Blog from January, 2012

Title: Large-Scale Multi-scale, Multi-Cell Simulations of Cancer Evolution and Toxicity using CompuCell3D
location: Room 1455A Biomedical and Physical Sciences Building (BPS)
Time: 11:00am on Thursday Feb 2nd

Abstract:
While modern biology faces a data deluge of molecular and genetic information, our ability to integrate this information to make biomedically meaningful predictions at the organ or organism level is still limited, because of the difficulty of predicting the emergent properties of large ensembles of cells from the cells’ molecular signatures. For the past 15 years, we have been developing computational tools and approaches to bridge the gap between molecule and physiological outcome. Our open-source CompuCell3D modeling environment enables rapid Python-scripted specification and refinement of complex biomedical simulations that combine subcellular molecular reaction kinetics models, the physical and mechanical behaviors of cells and the longer range effects of the extracellular environment. Such simulations are much easier to disseminate, support, share, test and reuse than classical low-level-code. I will illustrate two projects using CompuCell3D, the first, a collaboration with the US Environmental Protection Agency on toxicity effects in early embryonic development (which is a component of their CompTox project), the second, a collaboration with St. Judes hospital and others, on cancer evolution. Time permitting, I will briefly discuss our experience in training, outreach and standards setting, and the opportunities and issues in moving a project like CompuCell3D to a high-performance environment.

Biography:
Dr. Glazier received his B.A. in Physics and Mathematics from Harvard University and his M.S. and Ph.D. in Physics from the University of Chicago. His research focuses on experimental and computational approaches to pattern formation in embryology. He has held faculty appointments at the University of Notre Dame and Indiana University, Bloomington, where he is founding director of the Biocomplexity Institute, Professor of Physics and Adjunct Professor of Informatics and Biology

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Please join MathWorks for free MATLAB seminars on Wednesday, February 15, 2012.  Faculty, staff and students are all welcome to attend one or both sessions.
Parallel Computing and Medical Image Processing with MATLAB at Michigan State University
REGISTER now
INVITE a Colleague

Register for this seminar.
Agenda
9:30 a.m. – 12:00 p.m.

Session 1: Parallel Computing with MATLAB
Location: Brody Hall, Room 136

In this session you will learn how to solve computationally and data-intensive problems using multicore processors, GPUs, and computer clusters.  We will introduce you to high-level programming constructs that allow you to parallelize MATLAB applications and run them on multiple processors.  We will show you how to overcome the memory limits of your desktop computer by distributing your data on a large scale computing resource, such as a cluster.  We will also demonstrate how to take advantage of GPUs to speed up computations without low-level programming.


Highlights include:
Toolboxes with built-in support for parallel computing
Creating parallel applications to speed up independent tasks
Programming with distributed arrays to work with large data sets
Scaling up to computer clusters, grid environments or clouds
Employing GPUs to speed up your computations
1:30 p.m.  –  4:00 p.m.

Medical Image Processing with MATLAB
Location: Natural Sciences Building, Room 116

This seminar will be particularly valuable for anyone intending to use MATLAB to process, analyze and visualize medical images and video.  We will begin by showing you how to import, display and examine images in MATLAB.  We will then step you through series of examples designed to demonstrate how MATLAB can be used in a wide range of medical applications to explore ideas and automate your workflow.

Highlights include:

Quantification of tissue metastasis including workflow automation
Volume visualization from a brain MRI image stack
Measurement of vessel tortuosity
Video analysis and neural network-classification of a fluorescein angiogram

REGISTER now
INVITE a Colleague

Register for this seminar.
I hope you can join us. Please contact me with any questions at 508-647-7516 or angelo.damato@mathworks.com.

Sincerely,

Angelo D’Amato
Sr. Account Manager
MathWorks
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Title: Recent Adventures in Supernovae and Astrobiology
location: Room 1455A Biomedical and Physical Sciences Building (BPS)
Time: 11:00am on Monday January 30th

Abstract:
We'll explore the cyber-enabled frontier of exploding one or more white dwarf stars, and traverse a leading edge of astrobiology via the abundances of stars in the solar neighborhood.

Biography:
Frank Timmes is Director of the ASU Advanced Computing Center, Professor of Astrophysics in the School of Earth and Space Exploration, and a Scientific Editor for the Astrophysical Journal. He received his Bachelors degree in physics from UC Santa Barbara, and his Doctoral degree in Astronomy and Astrophysics from UC Santa Cruz. Frank has baled hay in San Diego, made power semiconductor devices in Silicon Valley, taught science at the School of the Art School of Chicago, bicycled across swaths of the America and Canada, and dabbled in weapons physics at Los Alamos. Frank enjoys cooking for his family, swimming, and baseball.

The next Mid-Morning Break topic is “Tips and Tricks for Shared Memory Parallelization: MKL, OpenMP and others”.  
The break is scheduled for Friday (January 27) from 10-11am in the new iCER Seminar Room (1445 BPS). More information and a schedule can be found at:

http://wiki.hpcc.msu.edu/display/Announce/HPCC+Mid-Morning+Break+Series

The Mid-Morning Break Series is designed to give users an opportunity to meet face-to-face with the HPCC and iCER staff. The staff will be giving a 10-20 minute presentation on topics of interest to users. The rest of the hour will be devoted to answering questions, trouble-shooting problems, and helping to connect individuals with others on campus who share similar research interests. We hope that you will encourage all members of your research team to participate in the HPCC Mid-Morning Breaks.

Look forward to seeing you there.

Please join MathWorks for free MATLAB seminars on Wednesday, February
15, 2012.  Faculty, staff and students are all welcome to attend one
or both sessions.

-Register now-

Register at www.mathworks.com/seminars/msu2012

-Agenda-

9:30 a.m. – 12:00 p.m.

Session 1: Parallel Computing with MATLAB

Location: Brody Hall, Room 136

In this session you will learn how to solve computationally and
data-intensive problems using multicore processors, GPUs, and computer
clusters.  We will introduce you to high-level programming constructs
that allow you to parallelize MATLAB applications and run them on
multiple processors.  We will show you how to overcome the memory
limits of your desktop computer by distributing your data on a large
scale computing resource, such as a cluster.  We will also demonstrate
how to take advantage of GPUs to speed up computations without
low-level programming.

Highlights include:

·         Toolboxes with built-in support for parallel computing

·         Creating parallel applications to speed up independent tasks

·         Programming with distributed arrays to work with large data sets

·         Scaling up to computer clusters, grid environments or clouds

·         Employing GPUs to speed up your computations

1:30 p.m.  – 4:00 p.m.

Medical Image Processing with MATLAB

Location: Natural Sciences Building, Room 116

This seminar will be particularly valuable for anyone intending to use
MATLAB to process, analyze and visualize medical images and video.  We
will begin by showing you how to import, display and examine images in
MATLAB.  We will then step you through series of examples designed to
demonstrate how MATLAB can be used in a wide range of medical
applications to explore ideas and automate your workflow.

Highlights include:

·         Quantification of tissue metastasis including workflow automation

·         Volume visualization from a brain MRI image stack

·         Measurement of vessel tortuosity

·         Video analysis and neural network-classification of a
fluorescein angiogram

I hope you can join us. Please contact me with any questions at
508-647-7516 or angelo.damato@mathworks.com.

Sincerely,

Angelo D’Amato

Sr. Account Manager

MathWorks
3 Apple Hill Drive
Natick, MA 01760
Direct: 508.647.7516
Fax: 508.652.8702
www.mathworks.com

Tutorials: learn how to get started with MATLAB and Simulink;

www.mathworks.com/academia/student_center/tutorials/

Webinars: learn more about using our products for specific
applications through online seminars;

www.mathworks.com/webinars

Connecting to hardware: learn more about using MATLAB and Simulink
with a variety of hardware platforms;

www.mathworks.com/academic/hardware-resources/

Parallel Computing: learn more about solving computational intensive
and data-intensive problems using multicore processors, GPU’s and
computers clusters;

www.mathwork.com/products/parallel-computing/?s_cid=global_nav

The next Mid-Morning Break topic is “Q and A: Rhel 6”. We will discuss the new generation Fermi cards now available at MSU, the architectures of our systems, and the basics of compiling GPGPU codes.
The break is scheduled for Friday (January 13) from 10-11am in the new iCER Seminar Room (1445 BPS). More information and a schedule can be found at:

http://wiki.hpcc.msu.edu/display/Announce/HPCC+Mid-Morning+Break+Series

The Mid-Morning Break Series is designed to give users an opportunity to meet face-to-face with the HPCC and iCER staff. The staff will be giving a 10-20 minute presentation on topics of interest to users. The rest of the hour will be devoted to answering questions, trouble-shooting problems, and helping to connect individuals with others on campus who share similar research interests. We hope that you will encourage all members of your research team to participate in the HPCC Mid-Morning Breaks.

Look forward to seeing you there.


Michigan State University was officially labeled a NVIDIA Teaching Center on Monday, January 9th.  The CUDA Teaching Center Program was created to encourage institutions to involve GPU Computing using CUDA in their curriculum.  As a new partner with NVIDIA, MSU will begin collaborating and may receive equipment and funding towards expanding education in GPU computing. 

The full announcement can be found on the NVIDIA page.

We have updated the default MATLAB version on HPCC to R2011b.