James Done Email & Phone Number

Trumbull, Connecticut, Us

• Examine miRNA feasibility as a cancer diagnostic employing Tensorflow, Keras and Scikit-learn artificial neural networks (ANNs) in python on macOS; tune hyper-parameters with keras-tuner• Employ XGBoost, SHAP, Linear Regression Correlation and Logistic Regression for feature extraction • Calculate p-values of biomarkers that imply pathology using Wilcoxon and Kolmogorov-Smirnov tests • Trained and tested models on imbalanced data using Synthetic Minority Oversampling Technique (SMOTE) variants • Determine protein biomarker measurement stability using mean-difference tests (e.g., Bland-Altman) and regression tests (e.g., Passing-Bablok) • Parse log files with pm4py • Document work using Microsoft Office on SharePoint • Maintain software configuration management using git, Gitlab and Github.

Los Angeles, Ca, Us

• Process Next Generation Sequencing Data in Pipelines using python on Linux clusters/AWS Parallel Cluster scheduling jobs with LSF, Torque/PBS and Sun Grid Engine; research Amazon FSx for Lustre• Auto-populate MediaWiki site in AWS supported docker container for genomics with text mined from reports and spreadsheets as well as text from a docker contained R/shiny user interface (using docker-compose).• Develop Perl (BioPerl), Julia, R, Ruby, Python and SQLite for Linux client/serverapplications • Employ GUI using Bootstrap web framework, that interacts with back-end software in R, written in HTML, CSS and Javascript to sort and analyze genetic variants; R/shiny• Deploy RESTful API for SQLite databases using flask and SQLAlchemy• Calculate overlap of sequenced genetic variants with Cancer Genomics Consortium Panels• Use parallel processing in Perl, Python, Ruby and R to support sequencing pipelines• Install, use and create R & python wrapper for samtools, bedtools, vt and bcftools• Acquire and maintain online cancer research literature and search utilities• Install & configure text mining software to support biological and medical research• Visualize databases using R/shiny, python dash and dash-bio• Implement key-value store NoSQL databases to support RNASeq pipeline• Create NLP models to support text mining projects using NLTK• Automate report generation using python; use of PharmCat for pharmacogenomics• Use gvcftools to convert gVCF to VCF• Use CrossMap.py to convert genome coordinates between different genomic assemblies

Pasadena, Ca, Us

•Collaborate with City of Hope to create text mining website for cancer research (using GeneCards for gene synonyms, HPO for phenotype ontology and UBERON for anatomy ontology)•Create text-mining site for OMIM•Employed Scribus to create poster for science conferences•Create Biocuration challenge GUI interface implemented in Javascript, Jquery, HTML and CSS to create and store scientific journal annotations hosted on Apache web server using PHP, perl and java•Develop Perl (BioPerl), Ruby, Python, PHP, SQLite, Javascript, JQuery, Linux client/server applications•Code Ruby (BioRuby) and Python (BioPython) scripts for biological laboratory applications for Linux and Mac OS X platforms•Write C/C++ extensions for R needed for experimental analysis•Use parallel processing in perl, python, ruby and R to support biological applications•Create gene ontology annotation tools for NIH NLM XML/HTML publications•Support annotation software for Genetic Society of America publication pipeline•Acquire and maintain online cancer research literature and search utilities•Install & configure text mining software to support biological and medical research•Present at Science Advisory Board, Gene Ontology Consortium and Genetic Society of America meetings•Design and write data-mining scripts to automate concise gene descriptions using GO, HGNC and Ensembl; http://med.stanford.edu/biocuration/scientific_program.html•Write software to support biological curation and annotation of genetics publications

Falls Church, Va, Us

•Supported NASA Aura, NASA NPP Suomi and NOAA JPSS climate missions ground data processing and calibration & validation of HDF5 data products using C++, Fortran 95, python, IDL and MATLAB employing parallel processing on Linux clusters•Reviewed design of optics used by space based instruments•Configured and used SGE & LSF batch queue systems on HPC Linux clusters •Configured and used OpenMPI and MVAPich on HPC Linux clusters •Performed configuration management with subversion and IBM Rational ClearCase •Tracked tasks of NASA NPP Suomi Ozone Measurement Profiler Suite (OMPS) using Gantt charts•Wrote, compiled and debugged C++ code modeling orbital attitude and location of satellites•Integrated legacy Fortran with modern python using f2py•Introduced Cygwin for all staff to compile code and run on MS Windows•Founded Northrop Grumman Linux Users Group to assist in developing scientific software

Arlington, Va, Us

• Science Data Systems Implementation and Operations (SDSIO) contract scientist at the NASA Jet Propulsion Laboratory supporting NASA Earth Observing Science (EOS) programs and NASA Aura• Implemented output of data products in Hierarchical Data Format (HDF) v4/v5 • Implemented single line application programming interfaces for scientific routines• Used PBS batch queue systems to submit and process scripts• Configuration management performed with CVS, Rational Clearcase, Harvest• Use of global map coordinate transforms, ephemeris and attitude routines in NASA Earth Observing System Toolkit• Created object-oriented designs of scientific software, databases using Unified Modeling Language (UML) in IBM Rational Rose • Wrote parallel processing scientific software and software designs for radiative transfer, surface emissivity and a priori matrices calculations based on inverse theory• Examined HDF5 output using the Interactive Data Language (IDL)• Created, lead Raytheon Linux Special Interest Group to sponsor discussions, presentations of open source software and operating systems for JPL aerospace community

Lemont, Il, Us

I contributed to physics experiments in the Physics and High Energy Physics divisions. Applied Mathematics; Computational Physics; Numerical Analysis; Numerical Methods; Nuclear Physics; Accelerator Physics; Unix/C; Fortran; Pascal; Finite Difference Methods; Nonlinear Partial Differential Equations

Lemont, Il, Us

I contributed to experiments in the Physics and High Energy Physics divisions. Applied Mathematics; Computational Physics; Numerical Analysis; Numerical Methods; Nuclear Physics; Accelerator Physics; Unix/C; Fortran; Pascal; Finite Difference Methods; Nonlinear Partial Differential Equations

Doctor Of Philosophy (Ph.D.), Physics

Master'S Degree, Engineering Applied Science

Bachelor'S Degree, Mathematics