Current Employment

04/2015 — present

Sr Engineer, Bioinformatics, BioMarin, San Rafael, CA.

My focus is in developing bioinformatics databases and applications to support research investigations and scientific analyses of rare diseases. In my time at BioMarin I have built systems used by researchers to explore genetic variants in rare diseases, and conducted analyses on EHR data collected by Optum. I have also built systems used to mine and curate disease annotations collected from numerous public and internal sources, which helps prioritize top lists of disease candidates. Additionally, I have built smaller databases and applications to support various workflows for groups in and around Research. This includes intranet sites using group templates in Sharepoint co-developed with IT and adopted by all of BioMarin. Together with IT, we built systems based on best practices for application source code management and automated application deployment, and have conducted various informal presentations and trainings in Research and other departments on the use of those systems.

Active Skills —

RDBMS: Postgres, MySQL

NoSQL: Neo4j, CouchDB

Javascript: Node, Hapi/Express, React/Hyperapp/Preact,

D3, DC, Highlight, Chart, Crossfilter, jQuery, many other 3rd party js libs

CSS: UIKit, Semantic UI, Material Design, Bootstrap

Builders: Parcel, Webpack, Grunt, Gulp, Brunch, Babel

Testing: NPM, Tape, Mocha, Chai/Sinon

Workflow & Doc: Docker, GitLab (with CI), Github, Puppet, Dox

Other languages & tools: R, Shiny, Python, Jupyter, Elm, Spotfire, Spark

ML/DL: Keras, Tensorflow

Evals: Infoworks, Cambridge Semantics, Linguamatics, Databricks, AWS, several others

Open Source Author:

myvariantjs (https://github.com/larryhengl/myvariantjs)

myvariantjs-demo (http://larryhengl.github.io/myvariantjs-demo/)

Other Interests:

Chasing my son...because it's fun

Coaching youth soccer

Ultra running, Ironman triathlons, skiing, basketball and golfing

Past Employment

12/2000 — 04/2015 (~15yrs)

Programmer Analyst IV, Novartis (formerly Chiron), NIBR IT, Emeryville, CA.

Database Specialist, Chiron, Bioinformatics, Emeryville, CA.

Focus: Informatics and IT support for cancer research.

SW: jQuery, React, Backbone, Marionette, D3, Crossfilter, Gephi, Cytoscape

Brunch, Jira, Confluence, SVN

SQL, PL/SQL, PHP, ASP, VB/VBA, IIS, Apache

DB: Oracle, MySQL, CouchDB, Neo4j, Redis, Solr, Semantic Web tools

5/1999 — 11/2000 (~1.5yrs)

Programmer Analyst III, Cancer Center, UC San Francisco, SF, CA.

Focus: Data collection and analysis systems for cancer research.

SW: PHP, ASP, VBA, JS, SQL, PL/SQL, Oracle and MS Forms, IIS, Apache

DB: Oracle, SQL Server, MS Access

10/1994 — 5/1999 (~5yrs)

Programmer Analyst and Assistant Statistician, UC San Francisco, SF, CA.

Focus: Data collection systems for oral studies, hiv studies, and cancer research.

SW: VB/VBA, ASP, MS Forms (double-entry validations), IIS

DB: MS Access, custom

4/1992 — 12/1993 (~1.5yrs)

Statistician, Santa Barbara Breast Cancer Institute, SB, CA.

Focus: Data inputation for breast cancer studies.

SW: SAS

DB: Double Helix

Other concurrent positions ...

4/1999 — 4/2001

Oracle Basics Instructor: SQL and PL/SQL

UC Berkeley (UCB) Extension

Muster Learning Architects (MLA), Berkeley, CA.

7/1999 — 1/2002

Volunteer Web Database Programmer, Cancerlinks LLC, Berkeley, CA.

6/1998 — 4/1999

Volunteer Unix Intern/Oracle Teaching Assistant, MLA, Berkeley, CA.

Education

Bachelor of Science, Statistics, UC Santa Barbara (UCSB), 1992.

Research Collaborations

Masouredis C., et al (1997).

A spit tobacco cessation intervention for college athletes: 3-month results.

Advances in Dental Research. 11(3):354-359.

Sartorius, O.W. (1995).

The biochemistry of breast cyst fluids and duct secretions.

Breast Cancer Research and Treatment 35: 255-266.

Walsh, M.W., et al. (1994).

Prevalence, patterns and correlates of spit tobacco use in a college athlete population.

School of Dentistry research paper.

Sartorius, O.W. (1994).

Age, body mass, and tumor aggressiveness in breast cancer.

Santa Barbara Breast Cancer Institute research paper.

Summarizing Prior Employment Duties

Web Development duties: Coded web apps utilizing Javascript, HTML/CSS, PHP, Apache and Ajax on Windows and Linux systems.

Performed DBA duties: monitor space, usage, and performance, tune instance parameters, check backups, version migrations, production and development data synchronizing.

Database development duties: data modeling, schema design, database creation, query programming and tuning, user security, strategize replication server scheme.

Developed relational databases for clinical cancer studies and genetics research utilizing Oracle and MS Access. Designed web interfaces using ASP on IIS web servers. Designed and implemented a data security model for shared information and collaboration. Coded PL/SQL module for legacy data migration. Generated reports and ad hoc query functions for local and web- based user tools. Performed Oracle DBA duties on production and development database servers. Installed and configured Oracle software and database applications. Maintained user and group accounts, user security, and database backups. Developed and modified web-generated forms and reports with Designer/2000 and WebDB, created and maintained Designer/2000 repositories, administered Oracle Application Servers and Report Servers, created and administered End User Layers in Oracle Discoverer. Supported Windows NT/2000 systems.

Instructed 10-week courses on SQL and PL/SQL language and programming concepts, Oracle database application design and development, Unix commands and utilities; developed and managed course curriculum, held tutorial sessions, evaluated student work and assign grades.

Installed, configured, and maintained Apache webservers and MySQL databases running on Linux platforms for the site http://www.cancerlinks.net and its sister sites; assisted with site content. (This non-profit portal site provides links and site information on cancer and related information.)

Assisted Unix and Oracle SQL classes: tutored on systems/programming concepts, troubleshot computer lab problems, assisted with curriculum development, tested skills and conducted grading.

Engineered relational databases for medical research studies. Programmed MS Access database quality control routines, double-entry modules, status reports, and SAS dataset exports. Administered databases and implemented user security. Provided desktop and server support, and administered a Novell network for PC and Macintosh clients.

Installed desktop and server hardware, software applications, Windows operating systems, and performed system troubleshooting. Created manuals and reports for DBMS review, data analysis, and data entry training. Conducted hardware/software tutorials for technical and administrative staff.

Performed statistical analysis and data management of breast cancer and breast biochemical information.