Interdisciplinary Computer Science
Our students' Masters in Interdisciplinary Science thesis papers cover a broad range of subjects. Displayed on this page are theses on the following topics:


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Amelia J. Parmidge, 2014

"NEPIC, a Semi-Automated Tool with a Robust and Extensible Framework that Identifies and Tracks Fluorescent Image Features"

As fluorescent imaging techniques for biological systems have advanced in recent years, scientists have used fluorescent imaging more and more to capture the state of biological systems at different moments in time. For many researchers, analysis of the fluorescent image data has become the limiting factor of this new technique. Although identification of fluorescing neurons in an image is (seemingly) easily done by the human visual system, manual delineation of the exact pixels comprising these fluorescing regions of interest (or fROIs) in digital images does not scale up well, being time-consuming, reiterative, and error-prone. This thesis introduces NEPIC, the Neuron-to-Environment Pixel Intensity Calculator, which seeks to help resolve this issue. NEPIC is a semi-automated tool for finding and tracking the cell body of a single neuron over an entire movie of grayscale calcium image data. NEPIC also provides a highly extensible, open source framework that could easily support finding and tracking other kinds of fROIs. When tested on calcium image movies of the AWC neuron in C. elegans under highly variant conditions, NEPIC correctly identified the neuronal cell body in 95.48% of the movie frames, and successfully tracked this cell body feature across 98.60% of the frame transitions in the movies. Although support for finding and tracking multiple fROIs has yet to be implemented, NEPIC displays promise as a tool for assisting researchers in the bulk analysis of fluorescent imaging data.

Lesley Evensen, 2004

"Computational Models for Alpha Helix Bundles"

We approximate free energy of a structure, in this case an alpha-helix bundle, using a program to build successive contact maps on a lattice structure to position the monomers or beads in the chain of molecules. The maps will contain pairs of beads indicating inter- and intra-helical contacts. A neighbor-avoiding walk over these nodes indicates whether the map is valid and the number of possible paths through the conformation. We ensure all possible conformations of these bundles are built and compute the density states per number of contacts. All conformations are not valid, however. We need to apply restrictions to avoid processing non-viable maps, since the program would otherwise require exponential time in the number of monomers. The aggregate values of path-counts found for the various conformations gives the density state for a contact map. We then plot the density states values against the number of contacts for a chain of up to N monomers, where N=20 for a 2-helix bundle, and N=24 for a 3-helix bundle.

I use these values to derive a partition function to use in predicting density states for higher numbers of monomers, which are computationally hard (exponential in N). Since this is a simplification of transition states, we aim to get a statistical sample of values within an order of 2 for prediction of density states. If the function appears to work well programmatically, it may be tested against a natural polymer.

Arina Fedorova, 2004

"Statistical Mechanics Studies of Triple Helix Bundle Polymers"

I modeled two- and three-helix bundles in a triangular lattice. An algorithm was developed so that a set of contact maps was generated representing a wide variety of different possible alpha helix bundles. For a chain length up to 25 beads the generated contact maps were physically viable in 75 percent cases. Using the program that I wrote in C language I computed the density of states for two- and three-helix bundles for chains of specified length. In collaboration with Lesley Evensen, ICS graduate student, I can predict the density of states for longer chains with good accuracy.

Prem Veeramani, 2004

"Vec2004 ~V: A robust and efficient vector screener and quality control tool"

DNA sequencing, the process of determining the exact order of millions or billions of bases that make up the DNA is a highly complex and multi-staged process. The resulting sequence could be contaminated with some segments from the vector during the multi-staged process. These segments need to be identified, removed and quality screened in order to acquire the pure sequence. The resulting pure sequence can be used for further research, which includes protein structure prediction, sequence alignment, building predictive models, etc. This research process understands the need for a better, robust and independent component that can identify and eliminate the vectors in the input sequences and also perform various quality control checks on the sequences thereby yielding the expected pure sequence. This component would replace the existing one and seamlessly integrate with the XGI pipeline and thereby increase the efficiency and quality of the existing pipeline.

Simona Carini, 2001

"ImagoSUs: A Database to Store Images and Data of Sea Urchins"

When we think of institutions having to solve the problem of digitizing and annotating their collections, we normally think of libraries or museums, large institutions with substantial means at their disposal. This thesis describes how a similar problem was addressed and solved by a small institution, the Biology department of Mills College, with limited means. The need to permanently store the rich image collection resulting from research on the larval development of sea urchins is the starting point of the project described in this thesis. The project achieved the development of a database that stores not only the images, but also the information they contain: ImagoSUs, a database to store Images of Sea Urchins, designed to be used as storage medium, knowledge discovery tool and teaching tool by researchers and students of the Biology department.

Cheryl Chambers, 1987

"The Biological World Beyond: An Educationally Manipulable Database for an Archival Biology Videodisk"


Tu Tran, 2004

"Lessons from Deploying Information Systems for Microfinance Transactions in Uganda"

The World Bank states that up to 500 million people could potentially benefit if the microfinance industry addresses the challenges of poor infrastructure and operational inefficiencies. Specifically, microfinance institutions must leverage information and communication technology to transition from manual record-keeping to standardized electronic client data and to connect electronically from rural points of exchange to regional credit organizations. The Remote Transaction System (RTS) is a technology solution initiated and designed by the Micro-development Finance Team (MFT) to help microfinance institutions transition from manual record-keeping and to electronically connect rural areas to regional microfinance institutions. The technology consists of a portable, point-of-sale (PoS) device with card reader, printing, and cellular networking capabilities. The objective of this research project is to present lessons learned from deploying the RTS solution in Uganda, based on three weeks of fieldwork in Uganda during August 2004. The principal findings are observations of cultural factors, training methodology, and the introduction of technology into existing microfinance infrastructures. It is hoped that the lessons highlighted in this paper offer the reader with positive guidance on mainstreaming microfinance in both developing and developed countries.

Deepa Madhavan, 1999

"An Online Tool for Market Research"

This thesis attempts to study the manner in which surveys are currently conducted and explore means of automating the entire process. Research will be carried out to determine whether the online survey is an improvement on the process currently followed. Furthermore, an attempt shall be made to demonstrate that the entire process of conducting a survey can be made more efficient.

Wei-Shine Patricia Kao, 1990

"A Rule-based System on Financial Statement Analysis"

Allan Miller, 1990

"Process Interaction Simulation Using Modula-2"

Discussion and design of a process interaction simulation system using Modula-2 to help programmers write discrete event model systems.

Narindar Pal Sandhu, 1988

"Goan: The Indian Village"

Development of a computer simulation of the economic system for a small village in India.

Randall I. Thomas, 1989

"The CONTRACT System with PQL: A Contract Management System for Hospitals"

Development of a contract management system using a query language to meet current and future needs of urban hospitals.

Mana Alemi, 1987

"Omphalos: A Prototype System to Evaluate Health Maintenance Organizations"

Development of a computer tool to help managers access appropriate and accurate information about health organizations.


Amy Dewey, 2007

"A Database to Preserve and Define Swing Dance Moves and Routines"

Swing dance, a social dance born in the late 1920s, is experiencing resurgence even as the first generation of swing dancers passes away. To preserve the dance and build communication and collaboration among swing dancers, I built a database-driven web site of swing dance moves and routines.