Volume 13, July 2016

Science Highlight

Using Beagle in an undergraduate biology course 

 

In addition to research, a core component of Beagle’s mission is education, as a hands-
on platform for introducing students in the biological sciences to quantitative methods 

and high performance computing. This past academic year, Beagle (in combination with 
the Research Computing Center’s cluster, “Midway”) was used in two undergraduate 
courses at the University of Chicago. Both of these two courses have attracted a large 
population of our students that have grown in numbers over years.

Multiscale Modeling of Biological Systems II (BIOS 106030): This course is the 
second part of the two-quarter long course that aims to introduce students majoring in 
quantitative sciences to elements of modern biology via quantitative modeling. It covers 
topics ranging from water solvation chemistry and amino acids, to the structure and 
function of proteins, DNA, and RNA. The students learned how to visualize 
macromolecules and measure their basic properties and to model their physical 
movements by means of molecular dynamic simulations running at university’s super 

computers.

Students in this course learned about high performance computing (HPC) via two 
lectures comprising an introduction to HPC and practical Linux by Lorenzo Pesce and 
Joe Urbanski from the Beagle team. Students also learned to use VMD 
(http://www.ks.uiuc.edu/Research/vmd/), a molecular visualization program for 
displaying, animating, and analyzing large biomolecular systems using 3D graphics and 
built-in scripting, and NAMD (http://www.ks.uiuc.edu/Research/namd/), a parallel 
molecular dynamics code designed for high-performance molecular dynamics 
simulation of large biomolecular systems. 

For their final project the students chose a protein system to simulate and analyze using 
NAMD and VMD packages. Students used a total of 360,000 core hours on their protein 
systems, and used Crerar Library’s Kathleen Zar room (part of the Research Computing 
Center’s facilities) to view the simulations in 3D. It was very pleasing to see the student 
fascinations when they saw the movements of their proteins at the atomistic detail. 
During finals week, students presented their results to the class and then submitted a 
write-up. 

Examples of final projects were:

 

 

 

Resouces:

 

Beagle Wiki

Get detailed usage information from 

the Beagle team

Beagle Support

Contact the Beagle experts for help

Globus

Get started moving files to/from 

Beagle using this fast service

Other CI resources

Learn about other computing 

resources available at the 

Computation Institute 

 

Intro to Beagle

September 14th, 10AM

Room 240A

at the Computation Institute of the 

University of Chicago

Topics will include:

General overview of Beagle2′s team 

and the Computation Institute

Overview of Beagle2′s Cray XE6 

system architecture

Basic access and navigation 

operations

Using compilers and applications

Appropriate use of local and network 

filesystems

Submitting jobs and monitoring jobs

Data transfer

Specific topics requested by users 

(e.g., using R or Matlab on Beagle2)

Beagle2 Events To learn more about 
Beagle2 trainings.

  

Training:

Esmael J. Haddadian

Beagle Wiki

Get detailed usage information from 

the Beagle team

Beagle Support

Contact the Beagle experts for help

Globus

Get started moving files to/from 

Beagle using this fast service

Other CI resources

Learn about other computing 

resources available at the 

Computation Institute 

 

Beagle2 Related Publications 

Z. Lou, J. Reinitz
Parallel simulated annealing using an 

adaptive resampling interval.

Parallel Computing; 53: 23-31

 

Searle Chemistry Laboratory
5735 South Ellis Avenue
Chicago, IL 60637 

Help E-Mail:

beagle-support@ci.uchicago.edu

Beage2 CI Website:

beagle.ci.uchicago.edu

 

 

An Introduction to Bioinformatics and Proteomics (BIOS 26120): This is a one-
quarter course devoted to understanding biological data and the models and 

computational techniques used to make sense of them. The course covered biological 
databases, algorithms for sequence alignment and phylogenetic tree building, and 
large-scale protein analysis techniques. Students learned how to use our in-house 
supercomputer facilities to process and analyze next generation sequencing (NGS) 
data.

Similarly, to the previous class, students received introductory HPC training including its 
application to the field of bioinformatics, how to practically use Beagle and its operating 
system. For their final project, students downloaded 1000 genomes raw NGS files, 
aligned raw NGS reads to the reference human genome, identified single nucleotide 
variant (SNV) and insertion-deletion (indel) mutations, and annotated these variants 
with biologically pertinent information. They then explored the annotated variants for 

their potential roles in human diseases. 

Overall students enjoyed using Beagle and Midway super computers as part of their 
coursework. "The HPC part of the class is useful because computation is a tool used by 
real researchers to make the discoveries studied in the rest of the class," one student 
said. "It’s as important as discussion of lab methods is to a Chemistry class." 

"The HPC aspect was the best part of the class," another student said. "While learning 
biological facts was interesting, it was through running the simulations that I feel I 
actually got some understanding of how computational biology is done, and it was fun 
to conduct a simulation on a protein of your own choosing. It wouldn't be possible if we 

didn't have access to a supercomputer large enough to allow each of us to run around 
40 hours of simulation." 
I am planning to use Beagle again in the coming academic year for the same classes. I 
am hoping to expand the educational role of Beagle with the support of Lorenzo and 
Joe.

 

R.C. Cockrell, M. E. Stack, G. An
Supercomputing ulcerative colitis-associated 
cancer simulations to bridge mechanism 
with epidemiology

Digestive Disease Week, San Diego, CA, 
5/21/2016

R.C.Cockrell,G. An
Characterizing the behavioral landscape of 

sepsis: supercomputing simulation of 40 
million in silico patients

Society of Critical Care Medicine Annual 
Congress, Orlando, FL 02/20/2016

R.C.Cockrell,G. An
Supercomputing sepsis simulations for in 
silico outcome prediction

Academic Surgical Congress 2016, 
Jacksonville, FL 02/03/2016

L. Waldron, J.D. Steimle, T.M. Greco et al.
The Cardiac TBX5 Interactome Reveals a 

Chromatin Remodeling Network Essential 
for Cardiac Septation

Developmental Cell 2016; 36(3), p262–275, 8 
February 2016

R.C.Cockrell,G. An
Investigating the development of ulcerative 

colitis-associated cancers through an agent-
based model

Academic Surgical Congress 2016, 
Jacksonville, FL 02/03/2016