PTMD.com

Led a team responsible for the web application integrated with the Selux Diagnostics antimicrobial susceptibility testing (AST) device:

• Architected a web-based infrastructure deployed at each customer site for storage and visualization of data from the SeLux antimicrobial susceptibility testing (AST) platform:
• Built ReactJS and ASP.NET Core web application for user review of test results
• Designed SQL Server schema and EF Core classes for storage of customer data
• Built secure RESTful ASP.NET Core web services to support integration of Selux instruments and Laboratory Information Systems (LIS)
• Contributed to multiple successful FDA clearances by delivering software releases employed during clinical trials, support of data analysis from trial results, and documentation towards 510K submissions.
• Led a team of 9 full-time and offshore contractors following Agile methodologies in the delivery of quarterly software releases to multiple US customer sites.
• Managed a dev-ops architect in the implementation of continuous integration (CI) using GitHub actions to enforce unit tests and code quality, TeamCity for build, test, and packaging pipelines, and continuous deployment (CD) using Octopus Deploy for internal test environments.
• Led an architecture redesign to leverage a microservice running as Docker container with RESTful API, health monitoring, and volume mount.
• Wrote and collaborated on design documentation with adherence to regulatory standards for software development of a Class II medical device (IEC 62304) and collaborated on risk analysis (ISO 14971) and quality management (ISO 13485).
• Responsible for cybersecurity monitoring and incident response using Software Bill of Materials (SBOM) analysis (IEC 62443).
• Incorporated and applied artificial intelligence (AI) machine learning (ML) algorithm models for processing instrumentation signals.
• Directed a dev-ops architect in the implementation of a data transformation pipeline leveraging Amazon AWS SFTP, S3 buckets, lambda functions, and IAM.
• Interfaced with product design, contract manufacturing, and software quality partners to specify, review, and test software documentation and code deliverables.
• Worked closely with staff scientists to define product features and implement complex business rules for data analysis and reporting of antimicrobial susceptibility results.
• Supported field service, application specialists, and customer support teams with instruction guides, release and technical documentation, and real time troubleshooting.

User Interface	.NET 8, C#, ASP.NET Core, HTML5, CSS, JavaScript, ReactJS, Bootstrap
Web Services	RESTful ASP.NET Core WebAPI, JSON, BSON
Database	SQL Server, Entity Framework Core, MongoDB
Cloud and Containers	AWS (S3, EC2, lambda, IAM), Azure, Docker, Compose, OpenTelemetry
Security	OAuth, JWT, Identity Server, Dependency Track, IEC 81001, X.509
Development Tools	Visual Studio 2022, GitHub, SVN, SSMS, Fiddler, Postman, Python
SDLC and QMS	ISO 13485, 14971, IEC 62304, Perforce Helix, ZenQMS

Architected and implemented a web-based infrastructure for capturing and analyzing data from Juno Therapeutics antibody discovery platform:

• ASP.NET MVC 5, HTML5, and JavaScript web interface to allow entry, upload, and display of outcomes from molecular biology, protein production, and cell-based assays generated during the discovery workflow.
• Web-based sequence analysis tools to parse DNA sequences and perform trimming, alignment, consensus, and validation, and render HTML5/SVG sequences and motifs.
• Web-based task tracking dashboard to capture and coordinate ongoing activities in protein production and cell sciences teams, including delivery dates and mail/text alerts.
• ASP.NET MVC Web API web services tier that provides RESTful exchange of JSON data from underlying data storage.

Designed and administered Oracle 12c instance to store workflow entities, DNA sequences, documents/reports, gel images, and assay metrics.

Interfaced with laboratory instruments and automation systems: label printer, liquid handler, flow cytometer, fluorescence plate reader.

Built a Next Generation Sequencing (NGS) pipeline to routinely process Illumina HiSeq/MiSeq FastQ files from antibody discovery campaigns:

• Developed .NET/C# high-throughput parsing of DNA sequences to identify antibody binding domain frameworks and CDR’s.
• Implemented ASP.NET MVC 5, HTML5, and JavaScript web interface to rank, compare, and search candidate sequences.

Built a catalog of nucleotide and amino acid sequences of antibody V,J genes from multiple species (culled from V-BASE and IMGT) and restriction enzyme recognition sites.

User Interface	.NET 4.6, C#, WPF, ASP.NET MVC 5, HTML5, CSS, JavaScript, jQuery, SVG
Web Services	RESTful ASP.NET MVC 5 WebAPI, JSON
Database	Oracle 12c, ODP.NET
Development Tools	Visual Studio 2015, TFS 2012, SQL Developer, Fiddler
Bioinformatics	.NET Bio Toolkit, R, BLAST, IgBLAST, Clustal, Entrez, exonerate, V-BASE
Infrastructure	VMware, ClickOnce, IIS 8

Architected and implemented a bioinformatics infrastructure for storage and analysis of antibody drug candidates from the X-BODY NGS (next-generation sequencing) discovery platform:

• Developed DNA sequence processing pipeline to parse millions of DNA sequences into constituent antibody components and calculate aggregate statistics.
• Sequence data was obtained from Illumina HiSeq (1x100) and MiSeq (2x250), Roche 454, and Sanger instrumentation.
• Designed and administered Oracle 11g database running on Windows 2012 Server for storage of sequences, sequence metadata, and statistics.
• Developed WCF and ASP.NET MVC 4 WebAPI web services that provided REST interface to sequence database.
• Developed WPF application, deployed via ClickOnce, that provided internal scientists with data analysis and visualization capabilities that included tabular display of lead antibodies, charts of antibody binding performance, and colorized display of nucleotide and protein sequences.
• Developed ASP.NET MVC 4 internal web site for browser-based functionality comparable to the Windows application described above.
• Implemented advanced data analysis capabilities for BIND® Scanner in support of in-house drug discovery campaigns. Developed documentation and supporting materials for technology transfer of BIND® instrumentation platforms.
• Worked closely with X-BODY scientists to provide timely support of ongoing customer collaborations, implementing as needed new features in the bioinformatics software, custom analysis tools, and database queries.
• Designed and developed X-BODY public website, and posted events, press releases, and updated content.

User Interface	.NET 4.5, C#, WPF, ASP.NET MVC 4, Telerik WPF/Kendo controls, JavaScript
Web Services	WCF, ASP.NET MVC 4 WebAPI
Database	PostgreSQL 8.4, Oracle 11g
Development Tools	Visual Studio 2012, TFS 2012, SQL Developer
Infrastructure	VMware, ClickOnce deployment, IIS 7

Architected and implemented BIND® View, a .NET 4.0 C# WinForms application for viewing images acquired from the SRU Biosystems BIND® Scanner:

• Implemented interactive display, manipulation, and export of very large images.
• Developed plug-in architecture for flexible and dynamic image processing and measurement.
• Implemented image processing algorithms for detecting, measuring, and tracking motion of cells.
• Designed binary file format and memory-mapping strategy for fast, low-memory access to acquired data.
• Developed custom C# user controls for charting and microtiter plate visualization.
• Implemented C/C++ libraries to control instrument hardware (motors and spectrophotometer).
• Developed and implemented SQL Server database for persistence of experimental data and user preferences.

Architected and implemented EMS™, a C++/MFC user interface for acquiring, displaying, and analyzing data from the SRU Biosystems BIND® Reader:

• Implemented 1-D signal processing algorithms for spectral peak estimation and function modeling.
• Developed custom ActiveX controls for charting and data visualization.
• Designed and implemented a C++/MFC user interface for hierarchical navigation of assay design and results.
• Designed and implemented a client database for on-demand access to acquired and analyzed data.

Software Development	C++, MFC, COM/ActiveX, .NET 4.0, C#, WinForms, WPF, MEF
Development Tools	Visual Studio 2010, InstallShield, VisualBuild
Design Tools	UML, Mindscape Lightspeed ORM
Source Code Control	Visual Source Safe
Database	MS Access, SQL Server 2008
Lifecycle Management	Seapine TestTrack, Mercury Quality Center

Managed several teams of software engineers in the development of ImageMatch™, a medical image search engine:

• Led successful company-wide preparation for product demonstration at industry trade show (Radiological Society of North America).
• Designed and implemented medical image processing C++ class architecture.
• Developed acquisition and processing pipeline for populating large-scale DICOM medical image database.

Software Development	C++, Java, Swing, JSP, JDBC, JNI, MFC, Perl, ASP, Visual Basic
Development Tools	Visual Studio, Visual Cafe, Forte, Rational Rose/Purify, UML
Source Code Control	CVS, VSS
Database	SQL, MS Access, Oracle 8i

• Developed software package for two- and three-dimensional interactive visualization of computed tomography (CT) data and radiation dose distributions for AcQSim™ and AcQPlan™ products.
• Built reusable software components for function plotting and tabular display of data.
• Wrote product design specifications and risk analyses for FDA review.