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

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.

Gravitation waves detected, again!

June 15, 2016 in blog, blog-general, blog-technical, for_press, for_researchers, for_users, in_the_news, news, success_story, Testimonials

We congratulate the LIGO and Virgo collaborations to the second-ever observation of gravitational waves from colliding black holes.

SciNet is proud to have contributed to the computation of the waveform templates that were used in this latest discovery of LIGO. LIGO measured about 55 gravitational wave cycles for this new binary black hole system. This large number of cycles made detailed computations of the expected wave-shapes more important than for the first detected black hole merger that was announced in February.

Canada is a leader of numerical calculations of colliding black holes, research led by Professor Harald Pfeiffer, Canada Research Chair for Numerical Relativity and Gravitational Wave Astrophysics at the University of Toronto. Pfeiffer states: I am very grateful for the sustained support of the SciNet team during the last 7 years; their support and the access to computing time on SciNet’s supercomputers have been crucial for my research program and its profound contributions to the LIGO discovery.


Above: The in-spiral and collision of two black holes similar to GW151226. The top portion of the frame shows the horizons of the two holes, in this case, at the moment close to the merger of the black holes. The middle portion of the frame shows the gravitational waveform projected onto the LIGO Livingston detector. The bottom part shows the frequency of the gravitational waves, gradually increasing from about 35Hz to above 700Hz. For this system, LIGO could observe many more gravitational wave cycles than for the first discoved system (named GW150914).

Visualization done by University of Toronto Undergraduate student Aliya Babul & Prof. Harald Pfeiffer, within the SXS Collaboration/

Ernest Ho: Thanks for the excellent work

March 21, 2014 in Testimonials

Dear SciNet administrators,

If you are still into keeping track of SciNet supported publications, here is one of mine that just got published. Thanks for the excellent work of all the SciNet staff members! Your team is really one of the most important reasons why this paper is even possible!


Joachim Harnois-Deraps: Staff remarkable, generous and dedicated

July 9, 2013 in Testimonials

Dear SciNet staff,

I am writing this letter to thank you all for your dedicated effort in providing SciNet users with such an excellent support service.

I have been using you High Performance Computing systems since the very first year of production, and was always impressed by the amount of help I received from your programming staff.

Being at the University of Toronto for five years, I had the chance to have close contact with the staff, I had to opportunity to sit down about a dozen time with one of your experts, which would patiently help me with a wide variety of programming aspects. “I should have come here last year!!!” would I say to myself every time. Read the rest of this entry →

Gaetan Kenway: You guys really got it right

July 7, 2013 in Testimonials

Hi Scott

I just wanted to personally thank you for all your help over the past couple of years with all things Scinet. I just convocated and I am now working with Dr. Martins as a post-doc at the University of Michigan. After using a couple of over HPC systems down here I can honestly say you guys really got it right and run a top-notch HPC system.



Nicholas Roberts: Scientific Computing Course 2013

April 9, 2013 in Testimonials

Hi both [Jonathan and Ramses],

I would like to thank you both for a very informative course, one from which I have learnt a lot and which is already been useful in my work. I only wish I had had more time to devote to it.

Thanks again,


Victor Chernov: A goodbye and thank you message

July 25, 2012 in Testimonials

Hello guys

For the last two years I’ve been a post-doctoral fellow with Thomson’s group and a SciNet user. Now, when my fellowship has came to an end (don’t close my account just yet – I need to finish some things), I wanted to say goodbye. I also wanted to say that I’ve seen a lot of computer system admins and mangers, from both sides. I have to say that you guys are the best of all these. Really, until I started using SciNet, I have never realized that the computer people can be responsive, professional and nice – in the best case scenario I thought I needed to pick two out of three. I was wrong, and I can hardly think of any way that SciNet staff can be better. You were nice, responded fast and to the point, and didn’t show your annoyance with users that clearly haven’t read Wiki (which you maintained great). The courses that you offered were great and even the upgrades actually made life easier.

So, thank you for your work, and if you want to forward it to the people that are responsible for the funding – feel free. People that are responsible for the funding – SciNet staff does a wonderful job. Keep that in mind.

All the best


Steven Schramm: Very educational

April 10, 2012 in Testimonials

Hi Ramses and Jonathan,

Thank you very much for setting up the [Scientific Computing] course! It was very educational, and will almost certainly be very practical in my future research. Hopefully many others will benefit from it in future years!

Best Regards,


Cai Durbin: Thanks for all the help

April 10, 2011 in Testimonials

Hey guys,

I just wanted to send you a quick note to say thanks for all the help you’ve given me over the last few weeks. I managed to get all the data I needed for the presentation and I think it went ok.I couldn’t have done it without your quick replies and understanding, not to mention the reservation on the TCS!

Thank you!!


Régis Pomès: Appreciation for your efforts

February 9, 2011 in Testimonials

Dear SciNet staff:

On behalf of my entire lab, I would like to express my appreciation for your efforts to keep the SciNet cluster operational. As you know, we rely very heavily on SciNet for our research. We appreciate that sporadic service outages are unavoidable and should be expected. We are consistently impressed by the speed at which the SciNet GPC is restored to active service whenever an outage occurs and I wanted to let you know how much we appreciate all of your hard work. For this, my entire group thanks all SciNet staff, especially Ching-Hsing and Joseph, who I understand were up all night restoring the computer.


Régis Pomès