Linux Cluster Institute Workshop, Urbana, IL — Aug. 4-7

The Linux Cluster Institute (LCI) Workshop is scheduled for August 4-7 2014 at the National Center for Supercomputing Applications (NCSA), Urbana IL.

Aimed at HPC users and those responsible for maintaining HPC resources, the workshop will address:

  • How to be an HPC cluster system administrator
  • How to be an effective HPC cluster user
  • The key issues of HPC
  • Current and emerging HPC hardware and software technologies

Workshop: High-Performance Networking for International Climate Science — July 14-16, Boulder, CO

ESnet and Internet2 in collaboration with key partners Indiana University (IU), National Center for Atmospheric Research (NCAR) and NOAA have announced a multi-day workshop that will bring together network and data management experts with the international climate community to discuss their pressing data challenges and emerging network requirements. The workshop will include a slate of invited speakers and panelists in a format designed to encourage lively, interactive discussions with the goal of developing a set of tangible next steps for supporting this data-intensive science community. Breakout sessions and many opportunities for professional networking are also planned.

For more information, visit

EarthCube All-Hands Meeting — June 24-26, Washington, D.C.

The EarthCube All-Hands Meeting will bring together project institutions, partners, collaborators, and scientists from across the globe to share their progress and experience with EarthCube thus far, and discuss and plan activities for the upcoming year. This meeting will be held from June 24-26, 2014 at the Renaissance Dupont Circle hotel in Washington, D.C.  

This event is designed in the collaborative spirit of EarthCube and will provide multiple opportunities for networking and meaningful work, as well as the chance to share your efforts and to learn from others.

Register Now!
To learn more about the meeting and register, please visit the EarthCube All-Hands Meeting website (a registration fee of $180 will cover a light breakfast, lunch, and coffee breaks for all 3 days, as well as a reception on the evening of June 24th).

Call for Proposals
We are pleased to invite proposals for sessions for the All-Hands Meeting. Proposed sessions should relate to EarthCube, the state of cyberinfrastructure in the geosciences, and innovative geoscience contributions to data management. Sessions in multiple formats will be considered, including:

•    Workshops or Hack-a-thons
•    Technology Presentations
•    Working Groups & Business (Project) Meetings
•    Panel discussions (Plenary or Breakout)
•    Presentations

NVIDIA offering workshop and symposium on CUDA, OpenACC and GPU programming — May 20-21

NVIDIA will offer a workshop and symposium on May 20-21 on GPU programming and computing. The events will be held at 1180 Duderstadt Center.

Registration is required; click here to register.

Day 1: Tuesday, May 20, 9am – 4pm

Presenter: Dr. Jonathan Bentz

Beginner to Intermediate GPU Programming Hands On Workshop

A full day of hands-on exercises in GPU Computing where you will learn how to program GPUs via the use of CUDA, OpenACC Compiler Directives, and Libraries.

No previous GPU programming experience is required. However, beginner-level C and Linux experience will be expected.

Participants must bring their own laptop with wireless connectivity


  1. Introduction to OpenACC
  2. Introduction to CUDA
  3. Memory optimization techniques
  4. Using NVIDIA Profilers
Day 2: Wednesday, May 21st, 9 a.m. – 4 p.m.

GPU Computing Symposium

Live sessions and remote presentations where you will hear from fellow researchers focused on best practices and trends, tools, research findings discovered using GPU computing for computational research.

9 – 10 a.m., Tesla & CUDA Updates, Jonathan Bentz, Jon Saposhnik – NVIDIA

10 – 10:30 a.m., OpenACC Status, Doug Miles – NVIDIA PGI

10:30 a.m. – noon, GPUs in Life Sciences, Molecular Dynamics/Bioinformatics, Mark Berger – NVIDIA.
Invited Guest Speaker  Dr. Jens  Glaser, University of Michigan: ”Multi-GPU Molecular Dynamics with HOOMD-blue”

Noon -1 pm, Lunch & Invited Guest Speaker  Dr. Raghuram Thiagarajan, University of Michigan: “GPU Enabled Reverse-Engineering of Genome-Scale Biological Networks”

1 – 1:30 p.m., GPU Math Solvers/Libraries NVIDIA AmgX, Joe Eaton – NVIDIA,

1:30 – 2:15 p.m., GPUs in Engineering -  FEA, CFD, Stan Posey – NVIDIA

2:15 – 2:45 p.m., Tegra K1 & Jetson for Automotive, David Anderson – NVIDIA

3 p.m.,  CONCLUDE

NCSA Blue Waters hosting “Symposium for Petascale Science and Beyond” — May 12-15, Champaign, IL

Hosted by the National Center for Supercomputing Applications, the “Symposium for Petascale Science and Beyond” will bring together leaders in petascale computational science and engineering and will be a tremendous opportunity for sharing successes, methods, and future challenges in petascale+ computing and analysis.

The symposium is scheduled for May 12-15 in Champaign, IL.

Along with presentations from the leaders of Blue Waters science teams, the symposium will provide forums for high-bandwidth information exchanges between teams and investigators. Charles Seife, author of “Decoding the Universe: How the New Science of Information is Explaining Everything in the Cosmos, From Our Brains to Black Holes,” will deliver the keynote address.

There is no fee to attend the symposium, but there is limited space and capacity so registration is required. If necessary, priority will be given to Blue Waters science team members. Online registration, along with a draft agenda and logistics details, can be found on the Blue Waters portal:

TACC Summer Supercomputing Institute — May 2 application deadline

The 2014 Texas Advanced Computing Center (TACC) Summer Supercomputing Institute will take place Monday, June 16 – Friday, June 20, 2014.

Apply Now


This week-long workshop is appropriate for all levels of researchers, faculty, staff, and graduate students, from new users of advanced computing technologies, to those who have research projects requiring powerful
computing, visualization, storage, or software. We encourage participation from Minority Serving Institutions,
Hispanic Serving Institutions, and Historically Black Colleges and Universities.

  • Researchers across disciplines: Mathematics, Engineering, Physics, Astronomy, Astrophysics, Cosmology, Geology & Geophysics, Computer Sciences, Biosciences, Nanosciences, and Data Analytics
  • Graduate and undergraduate students
  • Current TACC & XSEDE users
  • Industrial affiliates


The Institute will provide researchers with an intensive introduction to using TACC’s computing resources.
Senior TACC staff will deliver presentations and lead interactive lab sessions focused on using TACC’s advanced computing resources and technology.

  • Stampede: Dell PowerEdge C8220 Cluster with Intel Xeon Phi coprocessors
  • Lonestar: Dell Linux Cluster
  • Maverick: HP/NVIDIA Interactive Visualization and Data Analytics System
  • Ranch: Petascale archival facility

On January 7, 2013 TACC deployed a new compute cluster, Stampede. Funded by the National Science Foundation, this new cluster provides the community with access to 2 PFlops of Intel based microprocessor power and 8 PFlops of Intel MIC (Many Integrated Core) architecture technology. During the Institute students will receive a description of the system and TACC staff will present a session on how to use the new MIC architecture.

Lectures and Labs: Senior TACC staff will deliver presentations and lead interactive laboratory sessions:

  • Obtaining access to TACC resources and services
  • Reviewing the hardware and software available on TACC resources
  • Developing parallel programs with OpenMP and MPI
  • Using visualization and data analysis software and systems
  • GPGPU programming
  • Using the Intel Xeon Phi coprocessor (MIC)

Applications Seminars: Leading computational researchers will discuss their work, including examples of how they are utilizing TACC’s resources.

Consulting: During the Institute, TACC staff will be available to assist participants in applying the techniques and technologies covered in the Institute to their own applications.

Applying to Attend the Institute

Applications to attend the Institute must be submitted by Friday, May 2, 2014. Applicants will receive notification of the status of their application by Friday, May 9, 2014.

Apply Now

SC14 conference fellowships available for PhD students — May 1 deadline

The ACM/IEEE-CS George Michael Memorial HPC Fellowship is now open for submissions from exceptional PhD students whose research focus is on high-performance computing applications, networking, storage, or large-scale data analysis using the most powerful computers that are currently available.

Recipients receive a $5000 honorarium, travel and registration for SC14, and recognition at the SC14 Awards Ceremony.

For more information, visit the SC14 site at:

Submit applications via:

Applications due: May 1, 2014

Vijay Pande of Stanford University to speak on “Surprises in the Biophysics of Protein Dynamics” — April 30

As part of the Michigan Institute for Computational Discovery and Engineering Seminar Series, Vijay Pande of Stanford University will speak on “Some Surprises in the Biophysics of Protein Dynamics: simulating conformation change of kinases and GPCRs with Folding@home.”

Date: Wednesday, April 30

Time: 4 p.m.

Location: 1311 EECS Building (1301 Beal Ave.)

Abstract: A major challenge in molecular simulation is reaching experimentally relevant timescales.  We have developed a new approach for simulating long timescale dynamics using the Folding@home distributed computing project coupled to Markov State Models (MSMs) methods which can overcome these key challenges.  I will demonstrate this method with applications to all-atom molecular simulations on the millisecond timescale and beyond, with applications to protein conformational change in disease-relevant drug targets of GPCRs and kinases.  In particular, these simulations reveal novel druggable targets with the potential for more selective kinase drugs as well as give insight into the fundamental mechanisms of how these key proteins operate.

Bio: Vijay Pande is currently the Director of the Program in Biophysics and a Professor of Chemistry and (by courtesy) of Structural Biology and of Computer Science at Stanford University.  Prof. Pande received a BA in Physics from Princeton University in 1992 and PhD in physics from MIT in 1995.  Prof. Pande’s current research centers on the development and application of novel grid computing simulation techniques to address problems in chemical biology.  In particular, he has pioneered novel distributed computing methodology to break fundamental barriers in the simulation of kinetics and thermodynamics of proteins and nucleic acids.

Data Visualization and Exploration Tools: April 29 – May 1 conference, Boston

The BioIT World Conference and Expo in Boston, scheduled for April 29 – May 1, will feature a Data and Visualization Tools Track. The track will showcase how to design, implement and evaluate visualization techniques and tools that offer real value to the user both in support of genomics and sequencing research, as well as in drug discovery and development. The conference will present case studies that showcase approaches to data visualization and analysis that address important challenges in genomics, pathway analysis, oncology and drug discovery.

The program includes:

Variant View: Visualizing Sequence Variants in their Gene Context
Tamara Munzner, Ph.D., Professor, Computer Science, University of British Columbia
The Variant View visualization tool supports variant impact assessment with an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently-prevalent genome browsers… Read More

A Compendium of Next-Generation Clustered Heat Maps for Interactive Exploration of TCGA Data
John N. Weinstein, M.D., Ph.D., Professor & Chair, Bioinformatics & Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center
The Cancer Genome Atlas (TCGA) program is generating comprehensive molecular profiles of more than 25 clinical tumor types, the first 12 of which have been incorporated into a Pan-Cancer project. One challenge is statistical analysis of the resulting profiles; a second is the visual detective… Read More

Making the UCSC Genome Browser Work for You
Robert Kuhn, Ph.D., Associate Director, UCSC Genome Browser, Center for Biomolecular Science and Engineering University of California, Santa Cruz
The UCSC Genome Browser provides visualization tools for a large genomic database spanning more than 100 animals. New features include a tool to analyze sequence variant data and hosting organisms not part of the UCSC infrastructure. Browser views of user data may be saved and shared… Read More

Visualizing the Broad Institute’s Connectivity Map
Bang Wong, Creative Director, Broad Institute of MIT & Harvard; Adjunct Assistant Professor, Art as Applied to Medicine, Johns Hopkins University School of Medicine
The CMap is a catalog of a gene-expression data generated by exposing cells to chemical and genetic modifiers. Depicting findings from this 26 trillion point dataset requires thoughtful decisions about data presentation. I will describe how we apply design principles to develop… Read More

Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform
Nils Gehlenborg, Ph.D., Research Associate, Center for Biomedical Informatics, Harvard Medical School
Data sets with dozens or hundreds of samples are now common in molecular biology and the development of visualization tools for such large and complex data sets requires extensive software infrastructure. To address these challenges, we have developed the Refinery Platform… Read More

Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy
Jeremy Goecks, Ph.D., Computational Biology Institute, George Washington University
Learn about how to use the popular, web-based Galaxy platform to analyze and visualize your high-throughput genomics data. Galaxy visualizations require only a web browser to use and no software or data downloads. Galaxy visualizations include a genome browser, Circos plot… Read More

NetGestalt: Integrating Multidimensional Omics Data over Biological Networks
Bing Zhang, Ph.D., Associate Professor, Biomedical Informatics, Vanderbilt University School of Medicine
Node-link diagram-based network visualization becomes inadequate as network size and data complexity increase. NetGestalt exploits the inherent hierarchical modular architecture of biological networks to achieve high scalability. It allows simultaneous presentation… Read More

Caleydo Entourage: Visualizing Relationships between Biological Pathways
Alexander Lex, Ph.D., Researcher, Harvard School of Engineering & Applied Sciences
This talk will introduce Entourage, a visualization technique for analyzing interrelationships between multiple related biological pathways. We use a novel technique – contextual subsets – to determine and present parts of other pathways that are relevant in the context of a focus pathway… Read More

Visit for a complete agenda. For registration, visit

Hands-on Workshop on Computational Biophysics in Pittsburgh — Application deadline April 28

MMBioS Hands-on Workshop on Computational Biophysics 2014

Dates: May 19-23, 2014

Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA

Application Deadline: April 28, 2014

This workshop will be presented by members of the Theoretical and Computational Biophysics Group ( from the University of Illinois at Urbana-Champaign and the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh. It will cover a wide range of physical models and computational approaches for the simulation of biological systems including ProDy, NAMD and VMD. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.

The workshop is designed for students and researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Participants are encouraged to bring their own laptop (laptop requirements) for use in workshop tutorial sessions but computer workstations are also available.

Workshop Instructors:

  • Klaus Schulten (UIUC)
  • Alek Aksimentiev (UIUC)
  • Ivet Bahar (University of Pittsburgh)
  • Chakra Chennubhotla (University of Pittsburgh)
  • Tim Lezon (University of Pittsburgh)

Registration fee for accepted participants*: $150 fee for students; $250 non-student academics; $350 all others. The fee is non-refundable. Housing in double rooms* at the University of Pittsburgh Ruskin Hall and all course materials will be provided. The workshop can neither fund nor arrange participant travel.

Due to space constraints, the workshop will be limited to 25 participants. Please contact Pat Sudac, at for any questions.

*Workshop provides double-occupancy room housing for workshop participants only. Those preferring a single room or any other arrangements (e.g., early arrival or late departure) need to arrange and pay for their own housing. Participants are responsible for any incidental charges related to their stay in the residence hall. Visa or waiver holders must provide documentation of their status so that hotel costs can be covered. Please consult our visa page for more information.