UROP Research Opportunities

The Undergraduate Research Opportunities Program (UROP) cultivates and supports research partnerships between MIT undergraduates and faculty. If you have any questions please contact tluongo@csail.mit.edu or take a look at the How to UROP at CSAIL document (pdf format).  

This program is available to MIT students only.


 

  • Cloud computing for bioinformatics.

    he recent increase in quantity and complexity of high-throughput sequencing has made high-performance distributed computing important. This UROP would involve helping to design and implement a flexible high-performance computing infrastructure that can utilize both high-memory local compute clusters along with massively parallel cloud computing instances. Existing framework in our lab consists of a preliminary hybrid cluster architecture that opportunistically utilizes amazon ec2 nodes, as well as analysis tools which have been created to utilize primarily ec2 nodes. Our goal is to...

    Posted date: April 05, 2013
  • Computational yeast genetics

    Exploration of algorithms for model systems genetics, focusing on yeast. This study will use new high-throughput data from multiple sources to examine the inner workings of the cell. Depending on student interest, the project could focus more on the genetic history of a large population or specific questions of transcriptional regulation in a few individuals.

    Contact: Professor David Gifford, gifford@csail.mit.edu

    Posted date: April 05, 2013
  • Grammatical structure in developmental protein/DNA binding

    Cells choose their identity as a result of combinatorial expression of proteins called transcription factors that bind to specific DNA sequences and turn on and off sets of genes. Our understanding of this cellular programming is rudimentary, but a more complete characterization could enable the conversion of one cell type into another with transformative therapeutic consequences. We have devised a machine learning technique that identifies the genomic binding location of a large number of transcription factors in a given cell state based on an experimental dataset called DNase-Seq, and we...

    Posted date: April 05, 2013
  • Mechanisms of master regulator hand-off during red blood cell development

    So-called master regulators are transcription factor proteins whose individual expression can effect a change in cell identity by either directly co-binding with other factors to target specific gene regulation sites, or through the activation of broad signaling pathways. However, what precipitates the transition from one master-regulated state to another is typically not as well understood. For example, during the developmental transition from hematopoietic stem cells to red blood cells the Gata2 master regulator gives way to Gata1, binding different genomic sites despite their...

    Posted date: April 05, 2013
  • Reference-free genomics

    2 Developing and measuring algorithms for improved genomic studies. This project will use recently collected data that can improve on the standard and monolithic reference genomes that are currently employed. This project will seek to advance beyond that limitation and measure possible improvements on a wide variety of important experimental techniques.

    Contact: Professor David Gifford, gifford@csail.mit.edu

    Posted date: April 05, 2013
  • From Mockup to Web App: Building the Next-Generation Web Template Language

    Faculty Advisor: David Karger
    Mentor(s): Ted Benson
    Contact e-mail: karger@mit.edu
    Research Area(s): Graphics and Human-Computer Interfaces
    Think web frameworks like Node and Backbone are cool? Then help us develop the future of web templates. We are working on a web template language ( http://www.treesheets.org/ ) that continues to have benefits long after the page is rendered, including: rich copy-and-paste of...

    Posted date: April 04, 2013
  • Information Scraps, Quick Notetaking, and Personal Information Organization

    Faculty Advisor: David Karger
    Contact e-mail: karger@mit.edu
    Research Area(s): Graphics and Human-Computer Interfaces
    Our lives are filled with small, random scraps of information that seem to have no natural home. Where do we put them, and how do we find them later? We've created List.it (Link ), a fast, lightweight browser extension for capturing and organizing such scraps. Listit has over 25,000 active users who have recorded...

    Posted date: April 04, 2013
  • Interactive Data Visualization for Everyone the Web

    Faculty Advisor: David Karger
    Contact e-mail: karger@mit.edu
    Research Area(s): Graphics and Human-Computer Interfaces
    Exhibit (Link ) is an open source Javascript library that helps non-programmers author and publish rich interactive data visualizations on the web. We use Exhibit to push the boundaries of web authoring without programming, with our ultimate goal being to enable end-users to WYSIWYG-author complete web applications. Exhibit has been adopted on over a thousand web sites by hobbyists, scientists, merchants, and journalists...

    Posted date: April 04, 2013
  • Interactive Data Visualization for Journalists using Wordpress

    Faculty Advisor: David Karger
    Contact e-mail: karger@mit.edu
    Research Area(s): Graphics and Human-Computer Interfaces
    There's a new movement in journalism to incorporate rich data visualization in news stories, but many journalists lack that skills to create their own "news apps" for this purpose. We've prototyped a data visualization framework, Datapress (Link ) to support authoring (not programming) such...

    Posted date: April 04, 2013
  • The Future Textbook

    Faculty Advisor: David Karger
    Contact e-mail: karger@mit.edu
    Research Area(s): Graphics and Human-Computer Interfaces
    Now that we can put textbooks on the web, how can we change them to make them better? How can we make them more dynamic, more adaptable to individual students, more sociable, or more informative? We've tackled some of these questions with Nb (Link ), tool that lets students hold forum-type discussions in the margins of their...

    Posted date: April 04, 2013
  • Transparent Web Browsing

    Faculty Advisor: David Karger
    Contact e-mail: karger@mit.edu
    Research Area(s): Graphics and Human-Computer Interfaces
    Nowadays, all sorts of shady companies are collecting information about your browsing activities and using it for their own mysterious purposes. How could that information be used to your benefit? We propose to build Eyebrowse, a web browser extension that gathers information about your web browsing activities and shares that information (under your control) with...

    Posted date: April 04, 2013
  • Grammatical structure in developmental protein/DNA binding

    Cells choose their identity as a result of combinatorial expression of proteins called transcription factors that bind to specific DNA sequences and turn on and off sets of genes. Our understanding of this cellular programming is rudimentary, but a more complete characterization could enable the conversion of one cell type into another with transformative therapeutic consequences. We have devised a machine learning technique that identifies the genomic binding location of a large number of transcription factors in a given cell state based on an experimental dataset called DNase-Seq, and we...

    Posted date: April 02, 2013
  • Mechanisms of master regulator hand-off during red blood cell development

    So-called master regulators are transcription factor proteins whose individual expression can effect a change in cell identity by either directly co-binding with other factors to target specific gene regulation sites, or through the activation of broad signaling pathways. However, what precipitates the transition from one master-regulated state to another is typically not as well understood. For example, during the developmental transition from hematopoietic stem cells to red blood cells the Gata2 master regulator gives way to Gata1, binding different genomic sites despite their...

    Posted date: April 02, 2013
  • Investigating Natural Language Tools for Artificial Intelligence.

    The Infolab seeks UROPs interested in investigating natural language tools for artificial intelligence. The Infolab works on question answering, parsing, generating, and more, using both symbolic and statistical techniques. Introductory projects range from integrating knowledge sources to expanding automated methods to creating user interfaces and APIs; continuing opportunities for more in-depth research are available.

    Contact: Boris Katz, boris@csail.mit.edu

    Posted date: March 28, 2013
  • Segmentation of organs at risk in Head and Neck CT scans

    Do you want to contribute to improving the life of patients with head and neck cancer? Help us to develop a better algorithm for the segmentation of organs at risk. The accurate segmentation allows designing radiotherapy treatment plans that expose organs at risk to low radiation dose, leading to improved quality of life after the treatment. The segmentation is performed on 3D computed tomography (CT) images. We apply machine learning techniques to assign labels to patches based on a repository of manually labeled images. Implementation is mainly done in MATLAB. Our main goal is to refine...

    Posted date: March 27, 2013
  • iDiary

    Imagine an automatic private diary that records your life. For example, it allows you to:

    - Manage your time and get statistics about the time you spent with specific friends, family, or places.

    - Search it for all the restaurants that you visited last year and send to your guest.

    - See where you celebrated every birthday of your life.

    - Publish parts of your auto autobiography to the world, and to your grandchildren in the future.

    Our group at DRL is developing solutions towards these goals
    based on collected data from smartphone sensors. We build...

    Posted date: March 26, 2013
  • Printable Robots

    The goal of this project is to build a variety of flexible robotic systems from scratch using planar fabrication techniques. These systems include a number of origami inspired foldable robots, and pneumatically actuated elastomeric soft robots. Made of flat plastic sheets, these robots carry their own custom flexible circuit boards. Our aim is to achieve general, easy, and simple techniques for printing functional machines, and demonstrate that a suite of devices can be created and programmed this way. Another goal is to enable wireless programming, communication, and remote control...

    Posted date: March 26, 2013
  • A development environment for mobile apps, education, and entrepreneurship

    The goal of this project is to build and test an integrated development environment where undergraduates can generate ideas for mobile applications, build prototypes, and refine these to the point where they could be the basis for launching new ventures. Students' initial design work will be done using App Inventor for Android, which enables rapid investigation of working prototype apps.

    One challenge in this project is to create extension mechanisms for App Inventor so that students can smoothly bridge from their initial prototyping work to more refined use of the Android SDK....

    Posted date: March 26, 2013
  • Project: To program a model of fly's visual tracking.

    We are looking for a UROP to program the simulated behavior of several artificial flies, interacting visually with each other. Each fly is described by a simple tracking system (Buelthoff, Poggio and Wehrhahn 1980; Wehrhahn, Poggio and Buelthoff 1982) which summarizes behavioral experiments in which individual real flies track and chase targets. The model for this behavior is suggested by M. Poggio and T. Poggio in their paper: Cooperative physics of fly swarms: an emergent behavior. A.I Memo No. 1512, C.B.C.L Paper No. 103 (1994). We expect the model to be programmed and hopefully also...

    Posted date: March 21, 2013
  • Video Magnification

    We are developing algorithms to manipulate temporal variations in videos, to reveal small imperceptible changes (check out this video, and read more about it here) as well as automatically remove distracting changes (see here).

    We are looking for a strong and motivated student to work closely with us on exploring potential applications. This includes trying out our methods with different kinds of data, such as medical images (fMRI), satellite imagery, seismic data and time-lapse videos, developing tools to facilitate the experiments, and potentially helping us tune and improve the...

    Posted date: March 14, 2013