samuels-portfolio:~ User$ Hello, world! Type help for commands...
I spent two weeks taking classes on global changes in the ocean during the anthropocene, conservation & management for sustainable oceans, and basic ship skills (including safety and navigation) while on shore in Woods Hole, Massachusetts. During this time, I developed an independent research project on an aspect of ocean science. The class then joined the SSV Robert C. Seamans in Honolulu, Hawaii to depart for the Phoenix Islands Protected Area (PIPA). We spent six weeks at sea conducting regular sampling and data collection with a few brief stops on some of the Phoenix Islands, such as Kanton and Orona, and ended our voyage in American Samoa. (link)Sailing Life Python wget numpy matplotlib ADCP system Ocean Data View CTD-Carousel deployments Trucker Trawl deployments Neuston Net deployments Organism Identification
I had two main jobs as a laboratory assistant. I worked in the computer labs from 6-11 to assist anyone who needed help with their homework or lab assignments. I also attended a lab for another class from 2:30 to 4:30 to assist the students with general assignments.Explaining Code Abstractly Python
I spent five semesters as the Music Technology TA and one semester as a Music Theory TA. For the Music Tech TA I had five hours of computer lab time a week where students could come and get help on various music assignments that involved writing music with Finale, producing with Garageband, or recording with microphones. For the Music Theory TA I had the 8:30am Music Theory class and would help present and organize materials for the class as well as hold study sessions to assist students in improving the skills that they were most struggling with in the class.Music Theory GarageBand Finale
I recorded concerts and ran sound for Furman students and professors, visiting artist, and various events including Furmans TedX program. The recording involved straight to disk, and ProTools recording simultaneously to have hardcopy and digital editions. The sound engineering involved setting up microphones and monitors, checking levels with groups during rehearsals and before concerts, and running the sound board.Wire management Button pushing ProTools Sound Engineering
I helped Drs. Tartaro and Chosed (Computer Science and Biology, respectively) develop code for the class Introduction to Computer Science through Bioinformatics. In addition, I researched various tools and topics intended to assist teaching students about basic coding and more advanced bioinformatic techniques.Python
I worked on the My Salkehatchie website for the summer camp Salkehatchie Summer Service, which fixes hundreds of homes around South Carolina each year. This site has allowed thousands of campers to register and pay for camps, and has cut the amount of paper from six different paper forms to one form per camper. I was assigned various tasks on Producteev, logged my hours on Toggl, used Git to upload my work to Bitbucket, and tracked errors with Rollbar and ssh. My tasks ranged from simply adding components to forms, fixing broken components, or creating new forms, to editing and working with the custom designed MVC pattern and website, which has four unique portals for different user types. The models were written in PHP with both PostgreSQL and MongoDB to store user information and form data. The controllers were written in PHP and the Views were written in HTML5, CSS3, and JQuery.HTML5 CSS3 JQuery PHP MongoDB/MongoLab PostgreSQL Git Producteev Toggl Bitbucket Rollbar
I worked as part of a team of three to create a digital edition of the Iliad. Our work involved using a custom manuscript browser to identify regions of interest on a given page of the manuscript and obtain URNs. We identified individual characters, lines, and scholia then linked the regions on the manuscript to the text in csv files. After identifying regions, we edited XML files with the transcribed text to verify they matched the characters on each line. Finally, we would validate the page and edit any errors. Another important aspect of this work was using the issue tracker on Github to communicate when we found new occurrences of a word or name, and to ask for help on identifying tough characters and ligatures.Git Github Vagrant XML Oxygen XML Editor SPARQL Ancient Greek Glyph Identification Transcription
I worked with Dr. Tartaro, Computer Science and Dr. Kerstin Blomquist, Psychology, on my thesis project Self Monitoring Innovations (SMI). Our work focused on creating and testing a new application to assist in monitoring (recording what you eat). The USDA recommends a plate-based method for planning meals, but all current monitoring tools use traditional forms of calorie counting and serving sizes on its site. Our application uses a new technique called plate-based monitoring, which involves recoring the percentage of a plate each food group occupies. My job was to redesign and implement a new version of the site, and then test the system to see how usable a plate-based application would be and to determine how accurately it could represent a meal.
I worked with other students to create characteristic models of an underwater sea mountain (seamount), and to possibly observe island mass effect (IME) in action. The initial models were to be 3D using python, numpy, and matplotlib, but after some issues with the magnitude of currents and matplotlib rendering speed we decided to create several 2D models to characterize what is going on around the seamount. The parameters examined were: current flow, temperature and salinity (isohaline layers), and ocean productivity measured in phytoplankton and zooplankton. The data were collected in a 2 day track over Winslow Reef (our subject seamount) in an attempt to capture the most data and observe possible areas of interference.
I worked with Dr. Christopher Blackwell on botanical research in the Digital Humanities. During this time, I assisted in organizing data that was collected by the class and helped develop the structure that this data would reside in. The structure used a resource desription framework to add metadata like writter or geographic location to objects such as images of manuscripts and textual translations. In addition, Weston Catron (fellow research assistant) and I developed the SPARQL Environment to make querying our datasets easier. Later that summer I attended a two-week seminar at Harvard University’s Center for Hellenic Studies to work on digitizing the Illiad.Git Github Vagrant XML Oxygen XML Editor Botanical Identification SPARQL HTML5 CSS3 JQuery Ancient Greek Glyph Identification Transcription
I helped a molecular genetic biological research lab develop bioinformatic tools to examine a large dataset of gene expression profiles. Our goal was to create and utilize a data structure to allow for easy access to the data. The Hill labs possessed a transcriptomic data set obtained from the bioeroding and Symbiodinium-harboring sponge Cliona varians. The first step was to select information that might give the most relevant insights into our biological data set to include into the data structure. We used BLAST2GO to gather basic information such as BLAST hit, e value, GO terms, GO descriptions, KEGG annotations, PFAM, expression values, length, and nucleotide sequence for the transcriptome. Next we needed a way to consolidate and query this data set, and for that we used Python. With simple text processing we stripped the basic information from BLAST2GO and added it to a custom "contig" class. We developed an easy-to-use interface using Tkinter to allow for advanced searching of the database. We also wanted to allow for extendibility of our data structure to other possible biological data sets so all the code was generalized for use on any transcriptome.Python Tkinter Blast2Go
Awards & Distinctions
A group project for Graphics (mentioned above) which created new, more interactive models of the sea-mount I worked on during SEA semester. In the bottom left you can see the topography of Winslow Reef and towards the top of the mountains you can see stacks of arrows with various size, color, and direction. These stacks of arrows represent one scan from the Acoustic Doplar Current Profiler (ADCP) and each arrow represents the current measured at that depth. The size and color are correlated to magnitude to help visualize where strong currents are, while the direction of the arrows are linked to direction. Not pictured is an ocean surface layer to help gauge depth, but this can be toggled on and off with the GUI in the upper right corner. The GUI allows you to control a few parameters for the ocean and shows the magnitude, depth, and location of a selected current. To interact with the model you rotate with left-click and drag, pan with right-click and drag, zoom by scrolling, and select currents with left-click. To try the model click here. The code, including previous work with matplotlib, is on github here.
Self Monitoring Innovations
SPARQL Environment Backend
This project was part of my Database Management class and is built in a vagrant virtual environment (scotchbox) for stability and uses both MongoDB and MySQL to store user information. The database communication is handled in PHP. This system is intended to organize the backend and simplify the requirements for the original SPARQL-Environment (a project a fellow student and myself started while working with relational data for summer research). The code for the original SPARQL-Environment is on github here and the code for my backend is here.