Scott Miller

Software Engineer

scott.resume@boxtoast.com
GitHub: scott-a-miller

Software engineer with 25+ years experience collaborating on creative technical solutions in a variety of scientific and business domains. Strong fundamentals in data processing and web service protocol design. An academic background in network security with practical application in software development. Looking for an onsite position in Columbus, OH.

Work History

Consulting Software Engineer: Tonic Group — 2007 – Present

• full-stack engineer providing web service API design and implementation, front-end development, and devops across a variety of client business domains

Lead Development Engineer: Instem — 2025 – 2026

• principal engineer providing continued development, maintenance, and support for the Leadscope chem-informatics platform

Senior Software Engineer: Leadscope (under Instem in 2019) — 2001 – 2025

• career-long engineering position at a chem-informatics start-up turned leading provider of predictive toxicology software for regulatory submission
• involved with all aspects of software development: coding, feature definition, UI design, architecture, and technology evaluation

Developer: Single Source IT — 2000

• backend server developer at an exciting but ultimately short-lived start-up

Software Engineer: Marimba — 1999

• UI developer in the applications group - implemented document signing for the DocService application; later moved to core group supporting custom software packaging

Research Assistant: Computer Security Research Laboratory, UC Davis — 1997 – 1999

• collaborated on research projects including misuse detection, automated network defense, and network access policy specification

Teaching Assistant: Computer Science Department, UC Davis — 1996 – 1997

• led discussion sessions, lab consultation, and office hours for Artificial Intelligence and Introduction to Programming undergraduate courses

IS Summer Intern: Owens Corning — 1995

• developed and optimized Excel-based office applications on location for a fiber glass manufacturing plant

Mainframe Operator, Lab Consultant, Technical Writer: Computer Services, BGSU — 1991 – 1996

• provided basic administration for the academic mainframes and lab consultation for computer science students

Technologies Used in Production

Languages: Java, SQL, Ruby, Kotlin, JavaScript, HTML/CSS, PHP, C, Flex, C++

Frameworks/Libraries: Jersey (JAX-RS - JSON-based REST), SOAP (JAX-WS), Spring Boot, OAuth (Google API, MS Entra ID), JDBC, Jdbi, JPA, Hibernate, JUnit, Swing, React, MobX, jQuery, KNIME, XPP, iText, Nanoc, Ruby on Rails, JUNG, Protocol Buffers, StringTemplate

Tools: Git, IntelliJ, Claude Code, Emacs, Ant, Maven, AWS, Azure DevOps, Docker, Kubernetes, Unix tools

Databases: PostgreSQL, Derby, MySQL, Oracle, Lucene, Elasticsearch

Formal Education

1996 Bowling Green State University: B.S. Computer Science

1999 University of California, Davis: M.S. Computer Science — with thesis (Specification of Network Access Policy and Verification of Compliance Through Passive Monitoring)

A Sample of Projects

Leadscope Enterprise (Leadscope)

A flexible chem-informatics decision support platform with data warehousing capabilities.

• worked closely with toxicologists and other domain expert stakeholders to develop a series of novel tools for predictive toxicology and regulatory submissions
• redesigned client to a component-based architecture facilitating pivot from high-throughput screening to in silico predictive toxicology
• ported web services API supporting chem-informatics and toxicology data related functions from SOAP (JAX-WS) to REST (JAX-RS - JSON-based)
• provided API integration support and guidance to customers developing bespoke chem-informatics software solutions
• migrated build processes to Azure DevOps integrating with Pipelines and SonarQube

NIEHS ChemBioTox Predictions (Leadscope)

NIEHS project running 300+ million alogrithmically created chemical compounds through the full suite of Leadscope toxicity models and expert alerts

• designed and implemented a new architecture for orchestrating 100 AWS servers running in parallel to perform the 40+ billion predictions in a few months
• continually optimized performance while predictions were ongoing to ensure the project succeeded within its fixed budget for time and cost

KNIME Web Services Integration (Leadscope)

Integration of REST web services with KNIME, an open-source, data analytics workflow platform.

• created custom nodes in the KNIME framework allowing analysts to intuitively plug the Leadscope web services API into their custom informatics pipelines

Reporting Frameworks in JRuby and Kotlin (Leadscope)

A custom framework facilitating the rapid development of highly dynamic and data-rich scientific reports for regulatory submission

• designed an internal DSL for specifying templates, cascading styles, and hooks for testing
• initially implemented in Ruby for its flexibility, later ported to Kotlin for the maintainability of static typing

Insilicofirst (Leadscope)

A collaboratively developed web portal providing retail access to multiple vendors for chemistry-based predictive toxicity software

• designed the overall architecture, implemented the portal portion, and led the discussions defining the vendor web services

ToxML Community Site (Leadscope)

A community site for the collaborative development of ToxML, an open data exchange stanrd for toxicity data and chemical structure-related information

• designed and implemented the UI, lead requirements discussions, and implemented the export functions for the schema and reference parser library

ToxML ETL Framework (Leadscope)

A custom ETL framework for developing toxicity data pipelines; automates and documents the import from public archives, transformation to ToxML (with error correction and normalization), and compilation to Lucene indexes for inclusion in the Leadscope platform.

• designed the overall framework and command line interface
• extended Excel parsers with ergonomic methods for ToxML conventions

ToxML Repository (Leadscope)

A version-controlled repository and detailed user interface for composing and editing ToxML study data

• designed and implemented the component-based and XML form driven architecture

Toxbank User Interface (Leadscope)

A research and development collaboration with multiple European businesses and agencies supporting the SEURAT-1 research intiative to advance alternative methods for assessing safety

• implemented the web-based user interface accessing REST APIs utilizing semantic-web technologies (RDF)

VS+Company Representation App (Tonic)

An internal business application for a photography representation company handling common business tasks: scheduling, invoicing, as well as a work flow for usage rights negotiation

• developed the server-side operations: web services, business logic, persistence, and devops

Network Security Project (UC Davis)

A network security research project working with a prominent semiconductor company providing network monitoring in one of their research areas

• created a DSL for specifying network access policies; implemented its parser and compiler in Lex and Yacc
• extended Network Radar (a security product developed by one of the lab’s alumni) to apply the compiled rules to observed traffic, signalling alarms and/or laxing the security policy to fit acceptable observed patterns
• provided an audit with recommendations for improving security

Macintosh Games

A couple of games for the Macintosh (System 7), written in C, using the Sprite Animation Toolkit: a Spacewar/Scorched Earth mashup, and a remake of Labyrinth (originally for the Apple 2); the latter received a nice write-up in Inside Mac Games.

Publications

Alexander Amberg, Lisa Beilke, Joel Bercu, Dave Bower, Alessandro Brigo, Kevin P. Cross, Laura Custer, Krista Dobo, Eric Dowdy, Kevin A. Ford, Susanne Glowienke, Jacky Van Gompel, James Harvey, Catrin Hasselgren, Masamitsu Honma, Robert Jolly, Raymond Kemper, Michelle Kenyon, Naomi Kruhlak, Penny Leavitt, Scott Miller, Wolfgang Muster, John Nicolette, Andreja Plaper, Mark Powley, Donald P. Quigley, M. Vijayaraj Reddy, Hans-Peter Spirkl, Lidiya Stavitskaya, Andrew Teasdale, Sandy Weiner, Dennie S. Welch, Angela White, Joerg Wichard, and Glenn J. Myatt, (2016) Principles and procedures for implementation of ICH M7 recommended (Q)SAR analyses. Regulatory Toxicology and Pharmacology 77: 13–24. doi:10.1016/j.yrtph.2016.02.004

G.J. Myatt, E. Ahlberg, Y. Akahori, D. Allen, A. Amberg, L.T. Anger, A. Aptula, S. Auerbach, L. Beilke, P. Bellion, R. Benigni, J. Bercu, E.D. Booth, D. Bower, A. Brigo, N. Burden, Z. Cammerer, M.T.D. Cronin, K.P. Cross, L. Custer, M. Dettwiler, K. Dobo, K.A. Ford, M.C. Fortin, S.E. Gad-McDonald, N. Gellatly, V. Gervais, K.P. Glover, S. Glowienke, J. Van Gompel, S. Gutsell, B. Hardy, J.S. Harvey, J. Hillegass, M. Honma, J.-H. Hsieh, C.-W. Hsu, K. Hughes, C. Johnson, R. Jolly, D. Jones, R. Kemper, M.O. Kenyon, M.T. Kim, N.L. Kruhlak, S.A. Kulkarni, K. Kümmerer, P. Leavitt, B. Majer, S. Masten, S. Miller, J. Moser, M. Mumtaz, W. Muster, L. Neilson, T.I. Oprea, G. Patlewicz, A. Paulino, E. Lo Piparo, M. Powley, D.P. Quigley, M.V. Reddy, A.-N. Richarz, P. Ruiz, B. Schilter, R. Serafimova, W. Simpson, L. Stavitskaya, R. Stidl, D. Suarez-Rodriguez, D.T. Szabo, A. Teasdale, A. Trejo-Martin, J.-P. Valentin, A. Vuorinen, B.A. Wall, P. Watts, A.T. White, J. Wichard, K.L. Witt, A. Woolley, D. Woolley, C. Zwickl, C. Hasselgren, In silico toxicology protocols, Regul. Toxicol. Pharmacol. 96 (2018) 1–17. https://doi.org/10.1016/j.yrtph.2018.04.014.

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R. C., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J. and Hardy, B. (2013), The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Mol. Inf., 32: 47–63. doi:10.1002/minf.201200114

G.J. Myatt, A. Bassan, D. Bower, C. Johnson, S. Miller, M. Pavan, K.P. Cross, Implementation of in silico toxicology protocols within a visual and interactive hazard assessment platform, Comput. Toxicol. 21 (2022) 100201. https://doi.org/10.1016/j.comtox.2021.100201.

G.J. Myatt, A. Bassan, D. Bower, K. Crofton, K.P. Cross, J.C. Graham, C. Hasselgren, R.A. Jolly, S. Miller, M. Pavan, R.R. Tice, C. Zwickl, C. Johnson (2021), Increasing the acceptance of in silico toxicology through development of protocols and position papers, Computational Toxicology. 21 (2022) 100209. https://doi.org/10.1016/j.comtox.2021.100209

C. Johnson, L.T. Anger, R. Benigni, D. Bower, F. Bringezu, K.M. Crofton, M.T.D. Cronin, K.P. Cross, M. Dettwiler, M. Frericks, F. Melnikov, S. Miller, D.W. Roberts, D. Suarez-Rodrigez, A. Roncaglioni, E. Lo Piparo, R.R. Tice, C. Zwickl, G.J. Myatt, Evaluating confidence in toxicity assessments based on experimental data and in silico predictions, Computational Toxicology. 21 (2022) 100204. https://doi.org/10.1016/j.comtox.2021.100204. G