MIT: Independent Activities Period: IAP

IAP 2014 Activities by Category - Life Sciences: Hands-on

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A Look Inside the Human Brain

Dimitrios Pantazis, Director of MEG Lab

Enrollment: Limited: Advance sign-up required
Limited to 30 participants
Attendance: Participants welcome at individual sessions

Modern imaging technologies at MIT and MGH provide exciting new ways to understand the structure and function of the human brain. We will provide guided tours of our imaging facilities and show how we use these tools to look inside the brain. Our recently installed MEG scanner, capable of measuring magnetic fields a billionth of the magnetic field of earth, can record the simultaneous firing of thousands of cortical neurons as they form dynamic networks.  Our MRI scanners provide high resolution images of the human brain as subjects perform a wide range of perceptual and cognitive tasks. Our PET scanners can identify and localize specific molecules in the brain, revealing pathologies that may underlie many different brain disorders. TMS is a noninvasive method that uses electromagnetic induction to create weak electric currents and cause depolarization or hyperpolarization in the neurons of the brain. NIRS uses infrared light to illuminate tissue and infer brain activity through the diffusion and scattering of this light. We will introduce these technologies, offer lab tours and demonstrate data collection, and discuss their contribution to neuroscience and current projects at MIT and MGH.

Contact: Dimitrios Pantazis, 46-5147, 617 324-6292, PANTAZIS@MIT.EDU

Seminar on Magnetic Resonance Imaging

Jan/15 Wed 01:00PM-02:30PM 46-3015

Topics include MRI instrumentation, magnetic fields, safety, functional imaging with BOLD response, diffusion imaging, and others.

Anastasia Yendiki - Assistant Professor, Steven P Shannon - Operations Manager and MR Research Technologist, Sheeba Arnold Anteraper - MR Programmer, Atsushi Takahashi - Assistant Director, MR Physicist

A tour at the MRI Lab

Jan/17 Fri 11:00AM-12:00PM 46-1171

A tour at the MRI lab. Demo scan (finger tapping) and data analysis.

MRI Lab:

Steven P Shannon - Operations Manager and MR Research Technologist, Sheeba Arnold Anteraper - MR Programmer, Atsushi Takahashi - Assistant Director, MR Physicist

Seminar on Magnetoencephalography

Jan/22 Wed 01:00PM-02:30PM 46-3015

Electrophysiological basis of MEG signals; instrumentation; modeling; cortical rhythms; brain networks; combining MEG with fMRI, studying the human visual system. 

Dimitrios Pantazis - Director of MEG Lab, Yu-Teng Chang - Post-doctoral Associate, Radoslaw Cichy - Post-doctoral Associate

A tour at the MEG Lab

Jan/22 Wed 02:30PM-04:00PM 46-1147

A tour at the MEG Lab, demo scan and data analysis of an MEG experiment

MEG Lab:

Dimitrios Pantazis - Director of MEG Lab, Yu-Teng Chang - Post-doctoral Associate, Radoslaw Cichy - Post-doctoral Associate, Kleovoulos Tsourides - Research Associate

Seminar on Near Infrared Spectroscopy

Jan/24 Fri 01:00PM-02:30PM 46-3015

Near Infrared Spectroscopy (NIRS) instrumentation, principles of light scattering and absorption, imaging of oxygenated hemoglobin, NIRS applications.

Juliette Selb - Instructor

Seminar on Transcranial Magnetic Stim.

Jan/29 Wed 01:00PM-02:30PM 46-3015

Use of Transcranial Magnetic Stimulation to depolarize and hyperpolarize neurons of the brain, applications to treat depression and examine basic mechanisms of post-traumatic stress disorder and anxiety, among others.

Tommi Raij - Instructor

Seminar on Positron Emission Tomography

Jan/31 Fri 01:00PM-02:30PM 46-3015

Seminar on Positron Emission Technology. Introduction to PET technology and scanners at MGH; applications in tumor detection; brain metabolic activity; gene expression; neurological diseases, such as Alzheimer¿s and Parkinson¿s; pharmacology etc.

Quanzheng Li - Assistant Professor

BIOBASE Knowledge Library

Courtney Crummett, Bioinformatics and Biosciences Librarian

Jan/23 Thu 01:00PM-04:30PM 14N-132 DIRC, Lunch Provided

Enrollment: Unlimited: Advance sign-up required
Sign-up by 01/23

Interested in finding out what's known in the scientific literature about a particular gene, disease or drug? Want to apply that information to high-throughput data analysis? Interested in finding out about transcription factors related to your research? Learn to search the BIOBASE Knowledge Library (Proteome/TRANSFAC) by topic or multi-gene data sets. Lunch Provided!

Please register for this class.

Sponsor(s): Libraries, Biology
Contact: Courtney Crummett, 14S-134, 617 324-8290, CRUMMETT@MIT.EDU

Bioinformatics for Beginners

Courtney Crummett, Bioinformatics and Biosciences Librarian

Jan/08 Wed 03:00PM-04:30PM 14N-132 DIRC
Jan/10 Fri 10:00AM-11:30AM 14N-134 DIRC

Enrollment: Unlimited: Advance sign-up required
Attendance: Participants welcome at individual sessions

The National Center for Biotechnology Information (NCBI) Entrez family of databases is the foundation of knowledge for molecular level bioscience research. Class attendees will learn about the organization and interconnectedness of NCBI databases while focusing on several specific databases. The session is a hands-on practicum and an excellent starting point for people who are new to or curious about bioinformatics research tools. This session is offered twice covering the same material; participants welcome at either session. Registration required.

Wednesday January 8th 3-4:30PM Please register at:

Friday January 10th 10-11:30AM Please register at:

Sponsor(s): Libraries, Biology
Contact: Courtney Crummett, 14S-134, 617 324-8290, CRUMMETT@MIT.EDU

Get the most from your "omics" analysis: GeneGo MetaCore Software Training

Courtney Crummett, GeneGo Trainer

Jan/22 Wed 03:00PM-05:00PM 14N-132 DIRC

Enrollment: Unlimited: Advance sign-up required
Sign-up by 01/22

Attend this IAP session and learn how to use GeneGo, a bioinforamtics software tool licensed by MIT Libraries. GeneGo provides a solution for using "omics" gene lists to generate and prioritize hypotheses with MetaCore. Learn how to work with different types of data (genomics, proteomics, metabolomics and interaction data) beginning with how to upload gene lists and expression data. Use GeneGo software to: upload, batch upload, store, share and check data properties and signal distribution; extract functional relevance by determining the most enriched processes across several ontologies; emphasize the role of expression data in your analysis; visually predict experimental results, associated disease and possible drug targets; and compare data sets and work with experiment intersections. Please register. Need a GeneGo Account? Email

Sponsor(s): Libraries, Biology
Contact: Courtney Crummett, 14S-M48, x4-8290,

iGEM: Synthetic Biology IAP 2014

Katie Bodner, Kristjan Eerik Kaseniit, Kyle Lathem, Richard Nelson Hall, Brandon Nadres, Chamille Lescott

Enrollment: Apply online at:
Sign-up by 12/24
Attendance: Participants must attend all sessions
Prereq: 7.01x 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 to prepare you to join the MIT 2014 iGEM team!

iGEM is an international undergraduate competition in synthetic biology which MIT has competed in since 2004. To find out more about iGEM go to: and This is the special 10th anniversary of iGEM, and there will be a giant jamboree competition in Boston next November that will enable all teams to go directly to finals.

Through this hands-on class, you will go through the process of constructing DNA circuits, and by the end of IAP, you will create a bacterial lamp you can turn on and off! Guest lectures from synthetic biology professors and trips to local synthetic biology companies will supplement the curriculum.

No background experience is necessary, and all majors are welcome!

Send questions to

Visit to apply

Note: Times are roughly subject to change.

Sponsor(s): Biological Engineering
Contact: Katie Bodner, KBODNER@MIT.EDU

Lecture and Lab

Jan/13 Mon 11:00AM-05:00PM NE47
Jan/14 Tue 11:00AM-05:00PM NE47
Jan/15 Wed 11:00AM-05:00PM NE47
Jan/16 Thu 11:00AM-05:00PM NE47
Jan/17 Fri 11:00AM-05:00PM NE47
Jan/21 Tue 11:00AM-05:00PM NE47
Jan/22 Wed 11:00AM-05:00PM NE47
Jan/23 Thu 11:00AM-05:00PM NE47
Jan/24 Fri 11:00AM-05:00PM NE47

Introduction to Allopathy: The unique philosophy of non-alternative medicine

Dr. Louis Kuchnir, MD-PhD, MIT '87

Jan/31 Fri 06:00PM-07:00PM 4-163

Enrollment: Unlimited: No advance sign-up

Allopathic medicine is taught by the medical schools that award M.D. degrees. At its base, is the philosophy that medical therapy should be based on science. In this moderated discussion, we'll explore both the strengths and quirks of conventional medicine based on its foundation in the scientific method including peer review, controlled experimentation, and underpinnings in human biology. We'll also discuss how allopathic philosophy creates an antipathy toward euthanasia, prescribing placebo, integrating alternative therapies, etc. Finally, we'll consider the development of the standardized undergraduate, pre-medical core curriculum and extra-curriculars as prerequisites for studying medicine in an allopathic school. Preregistration requested on CareerBridge. 

For more information and to register visit CareerBridge at, click on the "Events" tab, and select "Info Session" from the "Category" drop-down menu.

Contact: Erin Scott, 12-185, 617-715-5328,

Learn to use IPA during IAP

IPA Trainer, Courtney Crummett

Jan/13 Mon 02:00PM-04:00PM 14N-132 DIRC

Enrollment: Limited: Advance sign-up required
Limited to 20 participants

Attend this introductory and hands-on training session and learn how to use Ingenuity Pathways Analysis (IPA), newly licensed by MIT Libraries and friends, for the analysis of your ‘omics data.  Build complete regulatory pictures and gain a better understanding of the biology underlying a gene expression.  Discover signaling cascades from predicted upstream regulators in your dataset.  Predict the effect of your gene expression changes on downstream biological processes and diseases. Interrogate networks and canonical pathways and generate hypotheses in the network or pathway. Please register for this event. Need an IPA account? Email

Sponsor(s): Libraries, Biology
Contact: Courtney Crummett, 14S-M48, x4-8290,

NIH Public Access Compliance Hands-on Working Session

Courtney Crummett, Biology and Biosciences Librarian

Jan/17 Fri 11:00AM-12:00PM 14N-132 DIRC

Enrollment: Unlimited: Advance sign-up required
Sign-up by 01/16

Missing a PMCID? Can't figure out why a paper isn't in compliance? Lost in NIH manuscript system? Join us for a problem solving session. 

This session is designed to provide an opportunity for hands on problem solving in the systems that need to be navigated in the process of submitting and authorizing manuscripts and reporting progress on NIH Funded Grants (eRA Commons; NIHMS, and MyNCBI). Please bring your NIH compliance problems to this session to work through together. Registration encouraged. 

Sponsor(s): Libraries
Contact: Courtney Crummett, 14S-134, 617 324-8290, CRUMMETT@MIT.EDU

The Lean Laboratory Startup

Dr John F. Carrier, Sloan School of Management

Jan/24 Fri 10:00AM-11:30AM E51-315

Enrollment: see eventbrite link below
Sign-up by 01/24
Limited to 80 participants


The Lean Laboratory Startup


Then The Lean Laboratory Startup is a must attend event for you!


In this session, we will look at how a few simple Continuous Improvement tools (5S and Value Stream Mapping) have been successfully applied in several laboratories at MIT. You'll learn how these simple techniques will have  immediate impact on the work in your lab today.  We will explain the rationale behind these techniques through the systems and psychological studies of several notable MIT faculty, including Jay Forrester, John DC Little, Ed Schein, Douglas McGregor, and Kurt Lewin.  


Finally, we'll present our “90 minute recipe” to assist you in kicking it off in your lab.  Come with your current “headaches” in your laboratories with the expectation that we can take control of where we work!

Pre-requisites: Curiosity 101 and Sense of Humor 202.

Sign up here:

Sponsor(s): Chemical Engineering
Contact: John Carrier, (617) 939-4396, JFCARRIE@MIT.EDU