# David Todd

> Scientific Software Engineer, Informatics

Location: San Francisco Bay Area, United States
Profile: https://flows.cv/davidtodd

Accomplished quantitative software engineer, analyst, and data scientist with expertise in bioinformatics, image processing, options trading systems, and technology acceleration. Skilled at resolving complex issues and deploying results into production. Experienced in object-oriented and functional software development in Python, C, and C++, machine learning, algorithm creation, business data modeling, quality systems, and the software development lifecycle. Regarded as a trusted advisor who is insightful, collaborative, with a high-level communication style and a commitment to excellence.

## Work Experience
### Senior Scientific Software Engineer @ Sigray, Inc.
Jan 2023 – Present | Benicia, California, United States
Creating image analysis tooling for x-ray laminography and micro-CT analysis.
Using NumPy, SciPy, scikit-learn, mutlithreading, multiprocessing, shared memory, and CuPy.
Focused on in-line semiconductor inspection and defect analysis.

### Informatics, Data Science, and Software Engineering - Consulting @ Christopher Roberts Consulting
Jan 2022 – Jan 2024

### Staff Software Engineer @ Sequencing Health / Genapsys
Jan 2019 – Jan 2022 | Redwood City, CA
As a member of the Bioinformatics team:
  - Optimized deep CNN machine learning models for improved DNA sequencing.
  - Generated, validated, and enhanced code for Phred quality models.
  - Researched the impact of filtering on homopolymer distribution, Q-score, and throughput.
  - NGS pipeline software development and configuration management for all steps.
  - Studied accuracy as a function of coverage for karect based correction module.
  - Implemented positive results of ad-hoc studies in Python software and algorithms.
  - Improved alignment tools and demultiplexing code.
  - Performed Verification and Validation testing and configuration management for software releases.
  - Supported new team members, reviewed pull requests, and documented processes.
for the continuous improvement of the base-calling pipeline.

Worked with BWA, BLAST, SAMtools, FASTQ, Karect, Cutadapt, Trimmomatic.

### Senior Software Engineer Consultant @ Intrexon Corporation
Jan 2018 – Jan 2019 | South San Francisco
Supported scientists genetically engineering microbes to create high value chemicals:
  - Integrated diverse data sets that tracked short and long term fermentation experiments.
  - Created back-end web services using NumPy, Pandas & Flask.
  - Enhanced next generation sequencing infrastructure, incorporating new sequencing platform.
  - Deployed services on Docker using Kubernetes on internal cloud.

### Senior Software Engineering Consultant @ Genapsys
Jan 2018 – Jan 2018 | Redwood City, CA
Implemented new modules in Python, and created software for bioinformatics pipeline used to process raw data from the GENIUS gene sequencing system.
  - Increased accuracy of 16s application using results from Hypervariable DNA regions.
  - Evaluated and improved Phred Q-score (Quality) metrics.
  - Added BWA as an option in the pipeline alignment module.
  - Sped up modules by up to two orders of magnitude.
  - Trained Q.A. team members and supported testing of software from Bioinformatics team.
Worked in Python, NumPy, SciPy, Pandas, Git, Docker, Google Cloud.

### Senior Software Engineering Consultant @ Protein Metrics, Inc.
Jan 2017 – Jan 2018 | Tiburon
- Developed algorithms to automate pattern recognition in mass spectrometry data to determine the composition of proteins and other macromolecules.
- Compared internal software to current open-source products. 
- Working with C++11 in Visual Studio on Windows and Git for version control.

### Lead Software Engineer @ O.N. Diagnostics
Jan 2011 – Jan 2017 | Berkeley, CA
Designed, developed and improved Python software on Linux and Windows to determine bone strength, fracture risk, and bone-implant stability from Patient CT scans. 
  - Used image processing and object-oriented design to solve challenging algorithmic problems in 3d segmentation and calibration of CT DICOM images.
  - Automated the calibration and segmentation of femurs, vertebrae, and the aorta.
  - Worked with data engineers and bone scientists to resolve challenging scientific problems.
  - Converted Matlab code to Python.
  - Designed database layout for FDA approved osteoporosis-analysis pipeline to handle orders from health care providers and return patient osteoporosis reports.
  - Wrote extensive set of automated unit tests and nightly regression & integration tests. 
  - Managed software and information technology (IT) team members.
  - Created and maintained software documentation and Standard Operating Procedures (SOPs) to FDA audit standards (HIPPA and CFR Title-21, 801, 820, and 830).
  - Generated Verification and Validation test reports and supporting quality documentation for every release.
  - Work with Numpy, Scipy, Eclipse, PyDev, Trac, Subversion, Tkinter, VTK, SQLite, JSON, DICOM.

Website: 
https://ondiagnostics.com/

### Scientific Programmer II & Analyst @ Center for Imaging of Neurodegenerative Diseases at UCSF & VA Medical Center
Jan 2009 – Jan 2011 | San Francisco, CA
Performed design and development work on the open source VeSPA project:
  - Created a pipeline in Python for designing RF pulses for magnetic resonance imaging (MRI) experiments.
  - Improved performance and updated the GAMMA MRI simulation package to work with a newer C++ compiler.
  - Export the C++ APIs to Python using SWIG, creating PyGamma.
  - Converted numerous algorithmic modules from Matlab to Python, using NumPy and SciPy.
  - Integrated Matpulse RF pulse system into the VeSPA package. 
  - Contributed to user interface and database design.
  - Worked with Eclipse, Bugzilla, Subversion, SQLite, DICOM, and wxWidgets. 
  - Created test libraries for Linux, Mac, and Windows.

For VeSPA information and details:
https://www.opensourceimaging.org/project/vespa-versatile-simulation-pulses-analysis/
http://scion.duhs.duke.edu/vespa/rfpulse
http://scion.duhs.duke.edu/vespa/rfpulse/wiki/Acknowledgements
http://scion.duhs.duke.edu/vespa/gamma
http://scion.duhs.duke.edu/vespa/gamma/wiki/GammaContributors

Publications:
1. Brian J. Soher, Philip Semanchuk, David Todd, Jyh-miin Lin, Xiao Ji, Dinesh Deelchand, James Joers, Gulin Oz and Karl Young, Vespa: Integrated applications for RF pulse design, spectral simulation and MRS data analysis, Magnetic Resonance in Medicine (May 15, 2023); http://doi.org/10.1002/mrm.29686
2. B. J. Soher, P. Semanchuk, D. Todd, J. Steinberg, K. Young. VeSPA: Integrated applications for RF pulse design, spectral simulation and MRS data analysis. Proc. Intl. Soc. Mag. Reson. Med. 19 (2011)

### Consulting (Project manager and Designer) @ Christopher Roberts Consulting
Jan 2009 – Jan 2009
Designed website for Personal Life Media.  Managed project to bring new products to market.

### Senior Software Engineering (Consulting) @ D2S, Inc.
Jan 2008 – Jan 2009 | San Jose, CA
Studied effectiveness of electron Beam technology for imaging current semiconductor designs:
 - Built tools for partitioning industry standard design files (GDSII) in C++/STL on Linux.
 - Informed change in company direction.
 - Used a test-driven development methodology.
 - Developed applications using the Silicon Integration Initiative (Si2) API’s.

### Senior Software Engineer (Consulting) @ Softagon
Jan 2007 – Jan 2008
Now part of Pariveda Solutions.
- Consulted on project management and design in the financial & hedge fund markets. 
- Worked on systems implemented in Microsoft SQL, stored procedures, XML/XSLT, and Visual Studio (C# and .NET).  
- Used Scrum/Agile development methodology.

### Team Leader & Assistant Vice President @ Newedge (Fimat)
Jan 2006 – Jan 2007 | San Francisco, CA
Managed and collaborated with a team of C#, C++, and .NET programmers to design, develop, and roll-out trading and risk management systems for stock, options, and futures. 
  - Designed and implemented a portfolio margining system. 
  - Responsible for enhancing a real time quotation system, middle tier infrastructure, and front office trading applications used by 1000s of professional traders in-house and via web infrastructure.
  - Worked with Visual Studio, Microsoft SQL server, Perforce, and UniVerse Pick BASIC.

### Team Leader @ Bank of America (Merrill Lynch Profesional Clearing Corp / Sage Clearing)
Jan 2004 – Jan 2005 | San Francisco, California, United States
Managed a team in charge of updating and supporting order execution, clearing systems, operations, and software development.

Results include:
 - Updated order management system to gain new business.
 - Managed the creation of mixed straddle tax reports and Sarbanes-Oxley compliance.
 - Responsible for business continuity, disaster recovery, and entitlements for real time quotes.
 - Migrated 20 years of trading data from a legacy multidimensional DB to Microsoft SQL (ETL).
 - Updated trading and clearing operations for penny option prices, Oats III, and new short sales rules.
 - Part of Risk Management team migrating key trading system to NY office.

### Senior Software Engineer and Quantitative Analyst @ Bank of America (MLPCC/Sage Clearing)
Jan 1998 – Jan 2004
Responsible for the risk management technology and software, used by real time traders and clearing clients. Improved models, created systems for new business, responded to SEC regulatory changes.

Highlights include:
  - Improved accuracy of binomial tree option pricing models and associated risk parameters - in C/C++.
  - Designed, developed, and implemented a multi-threaded financial information exchange (FIX) message server supporting new corporate clients.
  - Created reports to monitor and simplify clearing operations with the DTCC and the OCC.
  - Improved software quality by a factor of 30 by drastically reducing defects, greatly enhancing up-time.
  - Implemented high performance risk management and pricing tools for a Java based trading system.
  - Performed extensive pre-release software verification and validation.
  - Worked on architectural analysis, UI specification, implementation details. 
  - Analyzed Value at Risk (VAR): Reported shortcomings for handling derivatives.


## Education
### B.S. in Physics
Massachusetts Institute of Technology

### PhD in Chemical Physics
University of Chicago

### Machine Learning in Statistics, SQL
Continuing Education

### Continuing Education II

### Pre-college


## Contact & Social
- LinkedIn: https://linkedin.com/in/david-todd-rtts

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Source: https://flows.cv/davidtodd
JSON Resume: https://flows.cv/davidtodd/resume.json
Last updated: 2026-04-01