Student Research Opportunities

Please click on individual student research opportunity project titles to view additional details.  Also, please check back often as the positions on this page, and their status, will change continuously.

Faculty and staff can add new or modify existing student research opportunities.

 

Biology

Determinates of Lyme disease risk in Addison County

Position Status:
active/open/recruiting

Faculty or Staff Member:
David Allen

E-mail Address:
dallen@middlebury.edu

Department(s) and/or Program(s):
Biology

Project Title:
Determinates of Lyme disease risk in Addison County

Project Description:
Lyme disease is on the rise in the state of Vermont. In the last ten years the incidence rate has jumped 10-fold, and over the last three years VT has the highest incidence rate in the country. Lyme disease is a vector-borne, zoonotic disease. Vector-borne means that it is transmitted by a vector, in this case the black-legged tick, Ixodes scapulars. Zoonotic means that the bacterium that causes Lyme (Borrelia burgdorferi) can also live in other animal hosts. These two facts mean that the incidence of Lyme disease in an area is closely tied to the populations of those vectors and hosts. So Lyme disease risk to humans is partially controlled by ecological factors. In this research project we will examine this connection between ecology and Lyme disease. There are a tremendous number of possible biotic and abiotic factors that can affect Lyme disease risk: ticks are prone to desiccation so leaf litter humidity is important; tick development rate is controlled by temperature; mice are the best hosts for ticks; ... .

Project Location(s):
MBH lab and field sites throughout Addison County

Session Dates:
summer

Eligibility and Requirements:
None

Application Process:
Please fill out this form by Feb. 22. https://goo.gl/forms/ac9562wEAjYRteq32

Dynamics of a hemlock-hardwood forest

Position Status:
active/open/recruiting

Faculty or Staff Member:
David Allen

E-mail Address:
dallen@middlebury.edu

Department(s) and/or Program(s):
Biology

Project Title:
Dynamics of a hemlock-hardwood forest

Project Description:
Understanding the dynamics of forests is important for many reasons: we can better understand how the forest will respond to disturbance or climate change, we can set sustainable harvesting levels, we can predict how much carbon the forest will sequester, ... . But forest dynamics play out over a long time scales, so directly observing or measuring them is hard. One way around that is to create models that are realistic enough to capture those dynamics. This summer my research group will continue work developing and parameterizing a spatially explicit, individual-level mechanistic model to understand dynamics in this region's hemlock-hardwood forests. The hope is that this model will be realistic enough to do the things mentioned in the paragraph above. Be warned that this summer's work will continue a multi-year process and we won't be able to fully develop this model by the end of the summer. But we will get some exciting and interesting results this summer! The work will predominately be in the field.

Project Location(s):
My BiHall lab and local field sites (Battell Research Forest and Bread Loaf lands)

Session Dates:
summer

Eligibility and Requirements:
Prefer students how have taken BIOL0323

Application Process:
Fill out this form by Feb. 22nd. https://goo.gl/forms/ac9562wEAjYRteq32

Please contact department regarding other potential opportunities.

 

Chemistry & Biochemistry

Please contact department directly.

 

Computer Science

MySeq.js: A single page application for distributed genome analysis and education

Position Status:
active/open/recruiting

Faculty or Staff Member:
Michael Linderman

E-mail Address:
mlinderman@middlebury.edu

Department(s) and/or Program(s):
Computer Science

Project Title:
MySeq.js: A single page application for distributed genome analysis and education

Project Description:
Using React and other modern web technologies we will develop MySeq.js (https://github.com/mlinderm/myseq.js), a single page application for privacy protecting, hands-on analysis of genomic data that supports both self-guided exploration and structured laboratory exercises (such as predicting bitter tasting response from an individual’s genome). Modern browser APIs enable efficient querying of genome-scale variant files stored locally on the user’s computer or available remotely via URL (without downloading the entire multi-GB file). With the former, we can easily distribute sophisticated genome analysis tools that do not depend on local computational resources (other than the user’s web browser) nor require uploading sensitive data to external servers.

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Experience with object oriented programming is a prerequisite. Previous javascript/html/css experience, such as completion of CS321 or CS465, is highly desired.

Application Process:
Send your resume/CV including a list of relevant of coursework or other experience, the dates you will be available in Summer 2017, and a brief statement of interest to mlinderman@middlebury.edu.

Additional Information:
http://go.middlebury.edu/linderman

Non-parametric genotyping of structural variants in whole genome sequencing data

Position Status:
active/open/recruiting

Faculty or Staff Member:
Michael Linderman

E-mail Address:
mlinderman@middlebury.edu

Department(s) and/or Program(s):
Computer Science

Project Title:
Non-parametric genotyping of structural variants in whole genome sequencing data

Project Description:
Modern short-read DNA sequencers can’t directly detect variants, e.g. insertions or deletions of nucleotides, larger than the read length. These larger “structural” variants (SV), which can cause numerous genetic diseases, must be inferred from secondary, probabilistic, signals in the sequencing data. The existing parametric models for these signals do not take into account sample, region and pipeline-specific biases, reducing the accuracy of SV genotyping. Instead we will pursue a non-parametric approach using detailed simulations of the sequencing process. Specifically we will be bringing up a prototype simulation pipeline on Middlebury computing resources, and refining that pipeline into a practical tool for genotyping putative SVs in a cohort of children with congenital heart defects. As part of that pipeline we will implement annotators for the different types of evidence for SVs from raw sequencing data.

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Enrollment in (or completion of) CS321 Bioinformatics Algorithms or other advanced algorithms course and strong programming skills.

Application Process:
Send your resume/CV including a list of relevant of coursework or other experience, the dates you will be available in Summer 2017, and a brief statement of interest to mlinderman@middlebury.edu.

Additional Information:
http://go.middlebury.edu/linderman

Please contact department regarding other potential opportunities.

 

Environmental Studies

Please contact program directly.

 

Geography

Please contact department directly.

 

Geology

Please contact department directly.

 

Mathematics

Please contact department directly.

 

Molecular Biology & Biochemistry

Please contact program directly.

 

Neuroscience

Please contact program directly.

 

Physics

Biomedical Optics (closed)

This position is currently unavailable.

Position Status:
inactive/closed/filled

Faculty or Staff Member:
Prof. Michael Durst

E-mail Address:
mdurst@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Biomedical Optics

Project Description:
I study two-photon microscopy, which uses lasers to image deep within scattering tissue. Students gain hands-on experience with laser beam alignment, fiber coupling, and the development of breadboard optical systems. In addition, students will have the opportunity to become fluent in Matlab, Mathematica, and LabVIEW programming languages in order to create beam propagation simulations and operate equipment.

Project Location(s):
MBH -- Biomedical Optics Lab

Session Dates:
summer

Eligibility and Requirements:
Students majoring in physics are preferred, but I welcome students from other departments and majors, including neuroscience, MBB, chemistry, and biology, to apply if they have taken PHYS 0241: Biomedical Imaging.

Application Process:
Contact Prof. Durst, introduce yourself, and get an application form. Applications are due by the end of February.

Additional Information:
http://sites.middlebury.edu/durst/

Casimir Forces from Scattering Theory

Position Status:
active/open/recruiting

Faculty or Staff Member:
Noah Graham

E-mail Address:
ngraham@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Casimir Forces from Scattering Theory

Project Description:
Building computational tools based on wave mechanics to predict quantum-mechanical Casimir forces in nanotechnology.

Project Location(s):
MBH, Physics Department

Session Dates:
summer

Eligibility and Requirements:
PHYS 0212 is essential; other PHYS courses also are helpful, especially PHYS 0111, 0202, 0301, 0302, and/or 0401

Application Process:
please contact Prof. Graham if interested

Launching Laser-Cooled Atoms

Position Status:
active/open/recruiting

Faculty or Staff Member:
Anne Goodsell

E-mail Address:
agoodsell@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Launching Laser-Cooled Atoms

Project Description:
This is fundamental research in atomic and optical physics; most of the work is primarily experimental, with some elements of theory and calculation. The interaction of laser light and atoms in a gas results in slow-moving atoms that we characterize and control.

Project Location(s):
MBH -- Goodsell Lab

Session Dates:
summer

Eligibility and Requirements:
Appropriate for students majoring or planning to major in Physics who complete Phys 202 before Summer 2016; some aspects require additional coursework

Application Process:
Submit a list of your relevant coursework, relevant experience, weeks when you're available for Summer 2016, and roughly 250 word statement of interest to agoodsell@middlebury.edu by March 20; more materials may be requested.

Additional Notes:
I encourage interested students to come introduce yourself to me before applying, but this is not required.

Please contact department regarding other potential opportunities.

 

Psychology

Please contact department directly.

 

Director of Sciences
Pat Manley
McCardell Bicentennial Hall 427
802.443.5430
manley@middlebury.edu

Science & Mathematics
Middlebury College
Middlebury, VT 05753
802.443.5000
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