arXiv subjects

Sandra Gesing

Publications and source records attributed to Sandra Gesing.

14 recordsLinked to original sources

arXiv2025

Report of the 2025 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science

This report summarizes insights from the 2025 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science, which convened more than 40 experts from national laboratories, academia, industry, and community organizations to chart a path toward more powerful, sustainable, and collaborative scientific software ecosystems. To address urgent challenges at the intersection of high-performance computing (HPC), AI, and scientific software, participants envisioned agile, robust ecosystems built through socio-technical co-design--the intentional integration of social and technical components as interdependent parts of a unified strategy. This approach combines advances in AI, HPC, and software with new models for cross-disciplinary collaboration, training, and workforce development. Key recommendations include building modular, trustworthy AI-enabled scientific software systems; enabling scientific teams to integrate AI systems into their workflows while preserving human creativity, trust, and scientific rigor; and creating innovative training pipelines that keep pace with rapid technological change. Pilot projects were identified as near-term catalysts, with initial priorities focused on hybrid AI/HPC infrastructure, cross-disciplinary collaboration and pedagogy, responsible AI guidelines, and prototyping of public-private partnerships. This report presents a vision of next-generation ecosystems for scientific computing where AI, software, hardware, and human expertise are interwoven to drive discovery, expand access, strengthen the workforce, and accelerate scientific progress.

cs.CE↗

arXiv2023

Unleashing quantum algorithms with Qinterpreter: bridging the gap between theory and practice across leading quantum computing platforms

Quantum computing is a rapidly emerging and promising field that has the potential to revolutionize numerous research domains, including drug design, network technologies and sustainable energy. Due to the inherent complexity and divergence from classical computing, several major quantum computing libraries have been developed to implement quantum algorithms, namely IBM Qiskit, Amazon Braket, Cirq, PyQuil, and PennyLane. These libraries allow for quantum simulations on classical computers and facilitate program execution on corresponding quantum hardware, e.g., Qiskit programs on IBM quantum computers. While all platforms have some differences, the main concepts are the same. QInterpreter is a tool embedded in the Quantum Science Gateway QubitHub using Jupyter Notebooks that translates seamlessly programs from one library to the other and visualizes the results. It combines the five well-known quantum libraries: into a unified framework. Designed as an educational tool for beginners, Qinterpreter enables the development and execution of quantum circuits across various platforms in a straightforward way. The work highlights the versatility and accessibility of Qinterpreter in quantum programming and underscores our ultimate goal of pervading Quantum Computing through younger, less specialized, and diverse cultural and national communities.

quant-ph↗

arXiv2022

The Science Gateway Community Institute's Consulting Services Program: Lessons for Research Software Engineering Organizations

The Science Gateways Community Institute (SGCI) is an NSF Software Infrastructure for Sustained Innovation (S2I2) funded project that leads and supports the science gateway community. Major activities for SGCI include a) sustainability training, including the Focus Week week-long course designed to help science gateway operators develop sustainability plans, and the Jumpstart virtual short-course; b) usability and user experience consulting; c) a community catalog of science gateways and science gateway software; d) workforce development activities, including a coding institute for students, internship opportunities, and hackathons; e) an annual conference; and f) in-depth technical support for client gateway projects. The goals of SGCI's Embedded Technical Support component are to help the institute's clients to create new science gateways or to significantly enhance existing science gateways. Examples of the latter include helping to implement major new capabilities and to implement significant usability improvements suggested by SGCI's usability consultants. The Embedded Technical Support component was managed by Indiana University and involved research software engineers at San Diego Supercomputer Center, Texas Advanced Computing Center, Indiana University, and Purdue University (through 2019). Since 2016, the component has involved 20 research software engineers as consultants and has conducted 59 client consultations. This short paper provides a summary of lessons learned from the Embedded Technical Support program that may be useful for the research software engineering community.

cs.SE↗

arXiv2021

Biologists need modern data infrastructure on campus

Modern tools for biological research, especially microscopy, have rapidly advanced in recent years, which has led to the generation of increasingly large amounts of data on a regular basis. The result is that scientists desperately need state-of-the-art technical infrastructure for raw data storage, transfer, and processing. These scientists currently rely on outdated ways to move and store data, costing valuable time and risking loss of valuable data. While the community is aware of modern approaches to data management and high-level principles (including FAIR), highly-trained and highly-paid scientists are forced to spend time dealing with technical problems, which can ultimately costs more than providing storage and a fast network on campus. Here we provide concise arguments for better infrastructure, blueprints of possible solutions, and advice in navigating the political process of solving this issue. We suggest, as a broad solution, separate NIH-managed fund for supporting universities and institutes in deployment of data storage and long-term data sharing for all funded projects. This position statement is open for more contributors from imaging, life sciences, and other disciplines. Please contact us with your experience and perspective.

q-bio.OT↗

arXiv2021

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale HPC platforms. Workflows will play a crucial role in the data-oriented and post-Moore's computing landscape as they democratize the application of cutting-edge research techniques, computationally intensive methods, and use of new computing platforms. As workflows continue to be adopted by scientific projects and user communities, they are becoming more complex. Workflows are increasingly composed of tasks that perform computations such as short machine learning inference, multi-node simulations, long-running machine learning model training, amongst others, and thus increasingly rely on heterogeneous architectures that include CPUs but also GPUs and accelerators. The workflow management system (WMS) technology landscape is currently segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. Another fundamental problem is that there are conflicting theoretical bases and abstractions for a WMS. Systems that use the same underlying abstractions can likely be translated between, which is not the case for systems that use different abstractions. More information: https://workflowsri.org/summits/technical

cs.DC↗

arXiv2021

Addressing Research Software Sustainability via Institutes

Research software is essential to modern research, but it requires ongoing human effort to sustain: to continually adapt to changes in dependencies, to fix bugs, and to add new features. Software sustainability institutes, amongst others, develop, maintain, and disseminate best practices for research software sustainability, and build community around them. These practices can both reduce the amount of effort that is needed and create an environment where the effort is appreciated and rewarded. The UK SSI is such an institute, and the US URSSI and the Australian AuSSI are planning to become institutes, and this extended abstract discusses them and the strengths and weaknesses of this approach.

cs.SE↗

arXiv2021

Sustaining Research Software via Research Software Engineers and Professional Associations

Research software is a class of software developed to support research. Today a wealth of such software is created daily in universities, government, and commercial research enterprises worldwide. The sustainability of this software faces particular challenges due, at least in part, to the type of people who develop it. These Research Software Engineers (RSEs) face challenges in developing and sustaining software that differ from those faced by the developers of traditional software. As a result, professional associations have begun to provide support, advocacy, and resources for RSEs. These benefits are critical to sustaining RSEs, especially in environments where their contributions are often undervalued and not rewarded. This paper focuses on how professional associations, such as the United States Research Software Engineer Association (US-RSE), can provide this.

cs.SE↗

arXiv2019

Theory-Software Translation: Research Challenges and Future Directions

The Theory-Software Translation Workshop, held in New Orleans in February 2019, explored in depth the process of both instantiating theory in software - for example, implementing a mathematical model in code as part of a simulation - and using the outputs of software - such as the behavior of a simulation - to advance knowledge. As computation within research is now ubiquitous, the workshop provided a timely opportunity to reflect on the particular challenges of research software engineering - the process of developing and maintaining software for scientific discovery. In addition to the general challenges common to all software development projects, research software additionally must represent, manipulate, and provide data for complex theoretical constructs. Ensuring this process is robust is essential to maintaining the integrity of the science resulting from it, and the workshop highlighted a number of areas where the current approach to research software engineering would benefit from an evidence base that could be used to inform best practice. The workshop brought together expert research software engineers and academics to discuss the challenges of Theory-Software Translation over a two-day period. This report provides an overview of the workshop activities, and a synthesises of the discussion that was recorded. The body of the report presents a thematic analysis of the challenges of Theory-Software Translation as identified by workshop participants, summarises these into a set of research areas, and provides recommendations for the future direction of this work.

cs.SE↗

arXiv2019

Sustaining Research Software: an SC18 Panel

Many science advances have been possible thanks to the use of research software, which has become essential to advancing virtually every Science, Technology, Engineering and Mathematics (STEM) discipline and many non-STEM disciplines including social sciences and humanities. And while much of it is made available under open source licenses, work is needed to develop, support, and sustain it, as underlying systems and software as well as user needs evolve. In addition, the changing landscape of high-performance computing (HPC) platforms, where performance and scaling advances are ever more reliant on software and algorithm improvements as we hit hardware scaling barriers, is causing renewed tension between sustainability of software and its performance. We must do more to highlight the trade-off between performance and sustainability, and to emphasize the need for sustainability given the fact that complex software stacks don't survive without frequent maintenance; made more difficult as a generation of developers of established and heavily-used research software retire. Several HPC forums are doing this, and it has become an active area of funding as well. In response, the authors organized and ran a panel at the SC18 conference. The objectives of the panel were to highlight the importance of sustainability, to illuminate the tension between pure performance and sustainability, and to steer SC community discussion toward understanding and addressing this issue and this tension. The outcome of the discussions, as presented in this paper, can inform choices of advance compute and data infrastructures to positively impact future research software and future research.

cs.SE↗

arXiv2018

Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained

Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, software has evolved organically and inconsistently, with its development largely as by-products of other initiatives. Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics, multiscale modeling and outer-loop analysis. In recent years, community members have established a range of grass-roots organizations and projects to address these growing technical and social challenges in software productivity, quality, reproducibility, and sustainability. This article provides an overview of such groups and discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems.

cs.CY↗

arXiv2017

Report on the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

This report records and discusses the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4). The report includes a description of the keynote presentation of the workshop, the mission and vision statements that were drafted at the workshop and finalized shortly after it, a set of idea papers, position papers, experience papers, demos, and lightning talks, and a panel discussion. The main part of the report covers the set of working groups that formed during the meeting, and for each, discusses the participants, the objective and goal, and how the objective can be reached, along with contact information for readers who may want to join the group. Finally, we present results from a survey of the workshop attendees.

cs.SE↗

arXiv2016

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group's future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happen.

cs.SE↗

arXiv2015

Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and Reproducibility

Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data salvage to find answers for research questions, which would not have been feasible before, maybe even not feasible to ask before, the amount of data creates new challenges, which obviously need new software and data management systems. Such new solutions have to consider integrative approaches, which are not only considering the effectiveness and efficiency of data processing but improve reusability, reproducibility and usability especially tailored to the target user communities of genomic big data. In our opinion, current solutions tackle part of the challenges and have each their strengths but lack to provide a complete solution. We present in this paper the key challenges and the characteristics cutting-edge developments should possess for fulfilling the needs of the user communities to allow for seamless sharing and data analysis on a large scale.

cs.DC↗

arXiv2015

Enhanced Usability of Managing Workflows in an Industrial Data Gateway

The Grid and Cloud User Support Environment (gUSE) enables users convenient and easy access to grid and cloud infrastructures by providing a general purpose, workflow-oriented graphical user interface to create and run workflows on various Distributed Computing Infrastructures (DCIs). Its arrangements for creating and modifying existing workflows are, however, non-intuitive and cumbersome due to the technologies and architecture employed by gUSE. In this paper, we outline the first integrated web-based workflow editor for gUSE with the aim of improving the user experience for those with industrial data workflows and the wider gUSE community. We report initial assessments of the editor's utility based on users' feedback. We argue that combining access to diverse scalable resources with improved workflow creation tools is important for all big data applications and research infrastructures.

cs.DC↗