A5051814524- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Research Data Management Practices
- Immune Cell Function and Interaction
- Advanced Data Storage Technologies
- T-cell and B-cell Immunology
- vaccines and immunoinformatics approaches
- Cloud Computing and Resource Management
- Genetics, Bioinformatics, and Biomedical Research
- Parallel Computing and Optimization Techniques
- Advanced Sensor and Energy Harvesting Materials
- Immune Response and Inflammation
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Conducting polymers and applications
- Monoclonal and Polyclonal Antibodies Research
- Software System Performance and Reliability
- Analytical Chemistry and Sensors
- Reinforcement Learning in Robotics
- Biomedical and Engineering Education
- Protein Structure and Dynamics
- HIV Research and Treatment
- Biosensors and Analytical Detection
- Polydiacetylene-based materials and applications
Texas Advanced Computing Center
2013-2024
The University of Texas at Austin
2008-2018
Polypyrrole (PPy) is an inherently conducting polymer that has shown great promise for biomedical applications within the nervous system. However, to effectively use PPy as a biomaterial implant, it important understand and reproducibly control electrical properties, physical topography surface chemistry of polymer. Although there much research published on in various applications, no systematic study linking methodologies used synthesis PPy's basic polymeric properties (e.g.,...
CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven since 2010s. As technology landscape evolved with emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse enabled access by providing interfaces, Software as Service (SaaS), cloud-native Infrastructure Code (IaC) to leverage new technologies. services enable researchers integrate...
Background: Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive response dynamics various states health and disease. Immune produces large, highly complex data sets, however, which require specialized methods software tools their effective analysis interpretation. Results: VDJServer is a cloud-based portal sequence that provides access to suite complete workflow, including modules pre-processing quality...
We report the discovery of a novel small-molecule inhibitor dengue virus (DENV) protease (NS2B-NS3pro) using newly constructed Web-based portal (DrugDiscovery@TACC) for structure-based virtual screening. Our drug portal, an extension screening studies performed IBM's World Community Grid, facilitated access to supercomputer resources managed by Texas Advanced Computing Center (TACC) and enabled druglike commercially available libraries be rapidly screened against several high-resolution DENV...
The Agave Platform first appeared in 2011 as a pilot project for the iPlant Collaborative [11]. In its two years, Foundation saw over 40% growth per month, supporting 1000+ clients, 600+ applications, 4 HPC systems at 3 centers across US. It also gained users outside of plant biology. To better serve needs general open science community, we rewrote scalable, cloud native application and named it Platform. this paper present Platform, Science-as-a-Service (ScaaS) platform reproducible...
Abstract CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven since 2010s. As technology landscape evolved with emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse enabled access by providing interfaces, Software as Service (SaaS), cloud-native Infrastructure Code (IaC) to leverage new technologies. services enable researchers integrate...
Petascale computing systems have enabled tremendous advances for traditional simulation and modeling algorithms that are built around parallel execution. Unfortunately, scientific domains using data-oriented or high-throughput paradigms difficulty taking full advantage of these resources without custom software development. This paper describes our solution rapidly developing parametric studies sequential threaded tasks: The launcher. We detail how to get ensembles executing quickly through...
Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input downstream analysis. VDJPipe a flexible, high-performance tool that can perform multiple pre-processing tasks with just single pass over the files.Processing provided by include base composition statistics calculation, read filtering, homopolymer length and nucleotide paired-read merging, barcode demultiplexing, 5' 3' PCR primer matching, duplicate reads collapsing....
In the USA, national cyberinfrastructure refers to a system of research supercomputer and other IT facilities high speed networks that connect them. These resources have been heavily leveraged by scientists in disciplines such as energy physics, astronomy, climatology, but until recently they little used biomedical researchers. We suggest many 'Big Data' challenges facing medical informatics community can be efficiently handled using national-scale cyberinfrastructure. Resources Extreme...
The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. full set of an individual at single point time is referred to as repertoire. recombination distinguishing feature adaptive immunity enables effective responses against essentially infinite array...
Abstract Motivation Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments cover all possible combinations perturbations is infeasible. In this paper, we present the host model (HRM), a machine learning approach that maps single transcriptional combination Results The HRM combines high-throughput sequencing with infer links between experimental context, prior knowledge cell regulatory networks,...
In order to increase support for diverse projects amongst a wide range of research areas in accessing advanced computational and data resources, both local national, the University Hawai'i at Manoa (UH) Melbourne, Australia (Melbourne) partnered with Texas Advanced Computing Center (TACC) utilize Agave platform. However, due distance unique geographical locations it was necessary setup platform instances provide responsive robust middleware against which flexible science gateways could be...
Beginning with the initial release of DesignSafe JupyterHub in late 2015, TACC has been building and maintaining custom clusters for research groups across different domains science engineering. Today, maintains five production systems utilizing over half a terabyte memory hundreds CPU cores supporting nearly 1,600 unique users combined. In this paper, we describe our approach to these cyberinfrastructure projects collaborative integrating Jupyter into communities. For two such groups,...
Containers are becoming essential to support the diversity of scientific computing workloads at academic centers. Here, we offer perspectives and experiences from Texas Advanced Computing Center on: installation, configuration, select containerization platforms; incorporation containers into module system improve their discoverability usability; facilitation advanced use cases including MPI containers, GPU for multiple instruction set architectures; finally on best practices end users...
Software containers are an important common currency for portability and reproducibility in the modern world of computing. While they easy to share through public registries, usage documentation is often lacking, effectively leaving users with black boxes. RollingGantryCrane (RGC) open-source tool that takes generic software automatically exposes internal LMOD environment modules. Users provide container URLs wish use, RGC pulls containers, collects descriptive metadata from repositories,...
Abstract Despite the importance and widespread application of detailed antigen receptor repertoire profiling via high-throughput sequencing, there is currently no suite software tools for seamless, reproducible analysis sequence data. Tools exist only a subset tasks. They do not function together are difficult to reuse without modification that requires bioinformatics expertise. This leaves researchers perform repetitive error-prone tasks by hand, develop internal, idiosyncratic algorithms...
UT Austin-Portugal Program, a collaboration between the Portuguese Foundation of Science and Technology University Texas at Austin, award UTA18-001217
Virtual screening is a key step of the drug discovery process which utilizes computational resources to simulate behavior small molecules in binding site target protein. [13] Researchers often test millions when searching for an early hit compound, requiring significant CPU hours. An accessible, convenient, fast, and computationally efficient means virtual desirable order researchers conserve phase discovery. We developed application programming interface (API) integrated workflow that...
Abstract Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments cover all possible combinations perturbations is infeasible. In this paper, we present the host model (HRM), a machine learning approach that takes cell single as input predicts whole transcriptional combination inducers. We find HRM able qualitatively predict directionality dysregulation inducers with an accuracy >90% using data...
Abstract VDJServer is a comprehensive, web-accessible system for analysis of immune repertoire sequencing data. provides complete workflow from pre-processing sequence reads, to V(D)J assignment, characterization and comparison. Recent enhancements in include: --Automatic parallelization tools handle very large data sets running on high-performance supercomputer--Import export subject sample metadata. User-defined groups allows sophisticated group comparison.--Extensive functionality such as...