Résumé

MPublishing, University of Michigan

Extend and use open source software (e.g., archiving and content-management platforms including DLXS, WordPress and Drupal) and develop workflow applications to support electronic publishing at the University of Michigan.

ProteomeCommons.org, Dept. of Biological Chemistry, University of Michigan

Java developer employed to work as a core developer on the open source Tranche project, which is a secure, P2P distributed file system. Concerns such as annotation, pedegree and long-term preservation guided most of our work, and one of our greatest ambitions was the creation of a pipeline for proteomics data. In January 2008, I was promoted to the position of Intermediate Application Developer. 

Washtenaw Community College

Taught four courses — INP 150 (Web Coding I), INP 153 (Designing for the User Experience), INP 160 (Internet Technology), and INP 170 (Web Coding II).

• Designing for the User Experience was primarily an information architecture course, though we briefly covered other topics like accessibility, usability engineering and SEO.
• Internet Technology was a cursory overview to the technologies that make the Internet work.
• Web Coding I & II explored web page design with XHTML 1.0 Strict/CSS with modularity and ease of maintenance in mind, along with a little XML/XSL, WML and SGML.

Shapiro Undergraduate Library, University of Michigan

(734) 764-4481

Redesigned the undergraduate website, as well as updated subsites [e.g., Searchpath], as well as some information architecture and graphic design [for website, fliers and posters]. I also conducted user testing for the new website I created.

Knowledge Navigation Center, Hatcher Graduate Library, University of Michigan

(734) 647-5836

Assisted patrons with general technology issues such as web design, basic javascript coding, graphic arts applications like Illustrator and Photoshop, and other issues related to web and electronic-document creation.

Soar

Soar is a "general cognitive architecture for developing systems that exhibit intelligent behavior" (source), with features such as reinforcement learning, semantic memory, and episodic memory.

My work has exclusively focused on semantic memory, which is the storage and retrieval of facts about the world and their meaning. I have designed tools to help use ontologies such as the SUMO and OpenCyc ontologies as well as the WordNet lexical database, and have designed test agents to demonstrate the respective semantic memory knowledge base. Additionally, I have worked on performance tests to prepare for the use of very large knowledge bases.

For my final project, I developed a Soar agent that performed inductive reasoning for a subset of the properties from OWL.

De novo sequencing

To identify unknown proteins, tandem mass spectrometry-based proteomics uses instruments to fragment proteins into shorter peptides, which are they fragmented into series of smaller molecules (which are subsequently ionized so they can be measured). From these ion series, the instrument produces spectra with masses (molecular mass over charge) and the associated intensities of the recorded signals. The problem is that these spectra are often noisy; furthermore, though a great deal of fragmentation research has produced useful heuristics and models of how spectra should be produced, software applications have not been particularly successful in reliably producing appropriate sequences.

My first attempt to produce de novo sequences used genetic algorithms. Though this approach generally worked for smaller peptides of fairly good quality, the results were less predictable for longer sequences, and the run times were not appropriate for high throughput data processing.

My second approach produced the set of all candidate sequences described as a Cartesian product of all potential sub-sequences. (This approach relies on the problem exhibiting optimal substructure, which is true only when the ions can be correctly classified by their series.) Combined with some optimizations that were guided by fragmentation research (limited to tryptic digests) as well as some dynamic parameters to increase effeciency, I was able to sequence longer peptides in more reasonable times, measured in minutes instead of hours. However, for longer proteins, this approach produced increasingly larger sets of high scoring, tightly clustered candidates, making it unsuitable for fully automated batch processing.

One potential application would be to produce a plugin for a spectra visualization tool (such as Expedite) to identify candidate solutions, which experts could then review, potentially reducing the time spent identifying peptides. One benefit of using this tool is that the results are justified (i.e., labeled ion peaks and information about support for ion series classifications), and with a little more development, could produce meta information such as the quality of the spectra and the confidence of the tool. Alternative chemistries could also be supported, but would greatly increase the search space for each identification.

Though I worked unsupervised, I received some guidance and feedback from several research scientists in the field, and collaborated closely with a researcher who produced the Expedite visualization tool.

Ann Arbor Perl Mongers

Participate in the reorganization and development of the group. Visit the Ann Arbor PM website (http://annarbor.pm.org) for more information.

United Way University of Michigan campaign volunteer

I worked as a departmental volunteer for the 2010 University of Michigan United Way campaign. Additionally, I organized and directed the University of Michigan 2010 United Way charity tournament. As of 2011, I joined the Young Leaders society.

University of Michigan/Ann Arbor Go Club

Chief of staff since October 2010. Visit the UM Go club website (http://www.umich.edu/~goclub/) for more information.

WCC Reading Clinic

Tutored adult students who were learning basic reading and pronunciation skills.