Biowulf

A Computational Approach to Curbing Chemotherapy’s Side Effects

Study Identifies Compounds That Could Aid Body’s Removal of Toxic Cancer Drugs

computer binary code

When it comes to cancer, the treatment can sometimes feel worse than the disease. Not only do chemotherapy drugs cause grueling side effects, but certain products made by otherwise benign bacteria living in our digestive system can interfere with the body’s ability to get rid of those toxic chemicals. A new IRP study used a cutting-edge computational approach to help identify compounds that inhibit one of those meddling bacterial molecules, which could eventually lead to the creation of medications that reduce some of chemotherapy’s side effects.

The Virus vs the Machine

IRP Leverages Supercomputing to Combat Coronavirus

rows of computer servers

Over the past six months, a tiny virus has completely upended life in the United States and many other countries. To combat this microscopic threat, some IRP researchers have turned to a tool the size of a small building.

Biowulf, the NIH’s supercomputer, is supporting more than a dozen different IRP research projects focused on the novel coronavirus. As the world’s most powerful supercomputer solely dedicated to biomedical research, Biowulf allows scientists to analyze data and run simulations at unprecedented speed. Two weeks ago, a blog post described how IRP investigators are using Biowulf to elucidate the structure of the novel coronavirus and simulate how potential therapeutics might interact with it. Picking up where that post left off, this blog will explore the application of Biowulf to important questions about the spread of COVID-19 and the way that its genes, along with our own, might influence its impact on the body.

IRP Supercomputer Enables Rapid Response to Coronavirus

Biowulf Lends Massive Computing Power to NIH Research Efforts

rows of computer servers

Nations around the world are bringing every weapon in their arsenals to the fight against the COVID-19 pandemic: vaccines, new and existing therapeutics, personal protective equipment like face masks, and enough hand sanitizer to fill the Atlantic Ocean. The NIH community is contributing to this unprecedented effort with a tool that no other research institution can claim: Biowulf, the world’s most powerful supercomputer solely dedicated to biomedical research.

Plugging the Gaps in the Human Genome

Supercomputing Helps IRP Researchers Complete Our Genetic Blueprints

DNA sequence

While the Human Genome Project accomplished a remarkable feat in sequencing all the genes in the human genome, technological limitations still left significant swaths of our genetic blueprints unexplored. Recent advances in DNA sequencing are starting to fill in those gaps, but these new technologies require new computational tools to make sense of the data they generate. That’s where computer scientists like the IRP’s Adam Phillippy, Ph.D., come in.

Supercomputing Pushes Pregnancy Research Forward

mother with baby

Virtually all parents would agree that having kids is a massive undertaking, and not just after they’re born. Many couples struggle to conceive, and each year thousands of American women experience complications when giving birth. With the help of the NIH’s state-of-the-art supercomputer, Biowulf, IRP senior investigator Rajeshwari Sundaram, Ph.D., develops and refines statistical tools that can guide prospective parents and their doctors through these challenges.

Science by the Numbers: Modeling Complex Biological Processes

computer microchip with binary code

Science is a process of trial and error. Most successful research publications are preceded by at least a few false starts and perhaps weeks or even months of tinkering to get experiments to work. For IRP senior investigator Carson Chow, Ph.D., this process of testing and throwing out one potential solution after another is an essential part of his research, so much so that he may go through thousands of iterations before arriving at one that works. However, rather than test each approach himself, he leverages the IRP’s considerable computing power to considerably accelerate the process of sorting the wheat from the chaff.

Three Billion Base Pairs vs. One Powerful Computer

a stand of DNA

The human genome comprises roughly three billion base pairs and around 20,000 protein-coding genes, according to recent estimates. That’s a lot of information crammed into the tiny nucleus of a cell, and it doesn’t even include the many genes that do not produce a protein or the fact that most genes come in multiple flavors that vary in different individuals. Add to that the phenomenon of an identical gene being either more or less active in two different people and you can quickly end up with genomic datasets that would overload nearly any computer. Fortunately for IRP senior investigator Daniel Levy, M.D., the NIH IRP has one of the few computer systems in the world that can handle this mountain of information.

Top-of-the-Line Supercomputer Turbocharges NIH Research

Access to robust computing resources provides a critical foundation for advancing the wide variety of biomedical research taking place within the NIH’s Intramural Research Program (IRP). Whether performing molecular modeling simulations, generating whole-genome sequencing data, deducing the structures of biomolecules, or advancing drug discovery efforts, our ability to analyze large-scale biological and biomedical data strongly depends on our ability to employ computationally intensive approaches that produce interpretable results and advance translational efforts aimed at improving human health.

NIH's supercomputer, Biowulf

Labradors, Terriers, and Boxers — Oh My! IRP Researchers Delve Into Doggy DNA

two breeds of dog that have massively differing physical traits

For over a decade, my family shared our home with a short, fat beagle named Kayla Sue. She had big floppy ears, a tail as straight as an exclamation point, and a coat of fur that was a patchwork of white, brown, and black splotches. Her love of chasing small animals was matched only by her enthusiasm for eating, napping, and belly rubs. One of my best friends growing up, on the other hand, had a mean-spirited Dachshund named Rocky who would not let anyone outside his family touch his long, brown, sausage-shaped body. Meanwhile, one of my brother’s close childhood friends had two humongous, overly-friendly, black-and-brown German shepherds that would immediately bowl you over when you walked through the front door.

It doesn’t take a particularly sharp observer to notice that, despite being the same species, the more than 300 breeds of dog have remarkably different physical and behavioral traits. But what remains less clear even today are the specific biological roots that produce these widely varying attributes. And, perhaps more importantly, scientists seek to understand how learning about that immense diversity might help us improve the health of our canine companions – and ourselves.