October 24, 2008
-- Tao Yu

Location: Homewood Clark 110

Title: An introduction to Synthetic Biology and the iGEM competition

Abstract: Synthetic biology, a new discipline to "make biology easier to be engineered", is an emerging branch of biology in recent years. Though quite some researchers are participating the research in such a field, synthetic biology is still far from familiar to a broad range of investigators in biology, medicine and engineering scopes. iGEM, which is short for the international Genetically Engineered Machines competition, is an annual undergrad competition aiming to recruit more participants in the community of synthetic biology. Here, I would like to introduce you to some key concepts and typical research in synthetic biology, and share with you the great fun I had in the iGEM competition last year.

October 10, 2008
-- Suneil Hosmane

Location: Med Campus Talbot Library (Traylor 709)

Title: TBA

Abstract: Microfluidics has the potential to uncover mechanisms behind many neurodegenerative diseases by enabling engineers and scientists to recreate the diseased cellular microenvironment. By doing so, a repeatable, efficient, and quantitative approach can be taken to understand the neurobiology of disease in vitro. To this extent, we have developed a novel device platform that merges conventional macro-sized features with microfluidic technology to yield a hybrid device compatible with standard biological protocols. This device allows for numerous experimental modalities through the replication of a single master design using conventional polymethyldisiloxane (PDMS) soft lithography.


Laboratory: Biomedical Instrumentation and Neuroengineering Laboratory
http://www.jhu.edu/nthakor/

September 26 2008
-- Tri Ngo

A first year has stepped up and volunteered to present. How awesome is that?

Title: Stochastic White Matter Tractography

Abstract: Stochastic Tractography is a Bayesian approach for inferring nerve
fiber tract parameters from DTI (Diffusion Tensor Imaging) data. We
use this framework to calculate the posterior probability of the
existence of tracts given our observations. Additionally, the
Bayesian framework allows the algorithm to infer tracts which pass
through regions with uncertain fiber orientations, previously
unreachable by non-Bayesian methods, thereby revealing more details
about structural connectivity.

We have implemented the algorithm into the ITK medical image analysis
toolkit, an open source NIH supported medical image analysis toolkit.
Additionally we created a user interface which allows the program to
be integrated in the popular 3D Slicer medical image visualization
program. Finally we present some potential clinical studies for the
algorithm.
Location: Clark 110 Homewood

September 12 2008
-- Robert Jacques

Location: Med Campus Talbot Library (Traylor 709)

Title: Towards Real-Time Radiation Therapy:GPU Accelerated Superposition/Convolution

Abstract: We demonstrate the use of highly parallel graphics processing units (GPUs) to accelerate the Superposition/Convolution (S/C) algorithm to interactive rates while reducing the number of approximations. S/C first transports the incident fluence to compute the total energy released per unit mass (TERMA) grid. Dose is then calculated by superimposing the dose
deposition kernel at each point in the TERMA grid and summing the contributions to the surrounding voxels. The TERMA algorithm was enhanced with physically correct multi-spectral attenuation and a novel inverse formulation for increased performance, accuracy and simplicity. Dose deposition utilized a tilted poly-energetic inverse cumulative-cumulative kernel, with the novel option of using volumetric mip-maps to approximate solid angle ray-casting. Exact radiological path ray-casting decreased discretization errors. We achieved a speed-up of 34x-98x over a highly optimized CPU implementation.

Full Paper:
http://www.cse.buffalo.edu/hpmiccai/pdf/HPMICCAI2008-V1.pdf


Laboratory: The Computer Integrated Interventional Systems Laboratory
New page: http://ciis.lcsr.jhu.edu/Research
Old page: http://www.cisst.org/

Friday Sept 12 2008 at 5pm, Med Campus Talbot 709

Wow, that was a pretty fantastic FSSHH on Aug 13th. Great turnout -- I'd say 35 people or so, plus tons of first years. It was nice to have a happy hour after so many months off.

Next FSSHH is Friday Sept 12. Robert Jacques is giving the talk. Special thanks to him for volunteering, and thanks to John Issa for getting the refreshments.

STILL NEED VOLUNTEERS!

• We are looking for groups of 1-2 students to sign up to get the food
  and drinks for each week.
• NEED SPEAKERS! (20-30 minute informal talk) -- see schedule at right

Previous FSSHH

Friday Aug 13 2008 at 5pm, Homewood Clark 110

Super first-year (now second-year, I suppose) Laura Doyle is getting the food/drinks.

This is just a happy hour to get the ball rolling for this year. No seminar, though I may lock people in and not let them out until we get people committed to presenting and getting refreshments for the rest of the dates this semester.

Special invitation to the new incoming first-years! We are excited to meet you.

STILL NEED VOLUNTEERS!

• We are looking for one person to help Luke in scheduling FSSHH for the next year.
• We are looking for groups of 1-2 students to sign up to get the food
  and drinks for that week.
• NEED SPEAKERS! (20-30 minute informal talk) -- see schedule at right
  

The Future of FSSHH

We are looking for one person to help Luke in scheduling FSSHH for
the next year.

Tentative dates have been set, so responsibilities would include:
-- finding speakers for the scheduled dates
-- finding people to be in charge of getting food/drinks for the scheduled dates
-- reminding those people and the speaker about the happy hour as the
date approaches

We are looking for groups of 1-2 students to sign up to get the food
and drinks for that week.

Each happy hour a DIFFERENT group of 2 would be in charge of food/drinks and setup. This way more people could get involved, and they could get whatever they want (more variety from week to week). This has the added benefit that one person would not have to do everything (scheduling, purchasing, setting up) for the entire year.

Responsibilities include:
-- buying food and drinks
-- setting up the happy hour / cleaning up afterwards
-- make sure presenter has laptop and connector for projector
-- get reimbursed for expenses (simple process; ask Luke about it)
-- people who do the setup get to decide the location (med school / homewood)

Please see the tentative schedule below or at http://fsshh.blogspot.com/ and contact Luke (lukejohnson07@gmail.com) if you are interested in helping out. It is expected that many first-years would contribute by signing up to buy and setup for one of the days, and older year students would contribute by signing up to give a presentation.

However, if a first year wishes to present, that is great. If an older year wants to setup, fantastic.

Tentative Schedule for 2008

August 15
September 12
September 26
October 10
October 24
November 7
November 21