Study on the role of mediator complex in gene expression in collaboration with SciNet

September 10, 2019 in for_press, for_researchers, frontpage, in_the_news, news, science, success_story, Testimonials

For the last two years, SciNet has been collaborating with PhD candidate Alejandro Saettone from the Fillingham lab from Ryerson University. One of the research projects, which also involved the group of Dr. Ronald Pearlman at York University, deciphered some aspects of the mediator complex’s role in transcription and gene expression using the model organism Tetrahymena thermophila. See the EurekAlert! story on the matter, or the original paper in Current Biology.

The collaboration of SciNet’s Dr. Marcelo Ponce and Alejandro Saettone led to the development of the RACS (“Rapid Analysis of ChIP-Seq data”) pipeline, which serves to analyze data obtained from Chromatin Immunoprecipation followed by next generation Sequencing experiments (ChIp-Seq for short). The paper on this computational pipeline has been recently accepted for publication in BMC BioInformatics. The RACS pipeline, a set of bash shell scripts and R scripts, is open-source software available as a git repository at https://bitbucket.org/mjponce/RACS.

The RACS pipeline has been quite fruitful, having already resulted in two papers where it was applied to data from the model organism Tetrahymena thermophila. The pipeline is expected to result in a few more papers analyzing further data, and there are plans to make it suitable to target more general cases.

Alejandro Saettone: “Our group was very fortunate to collaborate with Dr. Ponce from SciNet. He helped our lab to solve bioinformatic problems involving big data. With this collaboration, we were able to advance knowledge in chromatin remodeling and gene expression.”

Learn more about SciNet’s research and opportunities to establish research collaborations visiting our research website.

SciNet’s webinar on “Trends and Strategies in Advanced Research Computing Education”

January 16, 2019 in for_educators, for_press, in_the_news, news

SciNet was invited to present our latest findings (see https://www.scinet.utoronto.ca/scinet-research) about “Trends and Strategies in Advanced Research Computing Education” in a SIGHPC Education webinar.

This webinar was based on our recent publications:



Trends in Demand, Growth, and Breadth in Scientific Computing Training Delivered by a High-Performance Computing Center,
Journal of Computational Science Education vol 10(1) (2019).
R.Van Zon, M.Ponce, E.Spence and D.Gruner
Presented at the Fifth Workshop on Best Practices for Enhancing HPC Training and Education (BPHTE18) @ SC18
Bridging the Educational Gap between Emerging and Established Scientific Computing Disciplines,
Journal of Computational Science Education, vol 10(1) (2019).
M.Ponce, E.Spence, R.Van Zon and D.Gruner
Presented at the Workshop on Strategies for Enhancing HPC Education and Training (SEHET18) @ PEARC18


Scientific Computing, High-Performance Computing and Data Science in Higher Education,
Journal of Computational Science Education, vol 10(1) (2019).
arXiv version (2016).
M.Ponce, E.Spence, D.Gruner and R.Van Zon
Presented at the Workshop on Strategies for Enhancing HPC Education and Training (SEHET18) @ PEARC18

SciNet Receives HPCwire Award

December 6, 2018 in blog, for_press, for_researchers, for_users, frontpage, in_the_news, news, Road_to_Niagara, success_story

We are very proud that SciNet has received the 2018 HPCwire Editor’s Award for Best Use of HPC in Physical Sciences. The award was announced at the 2018 International Conference for High Performance Computing, Networking, Storage and Analysis (SC18), in Dallas, Texas.

SciNet used Lenovo and Mellanox technologies on the new Niagara cluster to create spatial resolution models of the Pacific Ocean, helping to validate ocean waves movement and to assist in global warming calculations. These calculations were performed by a team of scientists involving University of Toronto’s Prof. W. Richard Peltier, University of Michigan oceanographer Prof. Brian Arbic, and NASA JPL’s Dr. Dimitris Menemenlis. More on this calculation can be found here.

This calculation was part of the “early science” program of the Niagara supercomputer at the SciNet HPC Consortion. In this short period in March of 2018, a number of scientists were given the opportunity to perform “heroic” calculations. These large scale calculation were essential to test, to tune and to get Niagara ready for use as a Canada’s fastest national academic supercomputer.

HPCwire: SciNet Launches Niagara, Canada’s Fastest Supercomputer

March 9, 2018 in in_the_news, news, Road_to_Niagara

HPCwire reports on the launch on the new supercomputer Niagara at Scinet.

Launch of the Niagara Supercomputer at SciNet

March 5, 2018 in for_educators, for_press, for_researchers, for_users, frontpage, in_the_news, news, Road_to_Niagara

The Niagara supercomputer was officially launched on March 5th, 2018. We were honoured by the presence and remarks of Reza Moridi (Ontario Minister of Research, Innovation and Science), Nizar Ladak (Compute Ontario President and CEO), Dr. Roseann O’Reilly Runte (CFI President and CEO), Prof. Vivek Goel (Vice-president of Research and Innovation at the University of Toronto), and Prof. W. Richard Peltier (Scientific Director of SciNet).

SciNet’s CTO Daniel Gruner gave an overview of the new system:

Niagara is located at University of Toronto and operated by the university’s high-performance computing centre SciNet, but the system is open to all Canadian university researchers.

Niagara is the fastest computer system in the country and is able to run a single job across all 60,000 cores thanks to a high-performance network which interconnects all the nodes. For more information on the configuration, see here.

A time-lapse of the building of Niagara is available (part of SciNet’s YouTube channel):

This system is jointly funded by the Canada Foundation for Innovation, the Government of Ontario, and the University of Toronto.

ZDNet: Lenovo gives a boost to the Canadian supercomputer Niagara

March 5, 2018 in in_the_news

zdnet reports on the launch on the new supercomputer Niagara at Scinet.

International HPC Summer School 2018 in Ostrava, by SciNet, XSEDE, PRACE and Riken

December 22, 2017 in for_educators, for_researchers, for_users, frontpage, in_the_news, news

A High-Performance Computing Summer Institute
July 8-13, Ostrava, Czech Republic
Expenses-paid program
Apply by February 13, 2018
Website: http://ihpcss18.it4i.cz


Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States are invited to apply for the ninth International Summer School on HPC Challenges in Computational Sciences, to be held July 8 to 13, 2018, in Ostrava, in the Czech Republic, and hosted by the IT4Innovations National Supercomputing Centre.

Applications are due Feb 13, 2018. The summer school is organized by the Partnership for Advanced Computing in Europe (PRACE), the Extreme Science and Engineering Discovery Environment (XSEDE), the RIKEN Advanced Insti­tute for Computational Science (RIKEN AICS), and the SciNet HPC Consortium.

Leading computational scientists and HPC technologists from the U.S., Europe, Japan and Canada will offer instructions on a variety of topics and also provide advanced mentoring. Topics include:

  • HPC challenges by discipline
  • HPC programming proficiencies
  • Performance analysis & profiling
  • Algorithmic approaches & numerical libraries
  • Data-intensive computing
  • Scientific visualization
  • Canadian, EU, Japanese and U.S. HPC-infrastructures

The expense-paid program will benefit scholars from Canadian, European, Japanese and U.S. institutions who use advanced computing in their research. The ideal candidate will have many of the following qualities, however this list is not meant to be a “checklist” for applicants to meet all criteria:

  • Familiar with HPC, not necessarily an HPC expert, but rather a scholar who could benefit from including advanced computing tools and methods into their existing computational work
  • A graduate student with a strong research plan or a postdoctoral fellow in the early stages of their research efforts
  • Regular practice with parallel programming (i.e., student utilizes parallel programming generally on a monthly basis or more)
  • May have a science or engineering background, however, applicants from other disciplines are welcome provided their research activities include computational work.

Students from underrepresented groups in computing are highly encouraged to apply (i.e., women, racial/ethnic minorities, persons with disabilities, etc.). If you have any questions regarding your eligibility or how this program may benefit you or your research group, please do not hesitate to contact the individual associated with your region below.

Interested students should apply by February 13, 2018. Participation, meals and housing will be covered for the selected participants, also support for intercontinental travel will be given (contingent to funding).

Further information and application, see http://ihpcss18.it4i.cz.

Bursting Through Limits with Peta-Scale Storage at SciNet

December 11, 2017 in in_the_news

Scientific Computing reports on SciNet’s Burst Buffer storage setup for the upcoming Niagara cluster.

Deployment Collaboration With Lenovo Will Power Canada’s Largest Supercomputer Center

December 7, 2017 in in_the_news

HPCwire reports on SciNet’s deployement collaboration with Lenovo for the upcoming Niagara cluster.

SciNet supercomputer’s GPFS trick: We node what you did, burst buffer

December 7, 2017 in in_the_news

The Register reports on SciNet’s storage solution for the upcoming Niagara cluster.