Students Apply HPC to Explore Regenerative Crickets

By Oliver Peckham

March 18, 2021

They may not be powered by a major supercomputing center or a national lab, but at Bowdoin College – a private liberal arts college in southern Maine – biology students are putting HPC to good use. Using Bowdoin’s in-house HPC cluster, the team is delving into the genome of a noisy mainstay of American life: the common field cricket.

Specifically, the students’ objective is to generate the most complete transcriptome – the range of messenger RNAs (mRNAs) in a given tissue – of the field cricket to date: and moreover, to do it within just a few months. The cricket was chosen for its startling ability to “reorganize” its auditory system if one of its ears has been incapacitated, which the researchers hope might be partially explained through mRNA analysis.

The Bowdoin cluster. Image courtesy of Bowdoin.

Bowdoin’s in-house cluster, which has been continuously upgraded since its initial installation in 2008, currently stands at 1,192 CPU cores and 9 GPU nodes. The racks are housed at the FirstLight datacenter, which connects to Bowdoin via a fiber line. 

Bowdoin is an undergraduate-only college, so the students involved in the project are all relatively new to high-performance computational biology. The professor organizing the project – Hadley Horch, a professor of biology and neuroscience at Bowdoin – worked with the nearby Mount Desert Island Biological Laboratory (MDIBL) to have a few of their bioinformaticians join the students weekly via Zoom. When the time comes to prepare and run the jobs, they are assisted by Dj Merrill, director of high-performance computing at Bowdoin.

“This is the first time we’ve seen the three [Bowdoin, MDIBL and Bowdoin’s HPC] coming together to actively teach a class,” Merrill said in an interview with Bowdoin’s Rebecca Goldfine.

Once the initial work is completed – which they plan on taking around three weeks – the students will work on annotating and curating the transcriptome, as well as using wet-lab work to identify gene expression before and after the field crickets’ auditory rewiring process.

“They’ll pick one gene to focus on, dissect tissue and do measurements on that gene to see if it is up- or down-regulated as we predicted,” Horch said. “These two strands will come together nicely – the bioinformatics and the wet lab research—so students can see how you build this resource and how you play with it experimentally as well.”

“It is ambitious what we’re trying to do,” Horch added. “And we have more plans, too, after we build this.”

For the students, this kind of hands-on HPC experience in their undergraduate careers represents important skill development.

“I spoke to a few neuroscience PhD candidates and researchers recently, and one of the questions I asked was ‘what is a skill that you didn’t get in college do you wish you had?’” said Lucy O’Sullivan, a student at Bowdoin. “And a lot of them said gaining proficiency in computer coding, especially as technology advances, that you have to keep up with the technology.”

Read Rebecca Goldfine’s reporting here.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Supercomputer-Powered Climate Model Makes Startling Sea Level Rise Prediction

April 19, 2021

The climate science community is tasked with striking a difficult balance: inspiring precisely the amount of alarm commensurate to the climate crisis. Make estimates that are too conservative, and the public might not re Read more…

San Diego Supercomputer Center Opens ‘Expanse’ to Industry Users

April 15, 2021

When San Diego Supercomputer Center (SDSC) at the University of California San Diego was getting ready to deploy its flagship Expanse supercomputer for the large research community it supports, it also sought to optimize Read more…

GTC21: Dell Building Cloud Native Supercomputers at U Cambridge and Durham

April 14, 2021

In conjunction with GTC21, Dell Technologies today announced new supercomputers at universities across DiRAC (Distributed Research utilizing Advanced Computing) in the UK with plans to explore use of Nvidia BlueField DPU technology. The University of Cambridge will expand... Read more…

The Role and Potential of CPUs in Deep Learning

April 14, 2021

Deep learning (DL) applications have unique architectural characteristics and efficiency requirements. Hence, the choice of computing system has a profound impact on how large a piece of the DL pie a user can finally enj Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

AWS Solution Channel

Research computing with RONIN on AWS

To allow more visibility into and management of Amazon Web Services (AWS) resources and expenses and minimize the cloud skills training required to operate these resources, AWS Partner RONIN created the RONIN research computing platform. Read more…

Nvidia Aims Clara Healthcare at Drug Discovery, Imaging via DGX

April 12, 2021

Nvidia Corp. continues to expand its Clara healthcare platform with the addition of computational drug discovery and medical imaging tools based on its DGX A100 platform, related InfiniBand networking and its AGX developer kit. The Clara partnerships announced during... Read more…

San Diego Supercomputer Center Opens ‘Expanse’ to Industry Users

April 15, 2021

When San Diego Supercomputer Center (SDSC) at the University of California San Diego was getting ready to deploy its flagship Expanse supercomputer for the larg Read more…

GTC21: Dell Building Cloud Native Supercomputers at U Cambridge and Durham

April 14, 2021

In conjunction with GTC21, Dell Technologies today announced new supercomputers at universities across DiRAC (Distributed Research utilizing Advanced Computing) in the UK with plans to explore use of Nvidia BlueField DPU technology. The University of Cambridge will expand... Read more…

The Role and Potential of CPUs in Deep Learning

April 14, 2021

Deep learning (DL) applications have unique architectural characteristics and efficiency requirements. Hence, the choice of computing system has a profound impa Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

Nvidia Aims Clara Healthcare at Drug Discovery, Imaging via DGX

April 12, 2021

Nvidia Corp. continues to expand its Clara healthcare platform with the addition of computational drug discovery and medical imaging tools based on its DGX A100 platform, related InfiniBand networking and its AGX developer kit. The Clara partnerships announced during... Read more…

Nvidia Serves Up Its First Arm Datacenter CPU ‘Grace’ During Kitchen Keynote

April 12, 2021

Today at Nvidia’s annual spring GPU Technology Conference (GTC), held virtually once more due to the pandemic, the company unveiled its first ever Arm-based CPU, called Grace in honor of the famous American programmer Grace Hopper. The announcement of the new... Read more…

Nvidia Debuts BlueField-3 – Its Next DPU with Big Plans for an Expanded Role

April 12, 2021

Nvidia today announced its next generation data processing unit (DPU) – BlueField-3 – adding more substance to its evolving concept of the DPU as a full-fledged partner to CPUs and GPUs in delivering advanced computing. Nvidia is pitching the DPU as an active engine... Read more…

Nvidia’s Newly DPU-Enabled SuperPod Is a Multi-Tenant, Cloud-Native Supercomputer

April 12, 2021

At GTC 2021, Nvidia has announced an upgraded iteration of its DGX SuperPods, calling the new offering “the first cloud-native, multi-tenant supercomputer.” Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl Read more…

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Saudi Aramco Unveils Dammam 7, Its New Top Ten Supercomputer

January 21, 2021

By revenue, oil and gas giant Saudi Aramco is one of the largest companies in the world, and it has historically employed commensurate amounts of supercomputing Read more…

Quantum Computer Start-up IonQ Plans IPO via SPAC

March 8, 2021

IonQ, a Maryland-based quantum computing start-up working with ion trap technology, plans to go public via a Special Purpose Acquisition Company (SPAC) merger a Read more…

Leading Solution Providers

Contributors

Can Deep Learning Replace Numerical Weather Prediction?

March 3, 2021

Numerical weather prediction (NWP) is a mainstay of supercomputing. Some of the first applications of the first supercomputers dealt with climate modeling, and Read more…

Livermore’s El Capitan Supercomputer to Debut HPE ‘Rabbit’ Near Node Local Storage

February 18, 2021

A near node local storage innovation called Rabbit factored heavily into Lawrence Livermore National Laboratory’s decision to select Cray’s proposal for its CORAL-2 machine, the lab’s first exascale-class supercomputer, El Capitan. Details of this new storage technology were revealed... Read more…

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

African Supercomputing Center Inaugurates ‘Toubkal,’ Most Powerful Supercomputer on the Continent

February 25, 2021

Historically, Africa hasn’t exactly been synonymous with supercomputing. There are only a handful of supercomputers on the continent, with few ranking on the Read more…

AMD Launches Epyc ‘Milan’ with 19 SKUs for HPC, Enterprise and Hyperscale

March 15, 2021

At a virtual launch event held today (Monday), AMD revealed its third-generation Epyc “Milan” CPU lineup: a set of 19 SKUs -- including the flagship 64-core, 280-watt 7763 part --  aimed at HPC, enterprise and cloud workloads. Notably, the third-gen Epyc Milan chips achieve 19 percent... Read more…

The History of Supercomputing vs. COVID-19

March 9, 2021

The COVID-19 pandemic poses a greater challenge to the high-performance computing community than any before. HPCwire's coverage of the supercomputing response t Read more…

HPE Names Justin Hotard New HPC Chief as Pete Ungaro Departs

March 2, 2021

HPE CEO Antonio Neri announced today (March 2, 2021) the appointment of Justin Hotard as general manager of HPC, mission critical solutions and labs, effective Read more…

Microsoft, HPE Bringing AI, Edge, Cloud to Earth Orbit in Preparation for Mars Missions

February 12, 2021

The International Space Station will soon get a delivery of powerful AI, edge and cloud computing tools from HPE and Microsoft Azure to expand technology experi Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire