generation sequencing and personalized medicine. -JNR
Diatom Software LLC (www.diatom.com) is a bio and
healthcare informatics consultancy providing scientific software and database
solutions for commercial, academic, and government clients. Our specialties are biological database
design and integration, graph & network visualization, multi-objective design
optimization, cloud computing, and software architecture best practices.
Some of Diatom’s recent projects include:
COMBREX (Computational
Bridge to Experiments) an
initiative based at Boston University to bring together computational
biologists who generate predictions of gene function, and laboratory
experimentalists who seek to validate those predictions in an effort to
accelerate the pace of functional annotation.
CDC/NEDSS (National
Electronic Disease Surveillance System). The US Centers for Disease Control and
Prevention (CDC) monitors cases of about 70 different diseases occurring across our
country, including Hepatitis, Chicken Pox, Measles, and various STDs. Information about each disease event is
transmitted to the CDC via various messaging protocols, stored in a database,
and then analyzed by CDC epidemiologists. Diatom Software, in collaboration with Brookline-based Epidemico, is
working to redesign and re-implement key components of the NEDSS infrastructure
in order to improve message validation, storage, analysis, and reporting.
CloudPCR (A
Cloud-based system for the design of multiplex PCR assays). The Polymerase Chain Reaction (PCR) is a
laboratory protocol for amplifying targets subsequences of DNA for downstream
sequencing or genotyping. In Multiplex
PCR, multiple DNA targets are amplified simultaneously in a single reaction
tube in order to save time and reagent costs. Multiplex PCR introduces certain constraints that make the design of the
assay computationally challenging, particularly as multiplexing levels
increase. Diatom Software collaborated
with Life Technologies / ION Torrent to develop cloud-based algorithms to
design multiplex PCR experiments that could amplifying exonic DNA as a sample
preparation precursor to their next-generation sequencing platform.
For more information, please contact us at (508) 429-1403,
or visit our website at www.diatom.com
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