As part of a set of connected activities under the banner of the US Research Software Sustainability Institute (URSSI), this grant will support the hiring of a full-time URSSI community manager who will focus on cultivating and growing URSSI’s community while identifying new needs and potential collaborations, as well as providing support with engagement and dissemination activities. This new position will draw on expertise and support from Code for Science and Society and the Center for Scientific Collaboration and Community Engagement, as well as PI Ram’s deep experience growing the rOpenSci community.  

As part of a set of connected activities under the banner of the US Research Software Sustainability Institute, this grant funds an effort by Kyle Niemeyer, mechanical engineering professor at Oregon State University, to develop and run four, weeklong “beyond introductory” winter/summer schools for researchers who want to deepen their software engineering skills. Beyond directly training an anticipated 130 scientific and engineering researchers in sustainable software development, Niemeyer will develop, hone, and release a scalable mid-level curriculum for the training of non-expert scientists in best practices in software engineering and his project will provide useful data on the size of demand for such skills training events.

Software has been critical to research for decades, but only in the past handful of years has it become a topic of broad national conversations about the scientific enterprise. Much of this discussion has centered on the difficulties of maintaining research software beyond initial grant funding, especially when funder support has historically focused on new projects rather than maintenance of existing research infrastructure. Unlike instruments, research software is rarely commercialized, and “sustainability” usually relies on persistent, ongoing engagement by developers cross-subsidized by institutions and other grants.   As part of a set of connected activities under the banner of the US Research Software Sustainability Institute, this grant funds a project led by Daniel S. Katz at the University of Illinois, Urbana-Champaign to collect and analyze research software sustainability policies across a host of key institutions. Katz’s targets are guidelines, rules, and practices related to research software created by institutions such as universities, laboratories, and industry as well as the funders, professional societies, and publishers that exert strong influence on the norms of scientific practice. Katz will then use the collected policies to answer several important big picture questions about research software sustainability, including characterizing the variation of strategies and institutional structures for the support of research software, the alignment or misalignment of such strategies, and funding sources and opportunities for the maintenance of research software.

In most contemporary software development, investments in user experience (UX) design are viewed as highly prudent expenditures that result in products that are intuitive, meaningful, and relevant for users. When it comes to scientific software projects, however, it’s rare to find a UX designer amongst any core set of contributors. Recent research on the topic suggests that greater investment in the UX of a piece of software (especially early in the lifecycle of a project) could have large positive downstream impacts: easier adoption of software, lowered barriers to its use by a broader set of scientists with different backgrounds and levels of training, diminishing maintenance costs, and healthy cycles of user feedback informing how to build more useful software.   This grant funds a project lead by Lavanya Ramakrishnan at the Lawrence Berkeley National Lab (LBL), to help codify how to effectively implement UX design in scientific software projects through the study of LBL’s extensive corpus of UX research on myriad scientific collaborations. Ramakrishnan’s team will use the research to generalize best practices for implementing UX into the development of a diverse typology of software types (i.e., data pipelines vs. instrument control systems), and then prototype a UX design system to be used for common scientific tasks and workflows.

The Emulation as a Service Infrastructure (EaaSI) project is an extensive platform for software curation and preservation. Beyond its core functionality, which builds and curates “virtual machines” that can execute any piece of archived software, regardless of the hardware on which it was originally designed to run, the project has responded to demand from partners and developed critical services like a hosted “reading room” for library CD-ROM collections and a Universal Virtual Interactor that can open any digital file natively in the appropriate application (and version) in which it was created. Anchored at the Yale University Library, the project team led by digital preservation manager Euan Cochrane and software preservation program manager Seth Anderson has built out a robust open source codebase, which in addition to production use at Yale has been piloted at 15 other universities and is being adopted by initiatives in Canada and Australia.   This grant supports the continued development and expansion of the EaaSI platform as it matures and moves towards long term sustainability.  Grant funds will support three streams of work: maintenance of the existing EaaSI services; development of automation and other approaches to lower costs for and appeal to new institutional users (with an emphasis on the archiving of computational research pipelines); and market development toward long term sustainability.

In 2020, the Sloan Foundation provided support for an effort led by the Rochester Institute of Technology’s Stephen Jacobs to design and launch an undergraduate-anchored program—LibreCorps—to support faculty software projects across the RIT campus. Aimed at both eliciting demand for and establishing the value of open source software projects, LibreCorps is an experiential learning program where students are deployed to work on real world open source software and data projects, supporting faculty partners with direct software development as well as community management, documentation, design, and other forms of non-code contribution. This pilot was successful, with LibreCorps having supported at least 24 faculty-driven software projects on topics ranging from computational astrophysics to ecology to data visualization to cybersecurity to Deaf education.   Funds from this grant provide continuing support for this effort under the broader Open@RIT initiative, supporting two core staff members who are tasked with building relationships, scoping projects, triaging requests, and otherwise ensuring that the program runs smoothly.

This grant funds efforts to develop and launch a set of core activities to support open source software engineering projects across CMU. Planned activities include creating a formal structure for managing software developer relations across the university, mapping the current open source activity across campus, and identifying opportunities which could simultaneously address faculty research needs and student training (including support for undergraduate research experiences).   In addition, the new CMU Open Source Program Office will leverage relationships with key collaborators at the Software Engineering Institute (SEI), a fully integrated Federally Funded R&D Center (FFRDC), and produce guidance and best practices for the development and maintenance of open source scientific software in the context of intramural federal research organizations. It will also explore how to support open source software developed to interface with a new “Cloud Laboratory” core facility on campus.

This grant provides ongoing support to Benjamin Dubin-Thaler, the founder of BioBus, and the team of 25 community scientists, educators, and nonprofit experts. BioBus started as a state-of-the-art science lab visiting schools in New York City to provide science opportunities aimed at K-12 students. BioBus brings a science field-trip-like experience to under-resourced schools and community groups, and has grown to include afterschool and weekend programs, summer camps, and paid high school and college research internships. Grant funds will allow BioBus to serve more than 115,000 diverse students (over half of their students identify as Latina/o/x and over a quarter as Black) from the Lower East Side to Harlem, as well as other locations in the Bronx, Brooklyn, Queens, and Staten Island, and explore a possible national expansion, while building annual financial support from NYC and New York State governments.

One challenge associated with building a life-like synthetic cell lies in how to power synthetic cell processes. A common mechanism used by natural cells to energize cell activities is the exploitation of an electrochemical gradient across a membrane. This grant funds a project led by Neal Devaraj at the University of California, San Diego to build an artificial system that couples the formation and maintenance of a pH gradient with anabolic chemistry to establish a primitive metabolism in a synthetic cell. Devaraj and his team will use photoacids encapsulated in lipid vesicles as the primitive protocells of this project. The photoacids release hydrogen ions (protons) when exposed to light, leading to an excess of protons within the vesicle. Reagent molecules will diffuse into the vesicle from the surrounding “environment” and become trapped as they acquire an electrical charge by bonding with hydrogen ions inside the proton-rich vesicle. These charged molecules will accumulate within the vesicle due to so-called ion-trapping, a phenomenon whereby a membrane that is permeable to neutral molecules becomes impermeable to charged molecules. The concentrating of reagent molecules within the vesicle will then stimulate an anabolic reaction: synthesis of phospholipids. The synthesized phospholipid molecules are building blocks for cell membranes and developing ways to synthesize these building blocks could prove useful for future efforts to build artificial cells that must be able to grow and divide. Devaraj expects that the synthesized lipids will—driven by hydrophobic interactions—associate into and thereby modify the pre-existing vesicle membrane. Microscopy will be used to characterize changes in membrane morphology, changes that could include membrane growth and division.

Recent improvements in electron microscopy have had a profound impact on cellular biology as they promise to bring a long-held 'holy grail' within reach: the ability to directly visualize nanoscale processes occurring within a cell. This goal—in situ visualization—is important because biological components often change their structure or function when removed from their native cellular environment. This grant supports a project by a team of five principal investigators to build a new type of microscope—a cryo-super-resolution microscope optimized for correlative light- and electron-microscopy (CLEM) that produces 3D snapshots (cryo-electron tomography; cryo-ET)—and to demonstrate the new microscope’s usefulness for the in situ visualization of intracellular structures and processes. Grant funds will support microscope design, construction of the super-resolution microscope, creation of software to run it, and the development of “workflows” defining how to implement CLEM when cryo-ET is the electron-microscopy technique of interest. Additionally, the principal investigators will conduct four demonstration projects in biology that leverage the capacities of the new microscope to obtain in situ structural explanations of a major cellular process. The first project, the clathrin project, seeks to understand force generation during clathrin-mediated endocytosis (CME), the taking-in of matter by invagination of a cell membrane. The second will produce images that improve our understanding of autophagy, the engulfment and degradation of various harmful objects within a cell. The third project seeks to understand the basic mechanisms behind the formation of a primary cilium, a hair-like entity that serves as an important sensory organelle on virtually all animal cells. The fourth project will use microscopy to visualize (polycomb-regulated) changes in chromatin structure during cellular development. The proposed work represents a next-logical-step in the development of electron-microscopy-for-biology and our corresponding ability to study the cell, the most basic unit of life. To help push this emerging technology out to a broad community, information on how to build and use the microscope will be made publicly available and access to the new microscope will be provided to scientists from across the globe through a visitor program.