Michael Elliott Smoot

Projects:

• Team leader managing four programmers. Responsible for hiring, firing, reviewing, and establishing work schedules. I try to make sure each programmer is happy and productive.
• Cytoscape Core Architect. I am responsible for overseeing the development, testing, release, and maintenance of the Cytoscape application. As an open source project I do not have the ability to dictate what work gets done, rather my role is as an adviser and resource for other developers. I do make design decisions and can reject code from the core.
• Presented Cytoscape at various conferences and institutions.
• Managed system administration of 40+ Linux, Windows, and Mac OS X computers including workstations, servers, and a RAID array.
• Helped write grants and grant renewals for different projects in the lab.
• All work done as a member of the Ideker Lab in the Department of Bioengineering.

Projects:

• Reimplemented PathBLAST using the Network Comparison Toolkit which I wrote for the purpose.
• Developed new code for the Cytoscape project. Refactored several aspects of the project to improve design and functionality. Re-established and expanded the unit testing framework for the project. Set up a system of nightly builds. Developed a Wiki/DocBook system for project documentation. Automated the release creation process.
• All work done as a member of the Ideker Lab in the Department of Bioengineering.

Projects:

• Implemented several near-optimal alignment generation algorithms in C++.
• Implemented software to visualize large sets of alternative protein sequence alignments in Java. The software provides animation and zooming facilities to effectively visualize both alignment details and set overviews. The software includes filtering features, customizable highlighting schemes, and mixed-initiative interaction.
• Performed various analyses comparing sets of near-optimal alignments with structural alignments. Developed a predictive, probabilistic model for determining which alignment edges are structurally relevant using logistic regression.
• Developed software to visualize various dynamic programming algorithms used in bioinformatics.

Projects:

• Developed the DisplayMUMs software package for visualizing genome assemblies based on output from suffix tree alignments (MUMmer).

Projects:

• Won the 2000 Darden Business Concept Competition and gained a spot in the Batten Institute Business Incubator.
• Helped define business plan, perform feasibility analysis, open office in Bangladesh (including hiring Bangladeshi employees, office rental, securing government permits), establish network communications with Bangladesh, design and perform data analysis, and procure venture capital funding. Among other things.
• Transitioned from company to pursue graduate studies.
• The company survived for 3 years before going out of business.

Projects:

• Designed and partially implemented a Probabilistic Quantitative Precipitation Forecast (PQPF) verification system in C++ for the National Weather Service.

Projects:

• Local Number Portability Products: Responsibilities included maintaining and enhancing Java graphical user interface to products. Implemented all system reports in Oracle Reports and C++
• Predictive Outbound Dialer: Tasks included code optimization, statistical analysis of predictive algorithm and various bug fixes. Implemented all changes in C++.
• Digital Cellular Base Station/Switch Translation: Rewrote the test environment such that all test cases could be generated and run together.
• Web Based Order Entry System: Project implemented in Smalltalk. Responsibilities included configuration management (source control), creating releases, writing and executing the system test plan, tracking defects and tracking requirements with a traceability matrix.
• Predictive Outbound Dialer: Wrote detailed system test plans, executed extended test periods, tracked system defects, maintained test environment including databases, assisted in requirement/code/design reviews, performed customer installations, assisted in configuration management, assisted in design of switch / VRU (Voice Response Unit) simulator, coordinated three other analysts.