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Cody Nash, Genomics Developer in Bratislava, Bratislava Region, Slovakia
Cody Nash

Genomics Developer in Bratislava, Bratislava Region, Slovakia

Member since April 11, 2017
Cody has experience in a range of fields from geobiology and medical genetics to data analytics for commercial clients. Along with validating genetic tests in a private clinic and developing software infrastructure to support analytics (including customizing Jupyter environments on Kubernetes clusters), he has assisted clients with experiment planning, data exploration, and model deployment. Cody's preferred languages include Python and R.
Cody is now available for hire

Portfolio

Experience

  • Genomics, 10 years
  • Statistics, 6 years
  • Perl, 5 years
  • Linux, 4 years
  • Python, 3 years
  • Docker, 3 years
  • Sklearn, 3 years
  • Jupyter, 3 years
Bratislava, Bratislava Region, Slovakia

Availability

Part-time

Preferred Environment

PyCharm, Jupyter, RStudio, Ubuntu, Windows

The most amazing...

...thing I've built was a 104 gene cancer panel for medical testing—including equipment selection, developing the analysis pipeline, validation, and maintenance.

Employment

  • Laboratory Director Assistant

    2010 - 2016
    Genetics Center
    • Developed and performed clinical genetic diagnostic laboratory tests.
    • Implemented and maintained data analysis pipelines.
    • Implemented application specific software in a clinical setting.
    • Developed new scripts as well as SQL and HTML interfaces for additional functionality.
    • Performed data analysis using Perl, R, and Excel.
    • Implemented microarray CGH assays for pre- and post-natal diagnosis.
    • Developed custom microarray designs for detection of clinically relevant loss of heterozygosity and exon-level deletions and duplications.
    • Developed a custom bait and capture kit for the 104 gene panel.
    • Implemented DNA sequencing assays using ABI 310, 3130xl, Illumina MiSeq, Ion Torrent PGM, Ion Proton, and Ion S5 instruments.
    • Developed quantitative PCR assays with Taqman and SYBR green methods (using a Roche Lightcycler 480 II instrument).
    • Developed fragment analysis for repeat-expansion disorders.
    • Implemented assays using MLPA, qPCR, RFLP, and Multiplex PCR.
    Technologies: Perl, R, Excel, Ion Torrent PGM/Proton/S5, Illumina MiSeq, Agilent CGH+SNP Arrays
  • Assistant Research Scientist

    2008 - 2010
    California Institute of Technology
    • Designed and led the gravity coring and SCUBA sampling expeditions in the hyper-saline, hyper-alkaline, high-altitude Mono Lake.
    • Extracted DNA from environmental samples then amplified, cloned, and sequenced.
    • Performed phylogenetic analyses with Phylip and ARB.
    • Analyzed samples with low temperature magnetometry and electron paramagnetic resonance spectroscopy.
    • Assisted with isolation of proteins for controlled magnetite precipitation, directed precipitation experiments and analysis.
    • Provided samples, strains, reagents and instruction to other researchers using magnetotactic bacteria.
    Technologies: Phylip, ARB

Experience

  • Create Data from Random Noise with Generative Adversarial Networks (Publication)
    Generative adversarial networks, among the most important machine learning breakthroughs of recent times, allow you to generate useful data from random noise. Instead of training one neural network with millions of data points, you let two neural networks contest with each other to figure things out. In this article, Toptal Freelance Software Engineer Cody Nash gives us an overview of how GANs work and how this class of machine learning algorithms can be used to generate data in data-limited situations.

Skills

  • Languages

    Python, Perl, R
  • Libraries/APIs

    Pandas, Sklearn, Matplotlib, NumPy, SciPy
  • Tools

    Jupyter, Google Kubernetes Engine (GKE), IPython Notebook, Microsoft Excel, Mathematica, Notepad++
  • Platforms

    Kubernetes, Linux, Docker, Jupyter Notebook, Windows, AWS EC2, Ubuntu Linux, RStudio
  • Storage

    Google Cloud
  • Other

    Statistics, Genomics, Color Science, Sequence Alignment, Bioinformatics

Education

  • PhD degree in Geobiology
    2001 - 2008
    California Institute of Technology - Pasadena, CA, USA
  • Master of Science degree in Space Science
    2000 - 2001
    International Space University - Strasbourg, France
  • Bachelor of Science degree in Biology
    1995 - 2000
    Rhodes College - Memphis, TN, USA
Certifications
  • Clinical Genetic Molecular Biologist Scientist (CLS)
    MAY 2012 - PRESENT
    California Department of Public Health
  • Technologist in Molecular Biology
    MAY 2012 - PRESENT
    American Society for Clinical Pathology
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