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    Rewarding excellence in open data

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    The second annual MIT Prize for Open Data, which included a $2,500 cash prize, was recently awarded to 10 individual and group research projects. Presented jointly by the School of Science and the MIT Libraries, the prize highlights the value of open data — research data that is openly accessible and reusable — at the Institute. The prize winners and 12 honorable mention recipients were honored at the Open Data @ MIT event held Oct. 24 at Hayden Library. 

    Conceived by Chris Bourg, director of MIT Libraries, and Rebecca Saxe, associate dean of the School of Science and the John W. Jarve (1978) Professor of Brain and Cognitive Sciences, the prize program was launched in 2022. It recognizes MIT-affiliated researchers who use or share open data, create infrastructure for open data sharing, or theorize about open data. Nominations were solicited from across the Institute, with a focus on trainees: undergraduate and graduate students, postdocs, and research staff. 

    “The prize is explicitly aimed at early-career researchers,” says Bourg. “Supporting and encouraging the next generation of researchers will help ensure that the future of scholarship is characterized by a norm of open sharing.”

    The 2023 awards were presented at a celebratory event held during International Open Access Week. Winners gave five-minute presentations on their projects and the role that open data plays in their research. The program also included remarks from Bourg and Anne White, School of Engineering Distinguished Professor of Engineering, vice provost, and associate vice president for research administration. White reflected on the ways in which MIT has demonstrated its values with the open sharing of research and scholarship and acknowledged the efforts of the honorees and advocates gathered at the event: “Thank you for the active role you’re all playing in building a culture of openness in research,” she said. “It benefits us all.” 

    Winners were chosen from more than 80 nominees, representing all five MIT schools, the MIT Schwarzman College of Computing, and several research centers across the Institute. A committee composed of faculty, staff, and graduate students made the selections:

    Hammaad Adam, graduate student in the Institute for Data, Systems, and Society, accepted on behalf of the team behind Organ Retrieval and Collection of Health Information for Donation (ORCHID), the first ever multi-center dataset dedicated to the organ procurement process. ORCHID provides the first opportunity to quantitatively analyze organ procurement organization decisions and identify operational inefficiencies.
    Adam Atanas, postdoc in the Department of Brain and Cognitive Sciences (BCS), and Jungsoo Kim, graduate student in BCS, created WormWideWeb.org. The site, allowing researchers to easily browse and download C. elegans whole-brain datasets, will be useful to C. elegans neuroscientists and theoretical/computational neuroscientists. 
    Paul Berube, research scientist in the Department of Civil and Environmental Engineering, and Steven Biller, assistant professor of biological sciences at Wellesley College, won for “Unlocking Marine Microbiomes with Open Data.” Open data of genomes and metagenomes for marine ecosystems, with a focus on cyanobacteria, leverage the power of contemporaneous data from GEOTRACES and other long-standing ocean time-series programs to provide underlying information to answer questions about marine ecosystem function. 
    Jack Cavanagh, Sarah Kopper, and Diana Horvath of the Abdul Latif Jameel Poverty Action Lab (J-PAL) were recognized for J-PAL’s Data Publication Infrastructure, which includes a trusted repository of open-access datasets, a dedicated team of data curators, and coding tools and training materials to help other teams publish data in an efficient and ethical manner. 
    Jerome Patrick Cruz, graduate student in the Department of Political Science, won for OpenAudit, leveraging advances in natural language processing and machine learning to make data in public audit reports more usable for academics and policy researchers, as well as governance practitioners, watchdogs, and reformers. This work was done in collaboration with colleagues at Ateneo de Manila University in the Philippines. 
    Undergraduate student Daniel Kurlander created a tool for planetary scientists to rapidly access and filter images of the comet 67P/Churyumov-Gerasimenko. The web-based tool enables searches by location and other properties, does not require a time-intensive download of a massive dataset, allows analysis of the data independent of the speed of one’s computer, and does not require installation of a complex set of programs. 
    Halie Olson, postdoc in BCS, was recognized for sharing data from a functional magnetic resonance imaging (fMRI) study on language processing. The study used video clips from “Sesame Street” in which researchers manipulated the comprehensibility of the speech stream, allowing them to isolate a “language response” in the brain.
    Thomas González Roberts, graduate student in the Department of Aeronautics and Astronautics, won for the International Telecommunication Union Compliance Assessment Monitor. This tool combats the heritage of secrecy in outer space operations by creating human- and machine-readable datasets that succinctly describe the international agreements that govern satellite operations. 
    Melissa Kline Struhl, research scientist in BCS, was recognized for Children Helping Science, a free, open-source platform for remote studies with babies and children that makes it possible for researchers at more than 100 institutions to conduct reproducible studies. 
    JS Tan, graduate student in the Department of Urban Studies and Planning, developed the Collective Action in Tech Archive in collaboration with Nataliya Nedzhvetskaya of the University of California at Berkeley. It is an open database of all publicly recorded collective actions taken by workers in the global tech industry. 
    A complete list of winning projects and honorable mentions, including links to the research data, is available on the MIT Libraries website. More

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      Understanding viral justice

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      In the wake of the Covid-19 pandemic, the word “viral” has a new resonance, and it’s not necessarily positive. Ruha Benjamin, a scholar who investigates the social dimensions of science, medicine, and technology, advocates a shift in perspective. She thinks justice can also be contagious. That’s the premise of Benjamin’s award-winning book “Viral Justice: How We Grow the World We Want,” as she shared with MIT Libraries staff on a June 14 visit. 

      “If this pandemic has taught us anything, it’s that something almost undetectable can be deadly, and that we can transmit it without even knowing,” said Benjamin, professor of African American studies at Princeton University. “Doesn’t this imply that small things, seemingly minor actions, decisions, or habits, could have exponential effects in the other direction, tipping the scales towards justice?” 

      To seek a more just world, Benjamin exhorted library staff to notice the ways exclusion is built into our daily lives, showing examples of park benches with armrests at regular intervals. On the surface they appear welcoming, but they also make lying down — or sleeping — impossible. This idea is taken to the extreme with “Pay and Sit,” an art installation by Fabian Brunsing in the form of a bench that deploys sharp spikes on the seat if the user doesn’t pay a meter. It serves as a powerful metaphor for discriminatory design. 

      “Dr. Benjamin’s keynote was seriously mind-blowing,” said Cherry Ibrahim, human resources generalist in the MIT Libraries. “One part that really grabbed my attention was when she talked about benches purposely designed to prevent unhoused people from sleeping on them. There are these hidden spikes in our community that we might not even realize because they don’t directly impact us.” 

      Benjamin urged the audience to look for those “spikes,” which new technologies can make even more insidious — gender and racial bias in facial recognition, the use of racial data in software used to predict student success, algorithmic bias in health care — often in the guise of progress. She coined the term “the New Jim Code” to describe the combination of coded bias and the imagined objectivity we ascribe to technology. 

      “At the MIT Libraries, we’re deeply concerned with combating inequities through our work, whether it’s democratizing access to data or investigating ways disparate communities can participate in scholarship with minimal bias or barriers,” says Director of Libraries Chris Bourg. “It’s our mission to remove the ‘spikes’ in the systems through which we create, use, and share knowledge.”

      Calling out the harms encoded into our digital world is critical, argues Benjamin, but we must also create alternatives. This is where the collective power of individuals can be transformative. Benjamin shared examples of those who are “re-imagining the default settings of technology and society,” citing initiatives like Data for Black Lives movement and the Detroit Community Technology Project. “I’m interested in the way that everyday people are changing the digital ecosystem and demanding different kinds of rights and responsibilities and protections,” she said.

      In 2020, Benjamin founded the Ida B. Wells Just Data Lab with a goal of bringing together students, educators, activists, and artists to develop a critical and creative approach to data conception, production, and circulation. Its projects have examined different aspects of data and racial inequality: assessing the impact of Covid-19 on student learning; providing resources that confront the experience of Black mourning, grief, and mental health; or developing a playbook for Black maternal mental health. Through the lab’s student-led projects Benjamin sees the next generation re-imagining technology in ways that respond to the needs of marginalized people.

      “If inequity is woven into the very fabric of our society — we see it from policing to education to health care to work — then each twist, coil, and code is a chance for us to weave new patterns, practices, and politics,” she said. “The vastness of the problems that we’re up against will be their undoing.” More

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      Celebrating open data

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      The inaugural MIT Prize for Open Data, which included a $2,500 cash prize, was recently awarded to 10 individual and group research projects. Presented jointly by the School of Science and the MIT Libraries, the prize recognizes MIT-affiliated researchers who make their data openly accessible and reusable by others. The prize winners and 16 honorable mention recipients were honored at the Open Data @ MIT event held Oct. 28 at Hayden Library. 

      “By making data open, researchers create opportunities for novel uses of their data and for new insights to be gleaned,” says Chris Bourg, director of MIT Libraries. “Open data accelerates scholarly progress and discovery, advances equity in scholarly participation, and increases transparency, replicability, and trust in science.” 

      Recognizing shared values

      Spearheaded by Bourg and Rebecca Saxe, associate dean of the School of Science and John W. Jarve (1978) Professor of Brain and Cognitive Sciences, the MIT Prize for Open Data was launched to highlight the value of open data at MIT and to encourage the next generation of researchers. Nominations were solicited from across the Institute, with a focus on trainees: research technicians, undergraduate or graduate students, or postdocs.

      “By launching an MIT-wide prize and event, we aimed to create visibility for the scholars who create, use, and advocate for open data,” says Saxe. “Highlighting this research and creating opportunities for networking would also help open-data advocates across campus find each other.” 

      Recognizing researchers who share data was also one of the recommendations of the Ad Hoc Task Force on Open Access to MIT’s Research, which Bourg co-chaired with Hal Abelson, Class of 1922 Professor, Department of Electrical Engineering and Computer Science. An annual award was one of the strategies put forth by the task force to further the Institute’s mission to disseminate the fruits of its research and scholarship as widely as possible.

      Strong competition

      Winners and honorable mentions were chosen from more than 70 nominees, representing all five schools, the MIT Schwarzman College of Computing, and several research centers across MIT. A committee composed of faculty, staff, and a graduate student made the selections:

      Yunsie Chung, graduate student in the Department of Chemical Engineering, won for SolProp, the largest open-source dataset with temperature-dependent solubility values of organic compounds. 
      Matthew Groh, graduate student, MIT Media Lab, accepted on behalf of the team behind the Fitzpatrick 17k dataset, an open dataset consisting of nearly 17,000 images of skin disease alongside skin disease and skin tone annotations. 
      Tom Pollard, research scientist at the Institute for Medical Engineering and Science, accepted on behalf of the PhysioNet team. This data-sharing platform enables thousands of clinical and machine-learning research studies each year and allows researchers to share sensitive resources that would not be possible through typical data sharing platforms. 
      Joseph Replogle, graduate student with the Whitehead Institute for Biomedical Research, was recognized for the Genome-wide Perturb-seq dataset, the largest publicly available, single-cell transcriptional dataset collected to date. 
      Pedro Reynolds-Cuéllar, graduate student with the MIT Media Lab/Art, Culture, and Technology, and Diana Duarte, co-founder at Diversa, won for Retos, an open-data platform for detailed documentation and sharing of local innovations from under-resourced settings. 
      Maanas Sharma, an undergraduate student, led States of Emergency, a nationwide project analyzing and grading the responses of prison systems to Covid-19 using data scraped from public databases and manually collected data. 
      Djuna von Maydell, graduate student in the Department of Brain and Cognitive Sciences, created the first publicly available dataset of single-cell gene expression from postmortem human brain tissue of patients who are carriers of APOE4, the major Alzheimer’s disease risk gene. 
      Raechel Walker, graduate researcher in the MIT Media Lab, and her collaborators created a Data Activism Curriculum for high school students through the Mayor’s Summer Youth Employment Program in Cambridge, Massachusetts. Students learned how to use data science to recognize, mitigate, and advocate for people who are disproportionately impacted by systemic inequality. 
      Suyeol Yun, graduate student in the Department of Political Science, was recognized for DeepWTO, a project creating open data for use in legal natural language processing research using cases from the World Trade Organization. 
      Jonathan Zheng, graduate student in the Department of Chemical Engineering, won for an open IUPAC dataset for acid dissociation constants, or “pKas,” physicochemical properties that govern how acidic a chemical is in a solution.
      A full list of winners and honorable mentions is available on the Open Data @ MIT website.

      A campus-wide celebration

      Awards were presented at a celebratory event held in the Nexus in Hayden Library during International Open Access Week. School of Science Dean Nergis Mavalvala kicked off the program by describing the long and proud history of open scholarship at MIT, citing the Institute-wide faculty open access policy and the launch of the open-source digital repository DSpace. “When I was a graduate student, we were trying to figure out how to share our theses during the days of the nascent internet,” she said, “With DSpace, MIT was figuring it out for us.” 

      The centerpiece of the program was a series of five-minute presentations from the prize winners on their research. Presenters detailed the ways they created, used, or advocated for open data, and the value that openness brings to their respective fields. Winner Djuna von Maydell, a graduate student in Professor Li-Huei Tsai’s lab who studies the genetic causes of neurodegeneration, underscored why it is important to share data, particularly data obtained from postmortem human brains. 

      “This is data generated from human brains, so every data point stems from a living, breathing human being, who presumably made this donation in the hope that we would use it to advance knowledge and uncover truth,” von Maydell said. “To maximize the probability of that happening, we have to make it available to the scientific community.” 

      MIT community members who would like to learn more about making their research data open can consult MIT Libraries’ Data Services team.  More

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      MIT to launch new Office of Research Computing and Data

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      As the computing and data needs of MIT’s research community continue to grow — both in their quantity and complexity — the Institute is launching a new effort to ensure that researchers have access to the advanced computing resources and data management services they need to do their best work. 

      At the core of this effort is the creation of the new Office of Research Computing and Data (ORCD), to be led by Professor Peter Fisher, who will step down as head of the Department of Physics to serve as the office’s inaugural director. The office, which formally opens in September, will build on and replace the MIT Research Computing Project, an initiative supported by the Office of the Vice President for Research, which contributed in recent years to improving the computing resources available to MIT researchers.

      “Almost every scientific field makes use of research computing to carry out our mission at MIT — and computing needs vary between different research groups. In my world, high-energy physics experiments need large amounts of storage and many identical general-purpose CPUs, while astrophysical theorists simulating the formation of galaxy clusters need relatively little storage, but many CPUs with high-speed connections between them,” says Fisher, the Thomas A. Frank (1977) Professor of Physics, who will take up the mantle of ORCD director on Sept. 1.

      “I envision ORCD to be, at a minimum, a centralized system with a spectrum of different capabilities to allow our MIT researchers to start their projects and understand the computational resources needed to execute them,” Fisher adds.

      The Office of Research Computing and Data will provide services spanning hardware, software, and cloud solutions, including data storage and retrieval, and offer advice, training, documentation, and data curation for MIT’s research community. It will also work to develop innovative solutions that address emerging or highly specialized needs, and it will advance strategic collaborations with industry.

      The exceptional performance of MIT’s endowment last year has provided a unique opportunity for MIT to distribute endowment funds to accelerate progress on an array of Institute priorities in fiscal year 2023, beginning July 1, 2022. On the basis of community input and visiting committee feedback, MIT’s leadership identified research computing as one such priority, enabling the expanded effort that the Institute commenced today. Future operation of ORCD will incorporate a cost-recovery model.

      In his new role, Fisher will report to Maria Zuber, MIT’s vice president for research, and coordinate closely with MIT Information Systems and Technology (IS&T), MIT Libraries, and the deans of the five schools and the MIT Schwarzman College of Computing, among others. He will also work closely with Provost Cindy Barnhart.

      “I am thrilled that Peter has agreed to take on this important role,” says Zuber. “Under his leadership, I am confident that we’ll be able to build on the important progress of recent years to deliver to MIT researchers best-in-class infrastructure, services, and expertise so they can maximize the performance of their research.”

      MIT’s research computing capabilities have grown significantly in recent years. Ten years ago, the Institute joined with a number of other Massachusetts universities to establish the Massachusetts Green High-Performance Computing Center (MGHPCC) in Holyoke to provide the high-performance, low-carbon computing power necessary to carry out cutting-edge research while reducing its environmental impact. MIT’s capacity at the MGHPCC is now almost fully utilized, however, and an expansion is underway.

      The need for more advanced computing capacity is not the only issue to be addressed. Over the last decade, there have been considerable advances in cloud computing, which is increasingly used in research computing, requiring the Institute to take a new look at how it works with cloud services providers and then allocates cloud resources to departments, labs, and centers. And MIT’s longstanding model for research computing — which has been mostly decentralized — can lead to inefficiencies and inequities among departments, even as it offers flexibility.

      The Institute has been carefully assessing how to address these issues for several years, including in connection with the establishment of the MIT Schwarzman College of Computing. In August 2019, a college task force on computing infrastructure found a “campus-wide preference for an overarching organizational model of computing infrastructure that transcends a college or school and most logically falls under senior leadership.” The task force’s report also addressed the need for a better balance between centralized and decentralized research computing resources.

      “The needs for computing infrastructure and support vary considerably across disciplines,” says Daniel Huttenlocher, dean of the MIT Schwarzman College of Computing and the Henry Ellis Warren Professor of Electrical Engineering and Computer Science. “With the new Office of Research Computing and Data, the Institute is seizing the opportunity to transform its approach to supporting research computing and data, including not only hardware and cloud computing but also expertise. This move is a critical step forward in supporting MIT’s research and scholarship.”

      Over time, ORCD (pronounced “orchid”) aims to recruit a staff of professionals, including data scientists and engineers and system and hardware administrators, who will enhance, support, and maintain MIT’s research computing infrastructure, and ensure that all researchers on campus have access to a minimum level of advanced computing and data management.

      The new research computing and data effort is part of a broader push to modernize MIT’s information technology infrastructure and systems. “We are at an inflection point, where we have a significant opportunity to invest in core needs, replace or upgrade aging systems, and respond fully to the changing needs of our faculty, students, and staff,” says Mark Silis, MIT’s vice president for information systems and technology. “We are thrilled to have a new partner in the Office of Research Computing and Data as we embark on this important work.” More