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11. EasyScienceGateway: A new framework for providing reproducible user environments on science gateways.

Author

Michels, Alexander, Padmanabhan, Anand, Li, Zhiyu, and Wang, Shaowen

Subjects
CYBERINFRASTRUCTURE, COMMUNITY life
Abstract

Summary: Science gateways have become a core part of the cyberinfrastructure ecosystem by increasing access to computational resources and providing community platforms for sharing and publishing education and research materials. While science gateways represent a promising solution for computational reproducibility, common methods for providing users with their user environments on gateways present challenges which are difficult to overcome. This article presents EasyScienceGateway: a new framework for providing user environments on science gateways to resolve these challenges, provides the technical details on implementing the framework on a science gateway based on Jupyter Notebook, and discusses our experience applying the framework to the CyberGIS‐Jupyter and CyberGIS‐Jupyter for Water gateways. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Monoclonal gammopathy of thrombotic/thrombocytopenic significance

Author

Kanack, Adam J., primary, Schaefer, Jordan K., additional, Sridharan, Meera, additional, Splinter, Noah P., additional, Kohlhagen, Mindy C., additional, Singh, Bandana, additional, De Lorenzo, Silvana B., additional, Mauch, Emily E., additional, Hussein, Maen A., additional, Shaikh, Marwan, additional, Kumar, Shaji, additional, Wen, Renren, additional, Wang, Demin, additional, Murray, David, additional, and Padmanabhan, Anand, additional

Published
2023
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16. Streamlined HPC Environments with CVMFS and CyberGIS-Compute

Author

Michels, Alexander C, Kotak, Mit, Padmanabhan, Anand, Wang, Shaowen, Michels, Alexander C, Kotak, Mit, Padmanabhan, Anand, and Wang, Shaowen

Abstract

High-Performance Computing (HPC) resources provide the potential for complex, large-scale modeling and analysis, fueling scientific progress over the last few decades, but these advances are not equally distributed across disciplines. Those in computational disciplines are often trained to have the necessary technical skills to utilize HPC (e.g. familiarity with the terminal), but many disciplines face technical hurdles when trying to apply HPC resources to their work. This unequal familiarity with HPC is increasingly a problem as cross-discipline teams work to tackle critical interdisciplinary issues like climate change and sustainability. CyberGIS-Compute is middle-ware designed to democratize to HPC services with the goal of empowering domain scientists, but a key challenge facing model developers on CyberGIS-Compute is creating a containerized software environment for their models. In this paper, we discuss our work to integrate the Cern Virtual Machine File System (CVMFS) into CyberGIS-Compute to provide consistent software environments across science gateways and HPC resources.

Published
2023

17. Venous thromboembolism after COVID ‐19 vaccination in patients with thrombophilia

Author

Houghton, Damon E., primary, Wysokinski, Waldemar E., additional, Padrnos, Leslie J., additional, Shah, Surbhi, additional, Wysokinska, Ewa, additional, Pruthi, Rajiv, additional, Ghorbanzadeh, Atefeh, additional, Ashrani, Aneel, additional, Sridharan, Meera, additional, McBane, Robert D., additional, Padmanabhan, Anand, additional, and Casanegra, Ana I., additional

Published
2023
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20. No Difference in Venous Thromboembolism Outcomes after COVID-19 and Influenza Vaccinations

Author

Houghton, Damon E., primary, Scott, David M, additional, Wysokinski, Waldemar E., additional, Pruthi, Rajiv K., additional, Sridharan, Meera, additional, Padrnos, Leslie, additional, Shah, Surbhi, additional, Ashrani, Aneel A., additional, Padmanabhan, Anand, additional, Wysokinska, Ewa, additional, McBane, Robert D., additional, and Baumann Kreuziger, Lisa, additional

Published
2022
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24. Monoclonal and oligoclonal anti-platelet factor 4 antibodies mediate VITT

Author

Kanack, Adam J., primary, Bayas, Antonios, additional, George, Gemlyn, additional, Abou-Ismail, Mouhamed Yazan, additional, Singh, Bandana, additional, Kohlhagen, Mindy C., additional, Splinter, Noah P., additional, Christ, Monika, additional, Naumann, Markus, additional, Moser, Karen A., additional, Smock, Kristi J., additional, Grazioli, Alison, additional, Wen, Renren, additional, Wang, Demin, additional, Murray, David L., additional, and Padmanabhan, Anand, additional

Published
2022
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25. Chemoenzymatic Synthesis of Homogeneous Heparan Sulfate and Chondroitin Sulfate Chimeras

Author

Stancanelli, Eduardo, primary, Liu, Wei, additional, Wander, Rylee, additional, Li, Jine, additional, Wang, Zhangjie, additional, Arnold, Katelyn, additional, Su, Guowei, additional, Kanack, Adam, additional, Pham, Truong Quang, additional, Pagadala, Vijayakanth, additional, Padmanabhan, Anand, additional, Xu, Yongmei, additional, and Liu, Jian, additional

Published
2022
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27. Persistence of Ad26.COV2.S‐associated vaccine‐induced immune thrombotic thrombocytopenia (VITT) and specific detection of VITT antibodies

Author

Kanack, Adam J., primary, Singh, Bandana, additional, George, Gemlyn, additional, Gundabolu, Krishna, additional, Koepsell, Scott A., additional, Abou‐Ismail, Mouhamed Yazan, additional, Moser, Karen A., additional, Smock, Kristi J., additional, Green, David, additional, Major, Ajay, additional, Chan, Clarence W., additional, Wool, Geoffrey D., additional, Reding, Mark, additional, Ashrani, Aneel A., additional, Bayas, Antonios, additional, Grill, Diane E., additional, and Padmanabhan, Anand, additional

Published
2022
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28. Vaccine-Induced Thrombocytopenia and Thrombosis (VITT) Antibodies Recognize Neutrophil-Activating Peptide 2 (NAP2) As Well As Platelet Factor 4 (PF4): Mechanistic and Clinical Implications

Author

Rauova, Lubica, primary, Wang, Andy, additional, Yarovoi, Serge, additional, Khandelwal, Sanjay, additional, Padmanabhan, Anand, additional, Oleshko, Olga, additional, Charman, Matthew J., additional, Tiede, Andreas, additional, Abrams, Charles S., additional, Weitzman, Matthew D., additional, Arepally, Gowthami M., additional, Cines, Douglas B., additional, and Poncz, Mortimer, additional

Published
2021
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31. Monoclonal and Oligoclonal Anti-PF4 Antibodies Mediate VITT

Author

Singh, Bandana, primary, Kanack, Adam, additional, Bayas, Antonios, additional, George, Gemlyn, additional, Abou-Ismail, Mouhamed Yazan Abou, additional, Kohlhagen, Mindy, additional, Christ, Monika, additional, Naumann, Markus, additional, Moser, Karen A, additional, Smock, Kristi J, additional, Grazioli, Alison, additional, Murray, David L, additional, and Padmanabhan, Anand, additional

Published
2021
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32. A Thrombospondin-1 Release Assay (TRA) Coupled to PF4-Treated Cryopreserved Platelets for the Detection of Pathogenic HIT and VITT Antibodies

Author

Kanack, Adam, primary, Jones, Curtis, additional, Singh, Bandana, additional, George, Gemlyn, additional, Abou-Ismail, Mouhamed Yazan, additional, Green, David L., additional, Grazioli, Alison, additional, Leger, Rachel, additional, Heikal, Nahla M., additional, Chen, Dong, additional, Pruthi, Rajiv K., additional, and Padmanabhan, Anand, additional

Published
2021
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33. Deep Vein Thrombosis after COVID-19 Vaccinations

Author

Houghton, Damon E., primary, Padmanabhan, Anand, additional, Ashrani, Aneel A., additional, Wysokinska, Ewa, additional, Chaudhary, Rahul, additional, Padrnos, Leslie, additional, Pruthi, Rajiv K., additional, Sridharan, Meera, additional, Shah, Surbhi, additional, and Wysokinski, Waldemar E., additional

Published
2021
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37. Towards Reproducible Research on CyberGISX with Lmod and Easybuild

Author

Michels, Alexander, Padmanabhan, Anand, Li, Zhiyu, and Wang, Shaowen

Subjects
Geospatial Software, cyberGIS, Easybuild, Jupyter
Abstract

JupyterHub [1] has become a popular choice in many scientific communities, offering an easy-to-use interface for users with little to no frontend development work while promoting reproducible and replicable (R&R) science [2]. In the broad geospatial science community, CyberGISX [3] provides such a gateway environment with many cyberGIS (i.e., geospatial information science and systems based on advanced cyberinfrastructure) and geospatial software packages prebuilt and ready to use. Like other JupyterHub-based solutions, CyberGISX also provides container-based access for its users and must balance a trade-off between providing a static compute environment which enhances R&R and continuously updating the software environment to keep up with advances in scientific software. Solutions such as Binder [4] have attempted to address this trade-off by having required dependencies encoded in the package and building the software environment at the time of use. However, such a solution comes with two major disadvantages: (a) software is built at the time it is needed, increasing startup time and introducing the possibility that some of the dependencies of the environment are no longer available or have changed; and (b) the onus of specifying and managing software installations is passed to notebook developers, many of whom are domain scientists and not comfortable with such responsibilities. To address these challenges and enhance R&R with minimal effort from end-users, we have designed and implemented a solution on CyberGISX that allows software to be kept on an external file server mounted into each user's environment. Scientific software is installed with Easybuild [5] and managed by Lmod [6] giving a variety of benefits: (1) the compute environment is more standardized and easily reproducible outside of the gateway; (2) multiple versions of software can be made available to users without increasing container size; and (3) the exact copies of software are always available on the gateway instead of being rebuilt for every release, further enhancing R&R. We also employ an Easybuild-installed Anaconda [7] to create and manage conda environments on the file server. The combination of the software stack from Easybuild and Python environment from conda provides end-users with kernels for their Jupyter notebooks which are persistent and unchanged as the gateway's container updates. This design enhances R&R and adds functionality for advanced users without introducing technical barriers to non-technical end-users. As such, domain scientists using this solution need not build their own software and specify dependencies, which helps prevent the notebooks they have developed from getting broken by the next software release. This talk explores the new architecture and applications of this solution to CyberGISX [3] and CyberGIS-Jupyter for Water (CJW) [8].

Published
2021
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38. Enabling computationally intensive geospatial research on CyberGIS-Jupyter with CyberGIS-Compute

Author

Padmanabhan, Anand, Xiao, Zimo, Vandewalle, Rebecca, Michels, Alexander, and Wang, Shaowen

Subjects
cyberGIS, GIScience, Cyberinfrastructure, Jupyter
Abstract

Geospatial research and education have become increasingly dependent on cyberGIS, defined as geographic information science and systems based on advanced cyberinfrastructure (CI), [1] to tackle computation and data challenges. However, the use of advanced cyberGIS capabilities has typically been constrained to a small set of research groups who have the technical expertise of using CI resources. Over the past few years CyberGIS-Jupyter [2,3] has been developed to provide access to cyberGIS capabilities through an easy-to-use Jupyter Notebook interface which has made cyberGIS more accessible. For many cyberGIS and geospatial applications accessing CI resources needed for solving complex problems at scale. However, leveraging CI resources for geospatial application is challenging both due to the steep learning curve and lack of appropriate tools. CyberGIS-Compute fills this gap by providing an easy-to-use middleware tool for using and contributing geospatial application codes that leverage CI resources. This substantially lowers the learning curve for both geospatial users and developers to access cyberGIS capabilities at scale. CyberGIS-Compute is backed by Virtual ROGER (Resourcing Open Geospatial Education and Research); a geospatial supercomputer with access to a number of readily available popular geospatial libraries. With CyberGIS-Compute we have designed an easy-to-use middleware and associated Python SDK to provide access to CyberGIS capabilities, allowing geospatial applications to easily scale and employ advanced cyberinfrastructure resources. This presentation will first describe the basics of CyberGIS-Jupyter and CyberGIS-Compute, then introduce the Python SDK for CyberGIS-Compute with a simple example. Then, we will take multiple real-world geospatial applications use-cases like spatial accessibility and wildfire evacuation simulation using agent based modeling. Lastly, we will also descrive mechanism to contribute applications to the CyberGIS-Compute framework.

Published
2021
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39. Developing Cohort Challenges: An Innovative Program for Training Graduate Students to Work in Transdisciplinary Teams.

Author

Marshall, Anna-Maria, Heemstra, Jill, Classen, John J., Cortus, Erin, Koziel, Jacek, Meyer, Deanne, Padmanabhan, Anand, Reed, Samuel Powers, and Walters, Riveraine

Subjects
GRADUATE students, ENGINEERING education, SCIENCE education, GRADUATES, ENGINEERING students
Abstract

"Wicked problems" in science and engineering demand transdisciplinary approaches drawing on multiple disciplines and perspectives, yet we continue to conduct graduate training largely within the confines of a single discipline. The INFEWS-ER is an NSF-funded virtual resource center designed to provide transdisciplinary graduate education to students working on problems at the intersection of food-energy-water systems. Relying on a conceptual framework that identifies several competencies -- the skills, knowledge, and pedagogical methods that are vital for successful transdisciplinary teamwork -- we designed an approach that capitalizes on faculty expertise, student interests, and teamwork. In this paper, we offer a model of an innovative approach to training graduate students -- Cohort Challenges offered by the INFEWS-ER. Specifically, we describe the fundamental elements that each Cohort Challenge shared: a broad theme related to a wicked problem that gives graduate students the flexibility and independence to formulate their own research questions and design their own projects; training in competencies for conducting transdisciplinary research; mentorship from faculty and peer experts outside their departments and outside their disciplines; and collaborative learning in a virtual environment. We also focus on important dimensions of the process of conducting a Cohort Challenge, including intentional team-building practices that foster trust and accountability among participants; meaningful stakeholder engagement throughout the research process, from design to sharing final products; and learning to communicate about science across varied audiences. We also describe some of the final projects the Challenges produced, including journal articles, conference presentations, and social media campaigns, all outside of the students' more traditional course of study. We conclude by offering several final observations about the opportunities and obstacles to successful Cohort Challenges, as well as our future plans to support others who want to design and deliver this mode of graduate education. [ABSTRACT FROM AUTHOR]

Published
2022

40. Understanding the multifaceted geospatial software ecosystem: a survey approach.

Author

Vandewalle, Rebecca C., Barley, William C., Padmanabhan, Anand, Katz, Daniel S., and Wang, Shaowen

Subjects
GEOSPATIAL data, SOFTWARE development tools, COMPUTER software, INTERNET forums, ECOSYSTEMS
Abstract

Understanding the characteristics of the rapidly evolving geospatial software ecosystem in the United States is critical to enable convergence research and education that are dependent on geospatial data and software. This paper describes a survey approach to better understand geospatial use cases, software and tools, and limitations encountered while using and developing geospatial software. The survey was broadcast through a variety of geospatial-related academic mailing lists and listservs. We report both quantitative responses and qualitative insights. As 42% of respondents indicated that they viewed their work as limited by inadequacies in geospatial software, ample room for improvement exists. In general, respondents expressed concerns about steep learning curves and insufficient time for mastering geospatial software, and often limited access to high-performance computing resources. If adequate efforts were taken to resolve software limitations, respondents believed they would be able to better handle big data, cover broader study areas, integrate more types of data, and pursue new research. Insights gained from this survey play an important role in supporting the conceptualization of a national geospatial software institute in the United States with the aim to drastically advance the geospatial software ecosystem to enable broad and significant research and education advances. [ABSTRACT FROM AUTHOR]

Published
2021
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42. Cerebral venous sinus thrombosis associated with spontaneous heparin-induced thrombocytopenia syndrome after total knee arthroplasty.

Author

Hwang, Steven R, Wang, Yuxiang, Weil, Erika L, Padmanabhan, Anand, Warkentin, Theodore E, and Pruthi, Rajiv K

Subjects
TOTAL knee replacement, VENOUS thrombosis, CRANIAL sinuses, ORTHOPEDIC surgery, SINUS thrombosis, THROMBOCYTOPENIA, SYNDROMES
Abstract

Spontaneous heparin-induced thrombocytopenia (HIT) syndrome, characterized by clinical and serologic features of HIT despite the absence of proximate heparin exposure, can be triggered by total knee arthroplasty (TKA). A 56-year-old female receiving aspirin thromboprophylaxis post-TKA presented with aphasia and thrombocytopenia on post-operative day 11. Imaging studies revealed cerebral venous sinus thrombosis (CVST) and intravenous bivalirudin was initiated. Her serum tested strong-positive for IgG anti-PF4/polyanion complexes and serotonin-release assay in the presence and absence of heparin; strong-positive IgG-specific chemiluminescent immunoassay; and moderate-positive latex immunoturbidimetric assay. Two 65 g doses of IVIG were administered. With the improvement of her platelet count, she was transitioned from bivalirudin to warfarin. At one-year follow-up, she remained free of recurrent thrombosis and neurologically stable with a normal platelet count. Previous reports of post-TKA spontaneous HIT syndrome include venous/arterial thrombosis and adrenal hemorrhage, and this report of CVST expands the clinical spectrum of this rare complication of orthopedic surgery. [ABSTRACT FROM AUTHOR]

Published
2021
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