IAP Independent Activities Period
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IAP 2012 Activities by Category

Life Sciences: Hands-on

BrainNavigator: Hands-On Introduction and Demo
Courtney Crummett
Thu Jan 19, 10-11:30am, 14N-132 (DIRC)

Enrollment limited: advance sign up required (see contact below)
Limited to 20 participants.
Single session event

BrainNavigator integrates accurate content and innovative tools to improve the productivity, efficiency and quality of research. It helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. Class attendees will learn how to access high resolution images, identify coordinates and calibrate those coordinates to their own animals, link their own images to BrainNavigator atlases, count cells using the cell marker tool, overlay schematic drawing onto atlas stained sections or their own images, and use the injection planner.

The session is a hands-on practicum. The training room has 20 PC terminals and a large table in the back for laptop use. Please register at http://libraries.mit.edu/sites/events/?p=349.
Web: http://libraries.mit.edu/get/brainnav
Contact: Courtney Crummett, 14S-134, x4-8290, crummett@mit.edu
Sponsor: Libraries
Cosponsor: Brain and Cognitive Sciences

Building Your Own Neuroscience Lab
Daniel Bendor, Carme Varela, Josh Siegle
Thu Jan 12, 19, 26, Feb 2, 03-06:00pm, 46-4062

Enrollment limited: advance sign up required (see contact below)
Signup by: 03-Jan-2012
Limited to 20 participants.
Participants requested to attend all sessions (non-series)

In this four-part course, you will learn how to build your own neuroscience lab, where you can collect data from living neurons, build a setup (from scratch) to collect behavioral data, and then analyze and plot this data in MATLAB. In the second class, you will have the opportunity to perform your own neural recordings in an anesthetized insect. In the third class, you will learn the basics of using an Arudino (http://www.arduino.cc), a microcontroller that allows you to control motors and sensors with your computer. Using the Arduino you will build a basic setup for running behavioral experiments. In the fourth class you will learn how to use MATLAB both for data analysis and to automate your experiments.

No previous experience in neuroscience, computer programming, or using MATLAB or an Arudino is required for this class. No purchase of equipment is required for this class.
Contact: Daniel Bendor, 46-5233, x2-1841, dbendor@mit.edu
Sponsor: Brain and Cognitive Sciences

High-level Visual Behaviors of the Fruit Fly Drosophila
Andrew Straw, Gadi Geiger, Tomaso Poggio
Mon-Fri, Jan 9-13, 17-20, 10am-02:00pm, 46-3189

Enrollment limited: advance sign up required (see contact below)
Limited to 20 participants.

Scientific background

The brain of a fly is capable of steering the animal through a complex environment at high relative speeds, avoiding stationary obstacles and moving predators. Because it is relatively easy to study how flies do this at several levels from the behavioral to the cellular, fly vision has long been recognized as an ideal system to address a fundamental question in neuroscience -- how does the distributed activity of neurons orchestrate animal-environment interactions to result in successful coordinated behavior? In this workshop we will investigate visual phenomena such as spatial attention and spatial working memory in flies. If successful, the results will inform future experiments using the molecular genetic toolbox of Drosophila to isolate the neural circuits involved and the relevant physiological mechanisms.

Applicants interested in participating in the workshop please e-mail Gadi at ggeiger@mit.edu before December 16 2011 to confirm their participation. The overview lecture will be free.
Web: http://bcs.mit.edu/BCS_IAP_2012.html
Contact: Gadi Geiger, 46-5162, x3-9646, gadi@AI.MIT.EDU
Sponsor: Brain and Cognitive Sciences

Intro to Synthetic Biology: Engineering Biological Circuits
Paul Muir, Andrew Yang, Ron Weiss
Mon-Fri, Jan 16-20, 23-27, 11am-05:00pm, TBD

Enrollment limited: advance sign up required (see contact below)
Signup by: 29-Dec-2011
Limited to 12 participants.
Participants requested to attend all sessions (non-series)
Prereq: 7.012 Preferred

Ever wonder if you could re-program cells to do whatever you wanted? With synthetic biology, the possibilities are endless!

Synthetic biology provides a unique opportunity to combine knowledge from electrical engineering, biological engineering, chemical engineering, and biology. In this class, through a combination of lectures and work in the lab you will learn many of the skills necessary for a UROP in biological engineering. This hands-on class will take you through the process of constructing DNA circuits, and by the end of IAP you will create an inducible baterial lamp!
Web: https://stellar.mit.edu/S/project/synbio-iap2011/
Contact: Paul Muir, Simmons 872, paulmuir@mit.edu
Sponsor: Biological Engineering

Practically Genomic
Charlie Whittaker, Paola Favaretto, Sebastian Hoersch, Courtney Crummett
Mon Jan 23, Wed Jan 25, Fri Jan 27, 11am-01:00pm, 14N-132

Enrollment limited: first come, first served
Limited to 20 participants.
Participants requested to attend all sessions (non-series)

Genomics, microarrays, and next generation sequencing have made biology research a highly quantitative field. As a result, most biologists must master computers and computational methods to effectively carry out their research. These sessions are designed to introduce students to some of the computational and bioinformatics tools and methods mandated by modern biological research. Practical and hands-on examples will be used to demonstrate some powerful aspects of the Unix operating system, more advanced Excel techniques, scripting with Perl and statistics with R. We will also introduce attendees to some of the many bioinformatics tools for genomics. Potential topics include the UCSC genome browser, GALAXY, IGV, Argo, GenePattern, Bioconductor and various functional annotation methods.
Web: http://rous.mit.edu/index.php/IAP_2012
Contact: Charlie Whittaker, 76-189B, x4-0337, charliew@mit.edu
Sponsor: David H. Koch Inst. for Integrative Cancer Researc
Cosponsor: Libraries

Repair of Basic Laboratory Equipment
Charles Moses
Wed Jan 11, Wed Jan 25, 06-08:00pm, 68-089

No enrollment limit, no advance sign up
Repeating event. Participants welcome at any session
Prereq: none

Sponsored by Graduate Women in Science.

Engineer Charles Moses will conduct a course on repair of laboratory equipment, geared toward but not limited to beginners. Equipment will include: electrophoresis units, spectrophotometers, motors on shakers and centrifuges, etc. General topics will also include: assessing the tools required to disassemble, fix and reassemble a piece of equipment; tool quality; and rational disassembly of equipment when the function of some component is not known. Bring broken equipment on which to practice. Session starts at 6:00 p.m. in Project Lab, room 089, Bldg 68.
Contact: Brenda Minesinger, 68-641, x3-4721, bminesin@mit.edu
Sponsor: Biology

Massachusetts Institute of Technology
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Last update: 7 Sept. 2011