The CSBG - LSU Gateway: Web based hosted gateway for computational system biology application tools from Louisiana state university

© 2018 Copyright held by the owner/author(s). Science gateways are identified as an effective way to publish and distribute software for research communities without the burden of learning HPC (High Performance Computer) systems. In the past, researchers were expected to have in-depth knowledge about using HPC systems for computations along with their respective science field in order to do effective research. Science gateways eliminate the need to learn HPC systems and allows the research communities to focus more on their science and let the gateway handle communicating with HPCs. In this poster we are presenting the science gateway project of CSBG (Computational System Biology Group - www.brylinski.org) of Department of Biological Sciences with Center for Computation & Technology at LSU (Louisiana State University). The gateway project was initiated in order to provide CSBG software tools as a service through a science gateway

The Event Horizon Telescope Science Gateway - Blackholes, High Throughput Computing, and User Experience Design

<p>The Event Horizon Telescope (EHT) recently used ten petabyte-scale observation data to construct the first images of black holes and 100 terabyte-scale simulation data to constrain the plasma properties around supermassive black holes. This work leveraged the Open Science Grid (OSG) high throughput resources provided by the Partnership to Advance Throughput Computing (PATh). While EHT has successfully utilized PATh to create the biggest black hole simulation library to date, the broad adoption of this resource for data processing has been slower. The sophisticated script/command-line-driven HTCondor environment creates barriers for less technical researchers, limiting PATh's reach and impact within the wider astronomy and science communities. In May of 2023, the Cyberinfrastructure Integration Research Center (CIRC) at Indiana University was awarded an NSF EAGER award to collaborate with EHT and PATh in implementing a targeted science gateway instance that will integrate three important EHT applications to leverage OSG within the Apache Airavata framework. The proposed session aims to introduce the project and present the progress of the design and development of the EHT Gateway, which will be underway during the Science Gateways 2023 Conference but has not started at the time of this paper submission.<br> </p&gt

Training and Workforce Development Through ScienceGateways: SEAGrid Use Case

<div><p>SEAGrid Science gateway is an infrastructure for computational science and engineering research and education primarily. It integrates computational chemistry application software and computational hardware resources and provides end to end environments with pre- and post- processing tools in a community oriented fashion. The environments are provided as web browser based interfaces and desktop clients where the former provides file upload and downloads required for computations while the latter provides molecular editors and graphical application input generation interfaces and output parsers to extract output components for visualization. The infrastructure is extensible such that other open tools can be integrated tightly or loosely. Such tools have been used in the classrooms for project oriented computational chemistry topics at undergraduate level. Here we discuss recent use of SEAGrid infrastructure for training and workforce development for computational chemistry, focused at Minority serving institutions.</p> </div

Experiences with managing data parallel computational workflows for High-throughput Fragment Molecular Orbital (FMO) Calculations

Fragment Molecular Orbital (FMO) calculations provide a framework to speed up quantum mechanical calculations and so can be used to explore structure-energy relationships in large and complex biomolecular systems. These calculations are still onerous, especially when applied to large sets of molecules. Therefore, cyberinfrastructure that provides mechanisms and user interfaces that manage job submissions, failed job resubmissions, data retrieval, and data storage for these calculations are needed. Motivated by the need to rapidly identify drugs that are likely to bind to targets implicated in SARS-CoV-2, the virus that causes COVID-19, we developed a static parameter sweeping framework with Apache Airavata middleware to apply to complexes formed between SARS-CoV-2 M-pro (the main protease in SARS-CoV-2) and 2820 small-molecules in a drug-repurposing library. Here we describe the implementation of our framework for managing the executions of the high-throughput FMO calculations. The approach is general and so should find utility in large-scale FMO calculations on biomolecular systems

Science Gateways with SciGaP Services

<p>The goal of the Science Gateways Platform as a service (SciGaP.org) project is to provide core services for building and hosting science gateways. Over the last two years, SciGaP services have been used to build and host over twenty science gateways. Hosted gateways include campus gateways that focus on providing cyberinfrastructure for university computing facilities, domain gateways that target a particular field of science, and science gateways that provide “software as a service” for newly developed applications. These gateways serve multiple purposes and audiences. Campus gateways seek to increase the efficient usage of campus computing facilities by a wider range of users for a diverse set of applications. Domain gateways leverage national cyberinfrastructure to deliver well-known scientific applications as services that target a specific field of research. Developers of new scientific applications who seek to make their software available to a larger audience without going through the traditional packaging, release, and support cycles for downloadable software constitute the third type of gateway. Supporting education and classroom usage as well as research is an important goal for all types of gateways.</p><div><br></div

Using Keycloak for Gateway Authentication and Authorization

<div> <div> <div> <div> <p>Establishing users’ identities before they access research infrastructure resources is a key feature of science gateways. With many science gateways now relying on general purpose gateway platform services, the challenges of managing identity-derived features have expanded to include authorization between science gateway tenants, middleware, and third party identity provider services. The latter include campus identity management systems. This paper examines the use of Keycloak as an implementation of an identity management system for Apache Airavata middleware, replacing our previous WSO2 Identity Server-based implementation. This effort raises larger issues that software-as-a-service communities should consider when embedding dependencies on third party software and services, including developing selection criteria and future-proofing systems. </p> </div> </div> </div> </div