Sandra Gesing

• Dr. rer. nat.
• Executive Director for US-RSE and Senior Researcher at SDSC at San Diego Supercomputer Center

The explosion of the data both in the biomedical research and in the healthcare systems demands urgent solutions. In particular, the research in omics sciences is moving from a hypothesis-driven to a data-driven approach. Healthcare is additionally always asking for a tighter integration with biomedical data in order to promote personalized medicin...

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user friendly web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined wo...

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The...

ABSTRACT: Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple ref...

The discrete dynamics of a one-dimensional non-hermitian zigzag waveguide array is studied theoretically. This system is characterized by unbalanced left/right nearest-neighbor hopping and reciprocal second-neighbor interactions in both hopping directions. The interplay between the unbalanced hopping amplitudes and the waveguide setup results in No...

Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models...

Quantum computing is a rapidly emerging and promising field with the potential to transform various research domains including drug design, network technologies, and sustainable energy solutions. Due to the inherent complexity and divergence from classical computing, several major quantum computing libraries have been developed to implement quantum...

A non-unitary transformation is applied to a non-Hermitian zigzag waveguide array, resulting in Hermitian dynamics that describe a reciprocal waveguide system. A comparison between the exact and numerical solution is performed.

We present Qubint-4Lexp, an integrated educational tool designed to illustrate fundamental concepts of the four Bell states in quantum computing. This tool is freely available and has already been integrated into the QUBITHUB platform.

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to...

Science gateways are a crucial component of critical infrastructure as they provide the means for users to focus on their topics and methods instead of the technical details of the infrastructure. They are defined as end-to-end solutions for accessing data, software, computing services, sensors, and equipment specific to the needs of a science or e...

Effective communication is vital for academic project success, particularly in multidisciplinary teams with diverse backgrounds and disciplines. Misunderstandings can arise from differing interpretations of terms, which may go unnoticed. VisDict aims to bridge this gap by creating a visual dictionary within a science gateway to facilitate clear com...

italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Researchers and educators in humanities such as computational linguists, digital humanists, and those doing historical reconstructions are increasingly heavy users of computational and/or data resources. Many know about activities, working groups, and i...

The research landscape has become increasingly interdisciplinary and complex with novel hardware, software, data, and lab instruments. Reproducibility of research results, the usability of tools, and sharing of methods are all crucial for timely collaboration for research and teaching. Hubzero is a widely used science gateway framework designed to...

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the devastating kinetoplastid parasites of the genus Leishmania , the causative agents of diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted t...

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 sustainabil...

To improve the sharing and reuse of research software,

Research software is a critical component of contemporary scholarship. Yet, most research software is developed and managed in ways that are at odds with its long-term sustainability. This paper presents findings from a survey of 1,149 researchers, primarily from the United States, about sustainability challenges they face in developing and using r...

Science gateways have been widely utilized by a large number of user communities to simplify access to complex distributed computing infrastructures. While science gateways are still becoming increasingly popular and the number of user communities is growing, the fast and efficient creation of new science gateways and the flexibility to deploy thes...

This paper summarizes the WORKS 2021 lightning talks, which cover four broad topics: (i) libEnsemble, a Python library to coordinate the concurrent evaluation of dynamic ensembles of calculations; (ii) Edu WRENCH, a set of online pedagogic modules that provides simulation-driven hands-on activity in the browser; (iii) VisDict, an envisioned visual...

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 curren...

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 curren...

The future for science gateways warrants exploration as we consider the possibilities that extend well beyond 'science' and high-performance computing into new interfaces, applications and user communities. In this paper, we look retrospectively at the successes of representative gateways thus far. This serves to highlight existing gaps gateways ne...

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 H...

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data A...

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 aro...

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 Engi...

Scholars worldwide leverage science gateways/VREs for a wide variety of research and education endeavors spanning diverse scientific fields. Evaluating the value of a given science gateway/VRE to its constituent community is critical in obtaining the financial and human resources necessary to sustain operations and increase adoption in the user com...

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data A...

Science gateways require a wide range of considerations to make them successful and sustainable. One important consideration is usability. Gateway creators typically lack usability expertise and do not know how to avoid common usability problems. The Science Gateways Community Institute (SGCI) has provided numerous workshops, webinars, and consulti...

Background : Software is now ubiquitous within research. In addition to the general challenges common to all software development projects, research software must also represent, manipulate, and provide data for complex theoretical constructs. Ensuring this process of theory-software translation is robust is essential to maintaining the integrity o...

The concept behind Science Gateways (SGs), Virtual Laboratories (VLs)and Virtual Research Environments (VREs) is to support researchers and educators with computational solutions that ease the use of complex research infrastructures, data infrastructures, lab instruments and sensor networks. The goal of SGs, VLs and VREs is to enable researchers an...

This is the final version of the Recommendations and Guidelines from the RDA COVID19 Working Group, and has been endorsed through the official RDA process.

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 with...

ICTBioMed, the International Consortium for Technology in Biomedicine is a consortium for biomedical collaborative research and the consortium partners believe in decentralization and democratization of science. The consortium works on strategies to develop ready-to-use research initiatives bridging the gap between research, implementation and read...

Cyberinfrastructure (CI) Facilitation is the process of helping researchers to use research computing systems and services to advance their computing-intensive/data-intensive research goals. The growing need for CI Facilitation isn't being met by traditional academic degree and certificate programs, so informal education is required. The Virtual Re...

The science gateway framework HUBzero® has been enhanced and further developed since its initial vision in 1996 -- always driven by requirements of the diverse communities applying HUBzero® for their research. HUBzero® is part of a computational landscape that has never evolved as fast as in the last decade. Novel frameworks and concepts on the use...

The Science Gateways Community Institute (SGCI), opened in August 2016, provides free resources, services, experts, and ideas for creating and sustaining science gateways. It offers five areas of services to the science gateway developer and user communities: the Incubator, Extended Developer Support, the Scientific Software Collaborative, Communit...

Science gateways, virtual laboratories and virtual research environments are all terms used to refer to community-developed digital environments that are designed to meet a set of needs for a research community. Specifically, they refer to integrated access to research community resources including software, data, collaboration tools, workflows, in...

The Regenstrief Center for Healthcare Engineering (RCHE), an interdisciplinary research center located at Purdue University, facilitated the development of a science community for medical device informatics, known as Regenstrief National Center for Medical Device Informatics (REMEDI). The community uses an online science gateway called REMEDI Centr...

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...

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, s...

The Science Gateway Bootcamp is designed to help teams in any stage for their gateway project-from planning to developing to maintaining their gateway-to learn core business strategy skills, technology best practices, and long-term sustainability strategies. The interactive sessions are planned to get an overview on basic strategies and develop for...

Introduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time consuming and therefore many research groups are moving from in-house solutions to remote distributed co...

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, s...

The challenges for creators of specific science gateways are manifold, and the expertise needed for well-designed science gateways is very diverse. The sustainability of science gateways is crucial to serve communities effectively, efficiently and reliably. One measure to achieve greater sustainability of science gateways is establishing on-campus...

Cyberinfrastructure facilitation – working directly with researchers Cyberinfrastructure facilitation – working directly with researchers 2 technical content that facilitators need is available via other opportunities). The VR consists primarily of (a) summer weeklong intensive workshops that provide both content and experiences in facilitation, (b...

In this column, the US Research Software Sustainability Institutes principal investigators introduce their conceptualization of an institute that would improve science and engineering research by supporting research softwares development and sustainability.

The amount of available data as well as computational methods for research have grown faster in the last decade than ever before. Methods that address compute-intensive and data-intensive challenges often apply sophisticated computing and data infrastructures such High-Performance Computing. Effectiveness and efficiency are the basis to achieve mea...

The challenges for creators of specific science gateways are manifold, and the expertise needed for well-designed science gateways is very diverse. The sustainability of science gateways is crucial to serve communities effectively, efficiently and reliably. One measure to achieve greater sustainability of science gateways is establishing on-campus...

This proposal is a response to NIH's call for creation of a Data Commons (RM-17-026). The Commons must support use cases of many stakeholders who need access to scholarly process, content, and outcomes in pursuit of knowledge. Moreover, the Commons must be flexible enough to respect researchers’ idiosyncratic workflows, yet specific enough to solve...

This special issue and our editorial celebrate 10 years of progress with data-intensive or scientific workflows. There have been very substantial advances in the representation of workflows and in the engineering of workflow management systems (WMS). The creation and refinement stages are now well supported, with a significant improvement in usabil...

To support scientists of different disciplines, different fields of Computer Science have developed tools and infras-tructures with the aim of giving them access to vast computational resources in the easiest possible way. Such extremely complex structures have evolved naturally in the last decades both in depth and breath and, in addition to scien...

Science gateways represent a community-specific set of tools, applications, and data collections that are integrated via a web portal or a desktop application, providing access to resources and services of distributed computing infrastruc-tures (DCIs). Science gateways offer the potential to open the utilisation of DCIs to wider audiences by provid...

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, exper...

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, exper...

The importance of Big Data and Open Data to achieve scientific advancements in precision medicine is beyond doubt and evident in many different projects and initiatives such as the Precision Medicine Initiative (All of Us), ICTBioMed, NCIP Hub, 100K Genomics England Project, and PatientsLikeMe.com. Companies from a wide spectrum such as Oracle Heal...

Compute-intensive simulations are often based on complex scientific theories and necessitate high-performance computing (HPC) infrastructures to deliver results in reasonable time. While domain researchers are experts in their field and apply sophisticated theoretical models in computational simulations, they are not necessarily also HPC experts or...

In the last 20 years, computational methods have become an important part of developing emerging technologies for the field of bioinformatics and biomedicine. Those methods rely heavily on large scale computational resources as they need to manage Tbytes or Pbytes of data with large-scale structural and functional relationships, TFlops or PFlops of...

Scientific workflows are routinely used in most scientific disciplines today, as they provide a systematic way to execute a number of applications in Science and Engineering. They are at the interface of end-users and computing infrastructures, often relying on workflow management systems and a variety of parallel and/or distributed computing resou...

Nowadays, research in various disciplines is enhanced via computational methods, cutting-edge technologies and diverse resources including computational infrastructures and instruments. Such infrastructures are often complex and researchers need means to conduct their research in an efficient way without getting distracted with information technolo...

Background Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a co...

Researchers can perform large-scale analyses on diverse computing and data infrastructures such as NGIs (National Grid Infrastructures), XSEDE (Extreme Science and Engineering Discovery Environment) and PRACE (Partnership for Advanced Computing in Europe). Some are national like NGIs and XSEDE, some are international like PRACE and all of them requ...

Collaborative research infrastructures on global scale for earth and space sciences face a plethora of challenges from technical implementations to organizational aspects. Science gateways – also known as virtual research environments (VREs) or virtual laboratories - address part of such challenges by providing end-to-end solutions to aid researche...

Background In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows...

Cyberinfrastructure including distributed and parallel computing infrastructures, Internet of Things (IoT) and instruments play a critical role in enabling research in many disciplines and often pushes the boundaries. Science gateways-also known as virtual research environments or virtual laboratories-allow researchers to focus on their respective...

Background: Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks...

Disaster prediction, community preparedness, infrastructure resilience, and costs are a subset of the reasons environmental disaster response and risk assessment collaboration tools are vital for preserving the future. Even using decision support and intelligent data, tools are often inhibited by specialized and even proprietary goals in the sense...

Accelerated architectures such as GPUs (Graphics Processing Units) and MICs (Many Integrated Cores) have been proven to increase the performance of many algorithms compared to their CPU counterparts and are widely available in local, campus-wide and national infrastructures, however, their utilization is not following the same pace as their deploym...

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-...

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-...

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-...

Virtual screening for active compounds has become an essential step within the drug development pipeline. The computer based prediction of compound-binding modes is one of the most time and cost efficient methods for screening ligand libraries and enrich results of potential drugs. Here we present an overview about currently available online resour...