Numerical Analysis and Scientific Computing Commons^™

Snowmass 2021 Computational Frontier Compf4 Topical Group Report Storage And Processing Resource Access, W. Bhimji, D. Carder, E. Dart, J. Duarte, I. Fisk, R. Gardner, C. Guok, B. Jayatilaka, T. Lehman, M. Lin, C. Maltzahn, S. Mckee, M. S. Neubauer, O. Rind, O. Shadura, N. V. Tran, P. Van Gemmeren, G. Watts, B. A. Weaver, F. Würthwein

Holland Computing Center: Faculty Publications

The Snowmass 2021 CompF4 topical group’s scope is facilities R&D, where we consider “facilities” as the hardware and software infrastructure inside the data centers plus the networking between data centers, irrespective of who owns them, and what policies are applied for using them. In other words, it includes commercial clouds, federally funded High Performance Computing (HPC) systems for all of science, and systems funded explicitly for a given experimental or theoretical program. However, we explicitly consider any data centers that are integrated into data acquisition systems or trigger of the experiments out of scope here. Those systems tend to have …

Collaborative Computing Support For Analysis Facilities Exploiting Software As Infrastructure Techniques, Maria Acosta Flechas, Garhan Attebury, Kenneth Bloom, Brian Bockelman, Lindsey Gray, Burt Holzman, Carl Lundstedt, Oksana Shadura, Nicholas Smith, John Thiltges

Holland Computing Center: Faculty Publications

Prior to the public release of Kubernetes it was difficult to conduct joint development of elaborate analysis facilities due to the highly non-homogeneous nature of hardware and network topology across compute facilities. However, since the advent of systems like Kubernetes and OpenShift, which provide declarative interfaces for building fault-tolerant and self-healing deployments of networked software, it is possible for multiple institutes to collaborate more effectively since resource details are abstracted away through various forms of hardware and software virtualization. In this whitepaper we will outline the development of two analysis facilities: “Coffea-casa” at University of Nebraska Lincoln and the “Elastic …

Discovery And Characterization Of Small Molecule Rac1 Inhibitors, Jamie L. Arnst, Ashley L. Hein, Margaret A. Taylor, Nick Y. Palermo, Jacob I. Contreras, Yogesh A. Sonawane, Andrw O. Wahl, Michel M. Ouellette, Amarnath Natarajan, Ying Yan

Holland Computing Center: Faculty Publications

Aberrant activation of Rho GTPase Rac1 has been observed in various tumor types, including pancreatic cancer. Rac1 activates multiple signaling pathways that lead to uncontrolled proliferation, invasion and metastasis. Thus, inhibition of Rac1 activity is a viable therapeutic strategy for proliferative disorders such as cancer. Here we identified small molecule inhibitors that target the nucleotide-binding site of Rac1 through in silico screening. Follow up in vitro studies demonstrated that two compounds blocked active Rac1 from binding to its effector PAK1. Fluorescence polarization studies indicate that these compounds target the nucleotide-binding site of Rac1. In cells, both compounds blocked Rac1 binding …

Image Harvest: An Open-Source Platform For High-Throughput Plant Image Processing And Analysis, Avi C. Knecht, Malachy T. Campbell, Adam Caprez, David R. Swanson, Harkamal Walia

Holland Computing Center: Faculty Publications

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources …

Distributed Caching Using The Htcondor Cached, Derek J. Weitzel, Brian Bockelman, David Swanson

Holland Computing Center: Faculty Publications

A batch processing job in a distributed system has three clear steps, stage-in, execution, and stage-out. As data sizes have increased, the stage-in time has also increased. In order to optimize stage-in time for shared inputs, we propose the CacheD, a caching mechanism for high throughput computing. Along with caching on worker nodes for rapid transfers, we also introduce a novel transfer method to distribute shared caches to multiple worker nodes utilizing BitTorrent. We show that our caching method significantly improves workflow completion times by minimizing stage-in time while being non-intrusive to the computational resources, allowing for opportunistic resources to …

Boscor: Extending R From The Desktop To The Grid, Derek J. Weitzel, Jaime Frey, Marco Mambelli, Dan Fraser, Miha Ahronovitz, David Swanson

Holland Computing Center: Faculty Publications

In this paper, we describe a framework to execute R functions on remote resources from the desktop using Bosco. The R language is attractive to researchers because of its high level programming constructs which lower the barrier of entry for use. As the use of the R programming language in HPC and High Throughput Computing (HTC) has grown, so too has the need for parallel libraries in order to utilize computing resources.

Bosco is middleware that uses common protocols to manage job submissions to a variety of remote computational platforms and resources. The researcher is able to control and monitor …

Designs Of Fullerene-Based Frameworks For Hydrogen Storage, Yi Gao, Xiaojun Wu, Xiao Cheng Zeng

Holland Computing Center: Faculty Publications

No abstract provided.

Designs Of Fullerene-Based Frameworks For Hydrogen Storage, Yi Gao, Xiaojun Wu, Xiao Cheng Zeng

Holland Computing Center: Faculty Publications

No abstract provided.

Functional Evolution Of Plp-Dependent Enzymes Based On Active-Site Structural Similarities, Jonathan Catazaro, Adam Caprez, Ashu Guru, David Swanson, Robert Powers

Holland Computing Center: Faculty Publications

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can …

Isptm: An Iterative Search Algorithm For Systematic Identification Of Post-Translational Modifications From Complex Proteome Mixtures, Xin Huang, Lin Huang, Hong Peng, Ashu Guru, Weihua Zue, Sang Yong Hong, Miao Liu, Seema Sharma, Kai Fu, Adam Caprez, David Swanson, Zhixin Zhang, Shi-Jian Ding

Holland Computing Center: Faculty Publications

Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear …