Category Archives: Software

Improvements in scaling of Bowtie2 alignment software and implications for RNA-Seq pipelines

 This is a guest post by Adam Marko, an IT and Biotech Professional with 10+ years of experience across diverse industries What is Bowtie2? Bowtie2 is a commonly used, open-source, fast, and memory efficient application used as part of a … Continue reading

CryoEM takes center stage: how compute, storage, and networking needs are growing with CryoEM research

 This is a guest post by Adam Marko, an IT and Biotech Professional with 10+ years of experience across diverse industries Background and history Cryogenic Electron Microscopy (CryoEM) is a type of electron microscopy that images molecular samples embedded in … Continue reading

NVIDIA Datacenter Manager (DCGM) for More Effective GPU Management

Managing an HPC server can be a tricky job, and managing multiple servers even more complex. Adding GPUs adds even more power yet new levels of granularity. Luckily, there’s a powerful, and effective tool available for managing multiple servers or … Continue reading

One-shot Learning Methods Applied to Drug Discovery with DeepChem

Experimental data sets for drug discovery are sometimes limited in size, due to the difficulty of gathering this type of data. Drug discovery data sets are expensive to obtain, and some are the result of clinical trials, which might not … Continue reading

DeepChem – a Deep Learning Framework for Drug Discovery

A powerful new open source deep learning framework for drug discovery is now available for public download on github. This new framework, called DeepChem, is python-based, and offers a feature-rich set of functionality for applying deep learning to problems in … Continue reading

GPU-accelerated HPC Containers with Singularity

Fighting with application installations is frustrating and time consuming. It’s not what domain experts should be spending their time on. And yet, every time users move their project to a new system, they have to begin again with a re-assembly … Continue reading

More Tips on OpenACC Acceleration

One blog post may not be enough to present all tips for performance acceleration using OpenACC. So here, more tips on OpenACC acceleration are provided, complementing our previous blog post on accelerating code with OpenACC. Further tips discussed here are: … Continue reading

Can I use Deep Learning?

If you’ve been reading the press this year, you’ve probably seen mention of deep learning or machine learning. You’ve probably gotten the impression they can do anything and solve every problem. It’s true that computers can be better than humans … Continue reading

Deep Learning Applications in Science and Engineering

Over the past decade, and particularly over the past several years, Deep learning applications have been developed for a wide range of scientific and engineering problems. For example, deep learning methods have recently increased the level of significance of the … Continue reading

Accelerating Code with OpenACC and the NVIDIA Visual Profiler

Comprised of a set of compiler directives, OpenACC was created to accelerate code using the many streaming multiprocessors (SM) present on a GPU. Similar to how OpenMP is used for accelerating code on multicore CPUs, OpenACC can accelerate code on … Continue reading