‘Strategies in Biomedical Data Science’ Advances IT-Research Synergies

By Tiffany Trader

March 23, 2017

“Strategies in Biomedical Data Science: Driving Force for Innovation” by Jay A. Etchings (John Wiley & Sons, Inc., Jan. 2017) is both an introductory text and a field guide for anyone working with biomedical data, IT professionals and as well as medical and research staff.

Director of operations at Arizona State University’s Research Computing program, Etchings writes the primary motivation for the book was to bridge the divide “between IT and data technologists, on one hand, and the community of clinicians, researchers, and academics who deliver and advance healthcare, on the other.” As biology and medicine move squarely into the realm of data sciences, driven by the twin engines of big compute and big data, removing the traditional silos between IT and biomedicine will allow both groups to work better and more efficiently, Etchings asserts.

“Work in sciences is routinely compartmentalized and segregated among specialists,” ASU Professor Ken Buetow, PhD, observes in the foreword. “This segregation is particularly true in biomedicine as it wrestles with the integration of data science and its underpinnings in information technology. While such specialization is essential for progress within disciplines, the failure to have cross-cutting discussions results in lost opportunities.”

Aimed at this broader audience, “Strategies in Biomedical Data Science” introduces readers to the cutting-edge and fast moving field of biomedical data. The 443-page book lays out a foundation in the concepts in data management biomedical sciences and empowers readers to:

Efficiently gather data from disparate sources for effective analysis;

Get the most out of the latest and preferred analytic resources and technical tool sets; and

Intelligently examine bioinformatics as a service, including the untapped possibilities for medical and personal health devices.

A diverse array of use cases and case studies highlight specific applications and technologies being employed to solve real-world challenges and improve patient outcomes. Contributing authors, experts working and studying at the intersection of IT and biomedicine, offer their knowledge and experience in traversing this rapidly-changing field.

We reached out to BioTeam VP Ari Berman to get his view on the IT/research gap challenge. “This is exactly what BioTeam [a life sciences computing consultancy] is focused on,” he told us.  “Since IT organizations have traditionally supported business administration needs, they are not always equipped to handle the large amounts of data that needs to be moved and stored, or the amount of computational power needed to run the analysis pipelines that may yield new discoveries for the scientists. Because of this infrastructure, skills, and services gap between IT and biomedical data science, many research organizations spend too much time and money trying to bridge that gap on their own through cloud infrastructures or shadow IT running in their laboratories. I’ve spent my career bridging this gap, and I can tell you first hand that doing it correctly has certainly moved the needle forward on scientists’ ability to make new discoveries.”

Arizona State University’s director of operations for research computing and senior HPC architect Jay Etchings

Never lost in this far-ranging survey of biomedical data challenges and strategies is the essential goal: to improve human life and reduce suffering. Etchings writes that the book was inspired by “the need for a collaborative and multidisciplinary approach to solving the intricate puzzle that is cancer.” Author proceeds support the Pediatric Brain Tumor Foundation. The charity serves the more than 28,000 children and teens in the United States who are living with the diagnosis of a brain tumor.

To read an excerpt, visit the book page on the publisher’s website.

A listing of Chapter headings:

Chapter 1 Healthcare, History, and Heartbreak 7

Chapter 2 Genome Sequencing: Know Thyself, One Base Pair at a Time 27

Chapter 3 Data Management 53

Chapter 4 Designing a Data-Ready Network Infrastructure 105

Chapter 5 Data-Intensive Compute Infrastructures 163

Chapter 6 Cloud Computing and Emerging Architectures 211

Chapter 7 Data Science 235

Chapter 8 Next-Generation Cyberinfrastructures 307

Subscribe to HPCwire's Weekly Update!

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

Edge-to-Cloud: Exploring an HPC Expedition in Self-Driving Learning

April 25, 2024

The journey begins as Kate Keahey's wandering path unfolds, leading to improbable events. Keahey, Senior Scientist at Argonne National Laboratory and the University of Chicago, leads Chameleon. This innovative projec Read more…

Quantum Internet: Tsinghua Researchers’ New Memory Framework could be Game-Changer

April 25, 2024

Researchers from the Center for Quantum Information (CQI), Tsinghua University, Beijing, have reported successful development and testing of a new programmable quantum memory framework. “This work provides a promising Read more…

Intel’s Silicon Brain System a Blueprint for Future AI Computing Architectures

April 24, 2024

Intel is releasing a whole arsenal of AI chips and systems hoping something will stick in the market. Its latest entry is a neuromorphic system called Hala Point. The system includes Intel's research chip called Loihi 2, Read more…

Anders Dam Jensen on HPC Sovereignty, Sustainability, and JU Progress

April 23, 2024

The recent 2024 EuroHPC Summit meeting took place in Antwerp, with attendance substantially up since 2023 to 750 participants. HPCwire asked Intersect360 Research senior analyst Steve Conway, who closely tracks HPC, AI, Read more…

AI Saves the Planet this Earth Day

April 22, 2024

Earth Day was originally conceived as a day of reflection. Our planet’s life-sustaining properties are unlike any other celestial body that we’ve observed, and this day of contemplation is meant to provide all of us Read more…

Intel Announces Hala Point – World’s Largest Neuromorphic System for Sustainable AI

April 22, 2024

As we find ourselves on the brink of a technological revolution, the need for efficient and sustainable computing solutions has never been more critical.  A computer system that can mimic the way humans process and s Read more…

Shutterstock 1748437547

Edge-to-Cloud: Exploring an HPC Expedition in Self-Driving Learning

April 25, 2024

The journey begins as Kate Keahey's wandering path unfolds, leading to improbable events. Keahey, Senior Scientist at Argonne National Laboratory and the Uni Read more…

Quantum Internet: Tsinghua Researchers’ New Memory Framework could be Game-Changer

April 25, 2024

Researchers from the Center for Quantum Information (CQI), Tsinghua University, Beijing, have reported successful development and testing of a new programmable Read more…

Intel’s Silicon Brain System a Blueprint for Future AI Computing Architectures

April 24, 2024

Intel is releasing a whole arsenal of AI chips and systems hoping something will stick in the market. Its latest entry is a neuromorphic system called Hala Poin Read more…

Anders Dam Jensen on HPC Sovereignty, Sustainability, and JU Progress

April 23, 2024

The recent 2024 EuroHPC Summit meeting took place in Antwerp, with attendance substantially up since 2023 to 750 participants. HPCwire asked Intersect360 Resear Read more…

AI Saves the Planet this Earth Day

April 22, 2024

Earth Day was originally conceived as a day of reflection. Our planet’s life-sustaining properties are unlike any other celestial body that we’ve observed, Read more…

Kathy Yelick on Post-Exascale Challenges

April 18, 2024

With the exascale era underway, the HPC community is already turning its attention to zettascale computing, the next of the 1,000-fold performance leaps that ha Read more…

Software Specialist Horizon Quantum to Build First-of-a-Kind Hardware Testbed

April 18, 2024

Horizon Quantum Computing, a Singapore-based quantum software start-up, announced today it would build its own testbed of quantum computers, starting with use o Read more…

MLCommons Launches New AI Safety Benchmark Initiative

April 16, 2024

MLCommons, organizer of the popular MLPerf benchmarking exercises (training and inference), is starting a new effort to benchmark AI Safety, one of the most pre Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Leading Solution Providers

Contributors

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, codenamed Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Eyes on the Quantum Prize – D-Wave Says its Time is Now

January 30, 2024

Early quantum computing pioneer D-Wave again asserted – that at least for D-Wave – the commercial quantum era has begun. Speaking at its first in-person Ana Read more…

The GenAI Datacenter Squeeze Is Here

February 1, 2024

The immediate effect of the GenAI GPU Squeeze was to reduce availability, either direct purchase or cloud access, increase cost, and push demand through the roof. A secondary issue has been developing over the last several years. Even though your organization secured several racks... Read more…

GenAI Having Major Impact on Data Culture, Survey Says

February 21, 2024

While 2023 was the year of GenAI, the adoption rates for GenAI did not match expectations. Most organizations are continuing to invest in GenAI but are yet to Read more…

Intel Plans Falcon Shores 2 GPU Supercomputing Chip for 2026  

August 8, 2023

Intel is planning to onboard a new version of the Falcon Shores chip in 2026, which is code-named Falcon Shores 2. The new product was announced by CEO Pat Gel Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire