Infotrack

Clinical Workflow Management Software

Technology used: Linux, Apache, MySQL, PHP, JavaScript(D3.js, jQuery, RequireJS), CSS3 (bootstrap), Python

Image of the Login page to Infotrack

Bed Trace

Interactive Timeline to Visualize Patient Hospital Stays

Technology used: Linux, Apache, MySQL, PHP, JavaScript(D3.js, Google Charts, jQuery, RequireJS), CSS3 (bootstrap)

An screen shot of the bed trace tool including some sample data.

Micro NGS Pipeline

Modular Clinical Microbiology NGS Pipeline for genomic investigation, surveillance, and outbreak tracing.

Technology used: Python (biopython), JavaScript (D3.js, jQuery), HTML, CSS3 (bootstrap)

A schema of micro pipeline including all of the bioinformatic software included in the the pipeline. The pipeline was designed to flexibly perform rapid analysis on a variety of datasets and questions while storing previously analyzed isolates allowing the user to build a local database of isolates discovered in their area. The pipeline consists of two steps written in Python, SQLiite3, and JavaScript. The first step performs quality control on the raw reads (trimmomatic, FastQC) followed by genome assembly (SPAdes) and plasmid assembly (PlasmidSPAdes). Quality of genome assembly is assessed (Quast), genus and species (strainseeker), and MLST of samples are identified. Common phenotyping blast databases are included in the pipeline but custom blast databases can be added making the pipeline relevant to any species or project. To rapidly identify the best species reference the genome coverage is calculated for every sample (Quast). Step two consists of a modified CFSAN SNP Pipeline for reference-based SNP Calling and Phylogenetic Analysis. Modifications include masking SNPs which occur inside phages, mobile elements, and transposons, only include sites where a consensus exists in every sample, to produce a maximum likelihood tree (FastTree), and an interactive web application is produced to visualize the coverage and SNP locations throughout the genome to ensure consistent coverage and no SNP clustering.

TurboStorage

Biological Freezer Inventory Management Software

Technology used: Linux, Apache, MySQL, PHP, JavaScript (D3.js, jQuery, RequireJS, QUnit), CSS3 (bootstrap)

An example image of my turbostorage view of samples info. All cells are clickable

Splicer App

Interactive Data visualization tool to investigate RNA splicing Variants

Technology used: JavaScript(D3.js, jQuery), HTML, CSS3 (bootstrap), Python (numpy, scipy, pandas)

An example image of my Splicer App output

Rainbow HiC

Web Application to Interactively Visualize DNA Folding in the Nucleus

Technology used: JavaScript (D3, jQuery, requireJS, QUnit), HTML, CSS3 (bootstrap), Python (numpy), inkscape, MapReduce, parallel processing

An example image of my Rainbow HiC App Graphing

IRS

Invented the First Interactive Single Cell RNA-SEQ Analyzer

Technology used: JavaScript (D3, jQuery), HTML, CSS3 (bootstrap), Python, SVG

An example a cell gating strategy in my IRS app

Experience

Genetics: 18 Years

Management Experience: 10 Years

Bioinformatic Analysis: 14 Years

Python: 12 Years

JavaScript: 11 Years

PHP: 10 Years

SQL: 10 Years

# Publications: 9

Select Skills

- PHP
- FPDF
- MVC
- JavaScript
- JQuery
- D3.js
- RequireJS
- MVC
- Python
- numpy
- scipy
- pandas
- matplotlib
- parallel processing
- MySQL
- SQLite
- Apache
- Inkscape
- GIMP