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    <title>Recent ucsc_gpm_oapdeposits items</title>
    <link>https://escholarship.org/uc/ucsc_gpm_oapdeposits/rss</link>
    <description>Recent eScholarship items from Department of Computational Media Open Access Policy Deposits</description>
    <pubDate>Thu, 25 Jun 2026 09:53:20 +0000</pubDate>
    <item>
      <title>Preparing and Experiencing Food During Life Events: Implications for Technology Supporting Social and Value Changes</title>
      <link>https://escholarship.org/uc/item/3z32c080</link>
      <description>Preparing and Experiencing Food During Life Events: Implications for Technology Supporting Social and Value Changes</description>
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      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Ha, Seung Wan</name>
      </author>
      <author>
        <name>Nurain, Novia</name>
      </author>
      <author>
        <name>Agapie, Elena</name>
      </author>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
    </item>
    <item>
      <title>Flight Incident Analysis Through Symbolic Argumentation</title>
      <link>https://escholarship.org/uc/item/9bj7m453</link>
      <description>Flight Incident Analysis Through Symbolic Argumentation</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9bj7m453</guid>
      <pubDate>Thu, 17 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>de Niz, Dionisio</name>
      </author>
      <author>
        <name>Andersson, Bjorn</name>
      </author>
      <author>
        <name>Klein, Mark H</name>
      </author>
      <author>
        <name>Lehoczky, John</name>
      </author>
      <author>
        <name>Kim, Hyoseung</name>
      </author>
      <author>
        <name>Romanski, George</name>
      </author>
      <author>
        <name>Preston, Jonathan</name>
      </author>
      <author>
        <name>Fazi, Floyd</name>
      </author>
      <author>
        <name>Shapiro, Daniel</name>
      </author>
      <author>
        <name>Schmidt, Douglas C</name>
      </author>
      <author>
        <name>Koontz, Ronald</name>
      </author>
      <author>
        <name>Procter, Sam</name>
      </author>
    </item>
    <item>
      <title>Microscope Upcycling: Transforming legacy microscopes into automated cloud-integrated imaging systems</title>
      <link>https://escholarship.org/uc/item/8kd6w2hd</link>
      <description>Computerized microscopes improve repeatability, throughput, antisepsis, data analysis and data sharing in the biological laboratory, but these machines are cost-prohibitive in most academic environments. This is a barrier into collecting the large and consistent datasets required for machine learning analyses of microscopy data. We demonstrate hardware modifications and software to bring the features of modern computerized microscopes to decades-old legacy laboratory inverted microscopes. We demonstrate automation of X-Y positioning, focus stacking, image acquisition and image storage.</description>
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      <pubDate>Fri, 18 Apr 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Ehrlich, Drew</name>
      </author>
      <author>
        <name>Rosen, Yohei</name>
      </author>
      <author>
        <name>Parks, David F</name>
      </author>
      <author>
        <name>Doganyigit, Kivilcim</name>
      </author>
      <author>
        <name>Fenimore, Ryan</name>
      </author>
      <author>
        <name>Vera-Choqqueccota, Samira</name>
      </author>
      <author>
        <name>Hernandez, Sebastian</name>
      </author>
      <author>
        <name>Toledo, Anna</name>
      </author>
      <author>
        <name>Haussler, David</name>
        <uri>https://orcid.org/0000-0003-1533-4575</uri>
      </author>
      <author>
        <name>Kurniawan, Sri</name>
      </author>
      <author>
        <name>Teodorescu, Mircea</name>
      </author>
    </item>
    <item>
      <title>Generating Together: Lessons Learned from Developing an Educational Visual Novel with AI Collaboration</title>
      <link>https://escholarship.org/uc/item/8pf7826g</link>
      <description>Visual novels are a popular game genre for educational games. However, they often feature pre-authored plot structures that cannot dynamically adjust to the player's progression through learning objectives. Employing procedural storytelling techniques boosts plot dynamism, but this comes at the cost of needing a larger repository of content (dialogue and images) to support different learning progressions and objectives. In this paper, we present postmortem-style case studies describing the lessons we learned from attempting to integrate large-language models (LLMs) and text-to-image models into the development of an educational visual novel about responsible conduct of research. Specifically, we discuss our experiences employing generative AI in our dialogue, character sprite, and background image creation processes.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8pf7826g</guid>
      <pubDate>Fri, 28 Feb 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Shields, Samuel</name>
      </author>
      <author>
        <name>Calderwood, Alexander</name>
      </author>
      <author>
        <name>Johnson-Bey, Shi</name>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
      <author>
        <name>Mateas, Michael</name>
      </author>
      <author>
        <name>Melcer, Edward</name>
      </author>
    </item>
    <item>
      <title>Academical: A Dynamic Interactive Narrative Game for Responsible Conduct of Research Training</title>
      <link>https://escholarship.org/uc/item/4s01k7f2</link>
      <description>Our demo showcases a choice-based interactive narrative game created to teach responsible conduct of research and research ethics. It re-imagines the experience of a game previously published in the literature, using a content-selection system that dynamically constructs dialogue choices during play. Our goal is to provide players with more opportunities to experience agency than they would have with the original game's hand-authored branching narrative structure. Primarily, our system implements a conversation thread-switching mechanic that allows players to fluidly enter/exit conversation topics as one would in a real-life conversation.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4s01k7f2</guid>
      <pubDate>Fri, 28 Feb 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Johnson-Bey, Shi</name>
      </author>
      <author>
        <name>Shields, Samuel</name>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
      </author>
      <author>
        <name>Melcer, Edward</name>
      </author>
    </item>
    <item>
      <title>Building Visual Novels with Social Simulation and Storylets</title>
      <link>https://escholarship.org/uc/item/21r7h0fq</link>
      <description>Simulationist interactive narrative systems allow game makers to craft reactive stories driven by simulated characters and their social dynamics. These systems produce narrative experiences that feel more emergent but may lack a coherent plot structure. We explored how to combine the emergent possibilities of social simulation with a procedural narrative system that affords writers strong authorial control over the plot. We did this by developing a Unity extension called Anansi that helps people create social simulation-driven visual novels. It enables users to inject simulation data into their story dialogue using logical queries and parameterized storylets written using Ink. The paper describes an overview of our extension and how we empower writers to drive narrative progression using cascading social effects from player choices.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/21r7h0fq</guid>
      <pubDate>Fri, 28 Feb 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Johnson-Bey, Shi</name>
      </author>
      <author>
        <name>Liao, Kira</name>
      </author>
      <author>
        <name>Shields, Samuel</name>
      </author>
      <author>
        <name>Hwang, Daeun</name>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
      <author>
        <name>Mateas, Michael</name>
      </author>
      <author>
        <name>Melcer, Edward</name>
      </author>
    </item>
    <item>
      <title>The feasibility, usability, and clinical utility of traditional paper food and symptom journals for patients with irritable bowel syndrome</title>
      <link>https://escholarship.org/uc/item/4vg7g9n0</link>
      <description>BACKGROUND: Paper food and gastrointestinal (GI) symptom journals are used to help irritable bowel syndrome (IBS) patients determine potential trigger foods. The primary aim of this study was to evaluate the feasibility, usability, and clinical utility of such journals as a data collection tool. A secondary aim was to explore a method for analyzing journal data to describe patterns of diet and symptoms.
METHODS: Participants (N=17) were asked to log three sets of 3-day food and symptom journals over a 15-day period. Feasibility was evaluated by journal completion rates, symptom logging compliance, and logging fatigability. The feasibility, usability, and clinical utility of journaling were also assessed by a customized evaluation and exit interview. For each journal, regression analyses were conducted to examine relationships between key meal nutrients and subsequent symptoms.
KEY RESULTS: Most participants were young (mean age 35±12) Caucasian (N=13) women (N=14). Journal completion...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4vg7g9n0</guid>
      <pubDate>Fri, 14 Feb 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Zia, JK</name>
      </author>
      <author>
        <name>Chung, C‐F</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Schroeder, J</name>
      </author>
      <author>
        <name>Munson, SA</name>
      </author>
      <author>
        <name>Kientz, JA</name>
      </author>
      <author>
        <name>Fogarty, J</name>
      </author>
      <author>
        <name>Bales, E</name>
      </author>
      <author>
        <name>Schenk, JM</name>
      </author>
      <author>
        <name>Heitkemper, MM</name>
      </author>
    </item>
    <item>
      <title>Opportunities to design better computer vison-assisted food diaries to support individuals and experts in dietary assessment: An observation and interview study with nutrition experts</title>
      <link>https://escholarship.org/uc/item/7tv17713</link>
      <description>Automatic visual recognition for photo-based food diaries is increasingly prevalent. However, existing tools in food recognition often focus on food classification and calorie counting, which may not be sufficient to support the variety of food and healthy eating goals people have. To understand how to better design computer-vision-based food diaries to support healthy eating, we began to examine how nutrition experts, such as dietitians, use the visual features of food photos to evaluate diet quality. We conducted an observation and interview study with 18 dietitians, during which we asked the dietitians to review a seven-day photo-based food diary and fill out an evaluation form about their observations, recommendations, and questions. We then conducted follow-up interviews to understand their strategies, needs, and challenges of photo diary review. Our findings show that dietitians used the photo features to understand long-term eating patterns, diet variety, eating contexts,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7tv17713</guid>
      <pubDate>Fri, 6 Dec 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Chiang, Pei-Ni</name>
      </author>
      <author>
        <name>Tan, Connie Ann</name>
      </author>
      <author>
        <name>Wu, Chien-Chun</name>
      </author>
      <author>
        <name>Schmidt, Haley</name>
      </author>
      <author>
        <name>Kotarski, Aric</name>
      </author>
      <author>
        <name>Guise, David</name>
      </author>
    </item>
    <item>
      <title>Identifying and Planning for Individualized Change</title>
      <link>https://escholarship.org/uc/item/8636p2dz</link>
      <description>Identifying and planning strategies that support a healthy lifestyle or manage a chronic disease often require patient-provider collaboration. For example, people with healthy eating goals often share everyday food, exercise, or sleep data with health coaches or nutritionists to find opportunities for change, and patients with irritable bowel syndrome (IBS) often gather food and symptom data as part of working with providers to diagnose and manage symptoms. However, a lack of effective support often prevents health experts from reviewing large amounts of data in time-constrained visits, prevents focusing on individual goals, and prevents generating correct, individualized, and actionable recommendations. To examine how to design photo-based diaries to help people and health experts exchange knowledge and focus on collaboration goals when reviewing the data together, we designed and developed Foodprint, a photo-based food diary. Foodprint includes three components: (1) A mobile...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8636p2dz</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Wang, Qiaosi</name>
      </author>
      <author>
        <name>Schroeder, Jessica</name>
      </author>
      <author>
        <name>Cole, Allison</name>
      </author>
      <author>
        <name>Zia, Jasmine</name>
      </author>
      <author>
        <name>Fogarty, James</name>
      </author>
      <author>
        <name>Munson, Sean A</name>
      </author>
    </item>
    <item>
      <title>Boundary Negotiating Artifacts in Personal Informatics</title>
      <link>https://escholarship.org/uc/item/6tw6w445</link>
      <description>Patient-generated data is increasingly common in chronic disease care management. Smartphone applications and wearable sensors help patients more easily collect health information. However, current commercial tools often do not effectively support patients and providers in collaboration surrounding these data. This paper examines patient expectations and current collaboration practices around patient-generated data. We survey 211 patients, interview 18 patients, and re-analyze a dataset of 21 provider interviews. We find that collaboration occurs in every stage of self-tracking and that patients and providers create boundary negotiating artifacts to support the collaboration. Building upon current practices with patient-generated data, we use these theories of patient and provider collaboration to analyze misunderstandings and privacy concerns as well as identify opportunities to better support these collaborations. We reflect on the social nature of patient-provider collaboration...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6tw6w445</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Dew, Kristin</name>
      </author>
      <author>
        <name>Cole, Allison</name>
      </author>
      <author>
        <name>Zia, Jasmine</name>
      </author>
      <author>
        <name>Fogarty, James</name>
      </author>
      <author>
        <name>Kientz, Julie A</name>
      </author>
      <author>
        <name>Munson, Sean A</name>
      </author>
    </item>
    <item>
      <title>When Personal Tracking Becomes Social</title>
      <link>https://escholarship.org/uc/item/5j2874dn</link>
      <description>Many people appropriate social media and online communities in their pursuit of personal health goals, such as healthy eating or increased physical activity. However, people struggle with impression management, and with reaching the right audiences when they share health information on these platforms. Instagram, a popular photo-based social media platform, has attracted many people who post and share their food photos. We aim to inform the design of tools to support healthy behaviors by understanding how people appropriate Instagram to track and share food data, the benefits they obtain from doing so, and the challenges they encounter. We interviewed 16 women who consistently record and share what they eat on Instagram. Participants tracked to support themselves and others in their pursuit of healthy eating goals. They sought social support for their own tracking and healthy behaviors and strove to provide that support for others. People adapted their personal tracking practices...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5j2874dn</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Agapie, Elena</name>
      </author>
      <author>
        <name>Schroeder, Jessica</name>
      </author>
      <author>
        <name>Mishra, Sonali</name>
      </author>
      <author>
        <name>Fogarty, James</name>
      </author>
      <author>
        <name>Munson, Sean A</name>
      </author>
    </item>
    <item>
      <title>Implementation of a New Kiosk Technology for Blood Pressure Management in a Family Medicine Clinic: from the WWAMI Region Practice and Research Network</title>
      <link>https://escholarship.org/uc/item/4rp38618</link>
      <description>BACKGROUND: Using a self-service kiosk to measure blood pressure (BP) has the potential to increase patients' awareness of their BP control and free up medical assistant (MA) time. The objective of this study was to evaluate BP kiosk acceptability and usability, as well as its effects on the workflow of patient BP self-measurement in a primary care clinic.
METHODS: We used qualitative and quantitative assessments of kiosk implementation via meetings with clinic leaders, focus groups with clinic providers and staff, observations of kiosk users, and surveys of kiosk users at 2 and 8 months.
RESULTS: Most patients were comfortable using the kiosk (82% at 2 months, 87% at 8 months). Initial provider concerns included accuracy, but most gained confidence after comparing it with other monitors and reviewing the literature supporting its accuracy. Patients and providers saw many benefits: easier BP checks, increased patient engagement, and saved MA time for other tasks. The clinic addressed...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4rp38618</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Munson, Sean A</name>
      </author>
      <author>
        <name>Thompson, Matthew J</name>
      </author>
      <author>
        <name>Baldwin, Laura-Mae</name>
      </author>
      <author>
        <name>Kaplan, Jeffrey</name>
      </author>
      <author>
        <name>Cline, Randall</name>
      </author>
      <author>
        <name>Green, Beverly B</name>
      </author>
    </item>
    <item>
      <title>The Importance of Starting With Goals in N-of-1 Studies</title>
      <link>https://escholarship.org/uc/item/4p91b0zn</link>
      <description>N-of-1 tools offer the potential to support people in monitoring health and identifying individualized health management strategies. We argue that elicitation of individualized goals and customization of tracking to support those goals are a critical yet under-studied and under-supported aspect of self-tracking. We review examples of self-tracking from across a range of chronic conditions and self-tracking designs (e.g., self-monitoring, correlation analyses, self-experimentation). Together, these examples show how failure to elicit goals can lead to ineffective tracking routines, breakdowns in collaboration (e.g., between patients and providers, among families), increased burdens, and even designs that encourage behaviors counter to a person's goals. We discuss potential techniques for eliciting and refining goals, scaffolding an appropriate tracking routine based on those goals, and presenting results in ways that advance individual goals while preserving individual agency....</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4p91b0zn</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Munson, Sean A</name>
      </author>
      <author>
        <name>Schroeder, Jessica</name>
      </author>
      <author>
        <name>Karkar, Ravi</name>
      </author>
      <author>
        <name>Kientz, Julie A</name>
      </author>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Fogarty, James</name>
      </author>
    </item>
    <item>
      <title>Survey on the Past Decade of Technology in Animal Enrichment: A Scoping Review</title>
      <link>https://escholarship.org/uc/item/20c876gs</link>
      <description>Environmental enrichment is adding complexity to an environment that has a positive impact on a captive animal as a necessity of care. Computing technology is being rapidly weaved throughout the space in both enrichment devices as well as evaluating enrichment outcomes. In this article, we present a scoping review of 102 captive animal enrichment studies and propose a contextual lens for exploring current practices. We discuss the importance of directed growth in species inclusion, transitioning beyond anthro-centric designs, and utilizing shared methodologies.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/20c876gs</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Kresnye, K Cassie</name>
      </author>
      <author>
        <name>Chung, Chia-Fang</name>
        <uri>https://orcid.org/0000-0002-3374-2073</uri>
      </author>
      <author>
        <name>Martin, Christopher Flynn</name>
      </author>
      <author>
        <name>Shih, Patrick C</name>
      </author>
    </item>
    <item>
      <title>Use of patient-generated health data across healthcare settings: implications for health systems</title>
      <link>https://escholarship.org/uc/item/1dp35413</link>
      <description>OBJECTIVE: The growing prevalence of chronic conditions requiring changes in lifestyle and at-home self-management has increased interest in and need for supplementing clinic visits with data generated by patients outside the clinic. Patient-generated health data (PGHD) support the ability to diagnose and manage chronic conditions, to improve health outcomes, and have the potential to facilitate more "connected health" between patients and their care teams; however, health systems have been slow to adopt PGHD use in clinical care.
MATERIALS AND METHODS: We surveyed current and potential users of PGHD to catalog how PGHD is integrated into clinical care at an academic health center. The survey included questions about data type, method of collection, and clinical uses of PGHD. Current users were asked to provide detailed case studies of PGHD use in research and care delivery.
RESULTS: Thirty-one respondents completed the survey. Seventeen individuals contributed detailed case studies...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1dp35413</guid>
      <pubDate>Fri, 25 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Austin, Elizabeth</name>
      </author>
      <author>
        <name>Lee, Jenney R</name>
      </author>
      <author>
        <name>Amtmann, Dagmar</name>
      </author>
      <author>
        <name>Bloch, Rich</name>
      </author>
      <author>
        <name>Lawrence, Sarah O</name>
      </author>
      <author>
        <name>McCall, Debbe</name>
      </author>
      <author>
        <name>Munson, Sean</name>
      </author>
      <author>
        <name>Lavallee, Danielle C</name>
      </author>
    </item>
    <item>
      <title>ENTRUST: A Serious Game-Based Virtual Patient Platform to Assess Entrustable Professional Activities in Graduate Medical Education.</title>
      <link>https://escholarship.org/uc/item/2mw6h31f</link>
      <description>Background: As entrustable professional activities (EPAs) are implemented in graduate medical education, there is a great need for tools to efficiently and objectively evaluate clinical competence. Readiness for entrustment in surgery requires not only assessment of technical ability, but also the critical skill of clinical decision-making.
Objective: We report the development of ENTRUST, a serious game-based, virtual patient case creation and simulation platform to assess trainees' decision-making competence. A case scenario and corresponding scoring algorithm for the Inguinal Hernia EPA was iteratively developed and aligned with the description and essential functions outlined by the American Board of Surgery. In this study we report preliminary feasibility data and validity evidence.
Methods: In January 2021, the case scenario was deployed and piloted on ENTRUST with 19 participants of varying surgical expertise levels to demonstrate proof of concept and initial validity evidence....</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2mw6h31f</guid>
      <pubDate>Thu, 19 Sep 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Lin, Dana T</name>
      </author>
      <author>
        <name>Melcer, Edward F</name>
        <uri>https://orcid.org/0000-0003-1760-5279</uri>
      </author>
      <author>
        <name>Keehl, Oleksandra</name>
      </author>
      <author>
        <name>Eddington, Hyrum</name>
      </author>
      <author>
        <name>Trickey, Amber W</name>
      </author>
      <author>
        <name>Tsai, Jason</name>
      </author>
      <author>
        <name>Camacho, Fatyma</name>
      </author>
      <author>
        <name>Merrell, Sylvia Bereknyei</name>
      </author>
      <author>
        <name>Korndorffer, James</name>
      </author>
      <author>
        <name>Liebert, Cara A</name>
      </author>
    </item>
    <item>
      <title>The Eyes, the Hands and the Brain: What can Text-to-Image Models Offer for Game Design and Visual Creativity?</title>
      <link>https://escholarship.org/uc/item/7tp7q651</link>
      <description>The Eyes, the Hands and the Brain: What can Text-to-Image Models Offer for Game Design and Visual Creativity?</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7tp7q651</guid>
      <pubDate>Thu, 12 Sep 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Zhou, Hongwei</name>
      </author>
      <author>
        <name>Zhu, Jichen</name>
      </author>
      <author>
        <name>Mateas, Michael</name>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
    </item>
    <item>
      <title>Designing Between Virtuality and Reality: Improving Inclusiveness in Hybrid Spaces</title>
      <link>https://escholarship.org/uc/item/4gr9t97x</link>
      <description>This experience report designs and introduces an application, PlantNet, which is based on hybrid spaces and combines augmented reality (AR) to help enhance the inclusiveness and accessibility of mobile application design. PlantNet is a hiking-focused application incorporating virtual plant cultivation and collection aimed at users with and without disabilities. This report first introduces the theoretical basis of this application and then introduces its main functions and gameplay. Finally, this report discusses the possibilities of hybrid spaces and AR to enhance the inclusiveness and experience of applications. The report concludes by describing the limitations of the current design and making recommendations to provide a foundation for future design.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4gr9t97x</guid>
      <pubDate>Fri, 2 Aug 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Liu, Peiyao</name>
      </author>
      <author>
        <name>Xie, Chenxing</name>
      </author>
    </item>
    <item>
      <title>Thought Chart: tracking the thought with manifold learning during emotion regulation</title>
      <link>https://escholarship.org/uc/item/98n6v76r</link>
      <description>The Nash embedding theorem demonstrates that any compact manifold can be isometrically embedded in a Euclidean space. Assuming the complex brain states form a high-dimensional manifold in a topological space, we propose a manifold learning framework, termed Thought Chart, to reconstruct and visualize the manifold in a low-dimensional space. Furthermore, it serves as a data-driven approach to discover the underlying dynamics when the brain is engaged in a series of emotion and cognitive regulation tasks. EEG-based temporal dynamic functional connectomes are created based on 20 psychiatrically healthy participants’ EEG recordings during resting state and an emotion regulation task. Graph dissimilarity space embedding was applied to all the dynamic EEG connectomes. In order to visualize the learned manifold in a lower dimensional space, local neighborhood information is reconstructed via k-nearest neighbor-based nonlinear dimensionality reduction (NDR) and epsilon distance-based...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/98n6v76r</guid>
      <pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Xing, Mengqi</name>
      </author>
      <author>
        <name>GadElkarim, Johnson</name>
      </author>
      <author>
        <name>Ajilore, Olusola</name>
      </author>
      <author>
        <name>Wolfson, Ouri</name>
      </author>
      <author>
        <name>Forbes, Angus</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
      <author>
        <name>Phan, K Luan</name>
      </author>
      <author>
        <name>Klumpp, Heide</name>
      </author>
      <author>
        <name>Leow, Alex</name>
      </author>
    </item>
    <item>
      <title>The Kappa platform for rule-based modeling</title>
      <link>https://escholarship.org/uc/item/8qv60198</link>
      <description>Motivation: We present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction.
Results: We discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8qv60198</guid>
      <pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Boutillier, Pierre</name>
      </author>
      <author>
        <name>Maasha, Mutaamba</name>
      </author>
      <author>
        <name>Li, Xing</name>
      </author>
      <author>
        <name>Medina-Abarca, Héctor F</name>
      </author>
      <author>
        <name>Krivine, Jean</name>
      </author>
      <author>
        <name>Feret, Jérôme</name>
      </author>
      <author>
        <name>Cristescu, Ioana</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
      <author>
        <name>Fontana, Walter</name>
      </author>
    </item>
    <item>
      <title>Exploring the Design Space of Social Physics Engines in Games</title>
      <link>https://escholarship.org/uc/item/5811p2s0</link>
      <description>Exploring the Design Space of Social Physics Engines in Games</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5811p2s0</guid>
      <pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Johnson-Bey, Shi</name>
      </author>
      <author>
        <name>Nelson, Mark J</name>
      </author>
      <author>
        <name>Mateas, Michael</name>
      </author>
    </item>
    <item>
      <title>A taxonomy of visualization tasks for the analysis of biological pathway data</title>
      <link>https://escholarship.org/uc/item/4f69s1dw</link>
      <description>BackgroundUnderstanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process. Visual representations can help researchers understand, interact with, and reason about these complex pathways in a number of ways. At the same time, these datasets offer unique challenges for visualization, due to their complexity and heterogeneity.ResultsHere, we present taxonomy of tasks that are regularly performed by researchers who work with biological pathway data. The generation of these tasks was done in conjunction with interviews with several domain experts in biology. These tasks require further classification than is provided by existing taxonomies. We also examine existing visualization techniques that support each task, and we...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4f69s1dw</guid>
      <pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Murray, Paul</name>
      </author>
      <author>
        <name>McGee, Fintan</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
    </item>
    <item>
      <title>The intrinsic geometry of the human brain connectome</title>
      <link>https://escholarship.org/uc/item/370500nq</link>
      <description>Abstract
This paper describes novel methods for constructing the intrinsic geometry of the human brain connectome using dimensionality-reduction techniques. We posit that the high-dimensional, complex geometry that represents this intrinsic topology can be mathematically embedded into lower dimensions using coupling patterns encoded in the corresponding brain connectivity graphs. We tested both linear and nonlinear dimensionality-reduction techniques using the diffusion-weighted structural connectome data acquired from a sample of healthy subjects. Results supported the nonlinearity of brain connectivity data, as linear reduction techniques such as the multidimensional scaling yielded inferior lower-dimensional embeddings. To further validate our results, we demonstrated that for tractography-derived structural connectome more influential regions such as rich-club members of the brain are more centrally mapped or embedded. Further, abnormal brain connectivity can be visually understood...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/370500nq</guid>
      <pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Ye, Allen Q</name>
      </author>
      <author>
        <name>Ajilore, Olusola A</name>
      </author>
      <author>
        <name>Conte, Giorgio</name>
      </author>
      <author>
        <name>GadElkarim, Johnson</name>
      </author>
      <author>
        <name>Thomas-Ramos, Galen</name>
      </author>
      <author>
        <name>Zhan, Liang</name>
      </author>
      <author>
        <name>Yang, Shaolin</name>
      </author>
      <author>
        <name>Kumar, Anand</name>
      </author>
      <author>
        <name>Magin, Richard L</name>
      </author>
      <author>
        <name>G. Forbes, Angus</name>
      </author>
      <author>
        <name>Leow, Alex D</name>
      </author>
    </item>
    <item>
      <title>Gamifying cell culture training: The ‘Seru-Otchi’ experience for undergraduates</title>
      <link>https://escholarship.org/uc/item/9d53v6fr</link>
      <description>Working in a stem cell laboratory necessitates a thorough understanding of complex cell culture protocols, the operation of sensitive scientific equipment, adherence to safety standards, and general laboratory etiquette. For novice student researchers, acquiring the necessary specialized knowledge before their initial laboratory experience can be a formidable task. Similarly, for experienced laboratory personnel, efficiently and uniformly training new trainees to a rigorous standard presents a significant challenge. In response to these issues, we have developed an educational and interactive virtual cell culture environment. This interactive virtual lab aims to equip students with foundational knowledge in maintaining cortical brain organoids and to instill an understanding of pertinent safety procedures and laboratory etiquette. The gamification of this training process seeks to provide laboratory supervisors in highly specialized fields with an effective tool to integrate students...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9d53v6fr</guid>
      <pubDate>Mon, 24 Jun 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Ly, Victoria T</name>
      </author>
      <author>
        <name>Ehrlich, Drew</name>
      </author>
      <author>
        <name>Sevetson, Jess</name>
      </author>
      <author>
        <name>Hoffman, Ryan N</name>
      </author>
      <author>
        <name>Salama, Sofie R</name>
      </author>
      <author>
        <name>Kurniawan, Sri</name>
      </author>
      <author>
        <name>Teodorescu, Mircea</name>
      </author>
    </item>
    <item>
      <title>It's usually not worth the effort unless you get really lucky": Barriers to Undergraduate Research Experiences from the Perspective of Computing Faculty</title>
      <link>https://escholarship.org/uc/item/4vk708gf</link>
      <description>It's usually not worth the effort unless you get really lucky": Barriers to Undergraduate Research Experiences from the Perspective of Computing Faculty</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4vk708gf</guid>
      <pubDate>Mon, 29 Apr 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Sharma, Rhea</name>
      </author>
      <author>
        <name>Nair, Atira</name>
      </author>
      <author>
        <name>Guo, Ana</name>
      </author>
      <author>
        <name>Palea, Dustin</name>
      </author>
      <author>
        <name>Lee, David T</name>
      </author>
    </item>
    <item>
      <title>Designing Spellcasters from Clinician Perspectives: A Customizable Gesture-Based Immersive Virtual Reality Game for Stroke Rehabilitation</title>
      <link>https://escholarship.org/uc/item/0nf117zh</link>
      <description>Developing games is time-consuming and costly. Overly clinical therapy games run the risk of being boring, which defeats the purpose of using games to motivate healing in the first place [
            10
            ,
            23
            ]. In this work, we adapt and repurpose an existing immersive virtual reality (iVR) game, Spellcasters, originally designed purely for entertainment for use as a stroke rehabilitation game—which is particularly relevant in the wake of COVID-19, where telehealth solutions are increasingly needed [
            4
            ]. In preparation for participatory design sessions with stroke survivors, we collaborate with 14 medical professionals to ensure Spellcasters is safe and therapeutically valid for clinical adoption. We present our novel VR sandbox implementation that allows medical professionals to customize appropriate gestures and interactions for each patient’s unique needs. Additionally, we share a co-designed companion app prototype...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0nf117zh</guid>
      <pubDate>Thu, 15 Feb 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Duval, Jared</name>
      </author>
      <author>
        <name>Thakkar, Rutul</name>
      </author>
      <author>
        <name>Du, Delong</name>
      </author>
      <author>
        <name>Chin, Kassandra</name>
      </author>
      <author>
        <name>Luo, Sherry</name>
      </author>
      <author>
        <name>Elor, Aviv</name>
      </author>
      <author>
        <name>El-Nasr, Magy Seif</name>
      </author>
      <author>
        <name>John, Michael</name>
      </author>
    </item>
    <item>
      <title>Being Social in VR Meetings: A Landscape Analysis of Current Tools</title>
      <link>https://escholarship.org/uc/item/868144wt</link>
      <description>Being Social in VR Meetings: A Landscape Analysis of Current Tools</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/868144wt</guid>
      <pubDate>Tue, 23 Jan 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Osborne, Anya</name>
      </author>
      <author>
        <name>Fielder, Sabrina</name>
      </author>
      <author>
        <name>Mcveigh-Schultz, Joshua</name>
      </author>
      <author>
        <name>Lang, Timothy</name>
      </author>
      <author>
        <name>Kreminski, Max</name>
      </author>
      <author>
        <name>Butler, George</name>
      </author>
      <author>
        <name>Li, Jialang Victor</name>
      </author>
      <author>
        <name>Sanchez, Diana R</name>
      </author>
      <author>
        <name>Isbister, Katherine</name>
      </author>
    </item>
    <item>
      <title>CogMod: Simulating Human Information Processing Limitation While Driving</title>
      <link>https://escholarship.org/uc/item/6kz4n4ht</link>
      <description>CogMod: Simulating Human Information Processing Limitation While Driving</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6kz4n4ht</guid>
      <pubDate>Sun, 8 Oct 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Jawad, Abdul</name>
      </author>
      <author>
        <name>Whitehead, Jim</name>
      </author>
    </item>
    <item>
      <title>A Modular Architecture for Procedural Generation of Towns, Intersections and Scenarios for Testing Autonomous Vehicles</title>
      <link>https://escholarship.org/uc/item/2bp6j85s</link>
      <description>A Modular Architecture for Procedural Generation of Towns, Intersections and Scenarios for Testing Autonomous Vehicles</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2bp6j85s</guid>
      <pubDate>Sun, 8 Oct 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Paranjape, Ishaan</name>
      </author>
      <author>
        <name>Jawad, Abdul</name>
      </author>
      <author>
        <name>Xu, Yanwen</name>
      </author>
      <author>
        <name>Song, Asiiah</name>
      </author>
      <author>
        <name>Whitehead, Jim</name>
      </author>
    </item>
    <item>
      <title>Large-Scale Analysis of Visualization Options in a Citizen Science Game</title>
      <link>https://escholarship.org/uc/item/7xt5r0jh</link>
      <description>Visualization is a valuable tool in problem solving, especially for citizen science games. In this study, we analyze data from 36,351 unique players of the citizen science game Foldit over a period of 5 years to understand how their choice of visualization options are affected by expertise and problem type. We identified clusters of visualization options, and found differences in how experts and novices view puzzles and that experts differentially change their views based on puzzle type. These results can inform new design approaches to help both novice and expert players visualize novel problems, develop expertise, and problem solve.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7xt5r0jh</guid>
      <pubDate>Fri, 15 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Miller, Josh Aaron</name>
      </author>
      <author>
        <name>Lee, Vivian</name>
      </author>
      <author>
        <name>Cooper, Seth</name>
      </author>
      <author>
        <name>El-Nasr, Magy Seif</name>
      </author>
    </item>
    <item>
      <title>“Because I'm Bad at the Game!” A Microanalytic Study of Self Regulated Learning in League of Legends</title>
      <link>https://escholarship.org/uc/item/2cj3v9gb</link>
      <description>Self-regulated learning (SRL) is a form of learning guided by the student's own meta-cognition, motivation, and strategic action, often in the absence of an educator. The use of SRL processes and skills has been demonstrated across numerous academic and non-academic contexts including athletics. However, manifestation of these processes within esports has not been studied. Similar to traditional athletes, esports players' performance is likely correlated with their ability to engage SRL skills as they train. Thus, the study of SRL in the context of esports would be valuable in supporting players' learning and mastery of play through specialized training and computational support. Further, an understanding of how SRL manifests in esports would highlight new opportunities to use esports in education. Existing work on SRL in games, however, predominantly focuses on educational games. In this work, we aim to take a first step in the study of SRL in esports by replicating Kitsantas...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2cj3v9gb</guid>
      <pubDate>Fri, 15 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Kleinman, Erica</name>
      </author>
      <author>
        <name>Gayle, Christian</name>
      </author>
      <author>
        <name>El-Nasr, Magy Seif</name>
      </author>
    </item>
    <item>
      <title>Implementing QR codes in academia to improve sample tracking, data accessibility, and traceability in multicampus interdisciplinary collaborations</title>
      <link>https://escholarship.org/uc/item/08f2g4rk</link>
      <description>The growing number of multicampus interdisciplinary projects in academic institutions expedites a necessity for tracking systems that provide instantly accessible data associated with devices, samples, and experimental results to all collaborators involved. This need has become particularly salient with the COVID pandemic when consequent travel restrictions have hampered in person meetings and laboratory visits. Minimizing post-pandemic travel can also help reduce carbon footprint of research activities. Here we developed a Quick Response (QR) code tracking system that integrates project management tools for seamless communication and tracking of materials and devices between multicampus collaborators: one school of medicine, two engineering laboratories, three manufacturing cleanroom sites, and three research laboratories. Here we aimed to use this system to track the design, fabrication, and quality control of bioelectronic devices, in vitro experimental results, and in vivo...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/08f2g4rk</guid>
      <pubDate>Fri, 15 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Hernandez, Cristian</name>
      </author>
      <author>
        <name>Aslankoohi, Elham</name>
      </author>
      <author>
        <name>Frolikov, Pavel</name>
      </author>
      <author>
        <name>Li, Houpu</name>
      </author>
      <author>
        <name>Kurniawan, Sri</name>
      </author>
      <author>
        <name>Rolandi, Marco</name>
      </author>
    </item>
    <item>
      <title>Cloud-controlled microscopy enables remote project-based biology education in underserved Latinx communities</title>
      <link>https://escholarship.org/uc/item/25j044h1</link>
      <description>Project-based learning (PBL) has long been recognized as an effective way to teach complex biology concepts. However, not all institutions have the resources to facilitate effective project-based coursework for students. We have developed a framework for facilitating PBL using remote-controlled internet-connected microscopes. Through this approach, one lab facility can host an experiment for many students around the world simultaneously. Experiments on this platform can be run on long timescales and with materials that are typically unavailable to high school classrooms. This allows students to perform novel research projects rather than just repeating standard classroom experiments. To investigate the impact of this program, we designed and ran six user studies with students worldwide. All experiments were hosted in Santa Cruz and San Francisco, California, with observations and decisions made remotely by the students using their personal computers and cellphones. In surveys...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/25j044h1</guid>
      <pubDate>Fri, 7 Jul 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Baudin, Pierre V</name>
      </author>
      <author>
        <name>Sacksteder, Raina E</name>
      </author>
      <author>
        <name>Worthington, Atesh K</name>
      </author>
      <author>
        <name>Voitiuk, Kateryna</name>
        <uri>https://orcid.org/0000-0002-6392-5188</uri>
      </author>
      <author>
        <name>Ly, Victoria T</name>
      </author>
      <author>
        <name>Hoffman, Ryan N</name>
      </author>
      <author>
        <name>Elliott, Matthew AT</name>
      </author>
      <author>
        <name>Parks, David F</name>
      </author>
      <author>
        <name>Ward, Rebecca</name>
      </author>
      <author>
        <name>Torres-Montoya, Sebastian</name>
      </author>
      <author>
        <name>Amend, Finn</name>
      </author>
      <author>
        <name>Duran, Natalia Montellano</name>
      </author>
      <author>
        <name>Vargas, Paola A</name>
      </author>
      <author>
        <name>Martinez, Guadalupe</name>
      </author>
      <author>
        <name>Ramirez, Sandra M</name>
      </author>
      <author>
        <name>Alvarado-Arnez, Lucia Elena</name>
      </author>
      <author>
        <name>Ehrlich, Drew</name>
      </author>
      <author>
        <name>Rosen, Yohei M</name>
      </author>
      <author>
        <name>Breevoort, Arnar</name>
      </author>
      <author>
        <name>Schouten, Tallulah</name>
      </author>
      <author>
        <name>Kurniawan, Sri</name>
      </author>
      <author>
        <name>Haussler, David</name>
        <uri>https://orcid.org/0000-0003-1533-4575</uri>
      </author>
      <author>
        <name>Teodorescu, Mircea</name>
      </author>
      <author>
        <name>Mostajo-Radji, Mohammed A</name>
      </author>
    </item>
    <item>
      <title>Printing the Polyphorm: Using 3D Printing to Manufacture Biologically Inspired Rhizomatic Structures</title>
      <link>https://escholarship.org/uc/item/1md0s4qv</link>
      <description>We present a pipeline for converting voxelized data generated by the Monte Carlo Physarum Machine (MCPM) based Polyphorm data visualization software into a mesh that can then be 3D printed. This reconstruction technique is based on the Marching Cubes algorithm paired with a suite of pre and post processing tools. Our process can be used to create both biomimetic structures and computational art, and can be tuned to create various visual effects based on the desired stylistic output.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1md0s4qv</guid>
      <pubDate>Fri, 2 Dec 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Ehrlich, Drew</name>
      </author>
    </item>
    <item>
      <title>AgentCraft: An Agent-Based Minecraft Settlement Generator</title>
      <link>https://escholarship.org/uc/item/83p272pq</link>
      <description>AgentCraft is an entry for the Generative Design in Minecraft (GDMC) AI Settlement Generation Competition, including the optional Chronicle Generation challenge. It makes use of an agent-based simulation to organically produce a plausible settlement and a written history of the settlement’s development. Uniquely, AgentCraft utilizes the HTTP Server version of the competition framework to show the agents constructing the settlement in real time—a visual technique that can’t be achieved with the earlier MCEdit framework. In this paper, we aim to provide a point of reference for future agent-based settlement generators by describing how our competition entry works and discussing the benefits and downsides of the agent-based approach. Additionally, we propose a new optional challenge for the GDMC competition, centering on the development of settlement simulations whose inhabitants can be directly observed or interacted with by the player.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/83p272pq</guid>
      <pubDate>Mon, 29 Nov 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Iramanesh, Ari</name>
      </author>
      <author>
        <name>Kreminski, Max</name>
      </author>
    </item>
    <item>
      <title>Generating Playable RPG ROMs for the Game Boy</title>
      <link>https://escholarship.org/uc/item/5c4068hq</link>
      <description>The handheld Game Boy console has seen widespread popularity, with over a hundred million sold. It continues to be relevant as a retro-computing platform, and through emulation a Game Boy ROM can be run in the browser. However, despite being a well-defined, stable platform, there have been very few procedural generation projects that target the Game Boy. By leveraging existing ecosystems of development tools for the Game Boy platform, we construct a game generator that outputs playable ROMs. Paired with this, we seek to improve the ecological validity of game generation by building a generator that acts as a bridge to an active community of non-academic developers. The system interprets and outputs the same data artifacts used in the wild, allowing it both learn from andcontribute to development communities, as well as tapping into the corpus of existing design work.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5c4068hq</guid>
      <pubDate>Wed, 24 Nov 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Karth, Isaac</name>
      </author>
      <author>
        <name>Duplantis, Tamara</name>
      </author>
      <author>
        <name>Kreminski, Max</name>
      </author>
      <author>
        <name>Kashyap, Sachita</name>
      </author>
      <author>
        <name>Kukutla, Vajaya</name>
      </author>
      <author>
        <name>Lo, Aaron</name>
      </author>
      <author>
        <name>Mittal, Anika</name>
      </author>
      <author>
        <name>Park, Harvin</name>
      </author>
      <author>
        <name>Smith, Adam M</name>
      </author>
    </item>
    <item>
      <title>Addressing the fundamental tension of PCGML with discriminative learning</title>
      <link>https://escholarship.org/uc/item/60h562kw</link>
      <description>Addressing the fundamental tension of PCGML with discriminative learning</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/60h562kw</guid>
      <pubDate>Fri, 23 Jul 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Karth, Isaac</name>
        <uri>https://orcid.org/0000-0003-4060-6077</uri>
      </author>
      <author>
        <name>Smith, Adam M</name>
      </author>
    </item>
    <item>
      <title>Generators that read</title>
      <link>https://escholarship.org/uc/item/5wn1g3hv</link>
      <description>Most discussions of procedural content generation have focused primarily on the artifacts that generators produce or the process by which these artifacts are created. Less focus, however, has been placed on the methods by which generators interpret their input. Many generators take complex input, act as part of a generative pipeline, are part of a mixed-initiative communication with the user, or otherwise need to take context into account during generation. In these cases, the process by which the generator reads and makes sense of its input is often just as interesting as the process by which it produces an output artifact. It is worthwhile to take a closer look at how generators read. Via a case study of two erasure poetry generators, we propose the concept of a generativist reading: a process of reading that produces generative models. Many existing generators have dual input/output or reading/writing processes that are presented as a monolithic unit, but our understanding...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5wn1g3hv</guid>
      <pubDate>Fri, 23 Jul 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Kreminski, Max</name>
      </author>
      <author>
        <name>Karth, Isaac</name>
        <uri>https://orcid.org/0000-0003-4060-6077</uri>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
    </item>
    <item>
      <title>Preliminary Poetics of Procedural Generation in Games</title>
      <link>https://escholarship.org/uc/item/56967354</link>
      <description>Procedural Content Generation (PCG) is deeply embedded in many games. While there are many taxonomies of the applications of PCG, less attention has been given to the poetics of PCG. In this paper we present a poetics for generative systems, including a descriptive framework that introduces terms for complex systems (Apollonian order and Dionysian chaos), the form that describes the shape of the generated output (formal gestalt, individual, and repetition), the locus of the generative process (structure, surface, or locus gestalt), the kind of variation the generator uses (style, multiplicity, and cohesion) and the relationship between coherence and the content used as input for the generator. Rather than being mutually exclusive categories, generators can be considered to exhibit aspects of all of these at once.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/56967354</guid>
      <pubDate>Fri, 23 Jul 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Karth, Isaac</name>
        <uri>https://orcid.org/0000-0003-4060-6077</uri>
      </author>
    </item>
    <item>
      <title>WaveFunctionCollapse: Content Generation via Constraint Solving and Machine Learning</title>
      <link>https://escholarship.org/uc/item/1fb9k44q</link>
      <description>WaveFunctionCollapse: Content Generation via Constraint Solving and Machine Learning</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1fb9k44q</guid>
      <pubDate>Fri, 23 Jul 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Karth, Isaac</name>
        <uri>https://orcid.org/0000-0003-4060-6077</uri>
      </author>
      <author>
        <name>Smith, Adam Marshall</name>
      </author>
    </item>
    <item>
      <title>WaveFunctionCollapse is constraint solving in the wild</title>
      <link>https://escholarship.org/uc/item/1f29235t</link>
      <description>WaveFunctionCollapse is constraint solving in the wild</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1f29235t</guid>
      <pubDate>Fri, 23 Jul 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Karth, Isaac</name>
      </author>
      <author>
        <name>Smith, Adam M</name>
      </author>
    </item>
    <item>
      <title>Disentangling the Cosmic Web toward FRB 190608</title>
      <link>https://escholarship.org/uc/item/9cx8t0wm</link>
      <description>FRB 190608 was detected by ASKAP and localized to a spiral galaxy at
$z_{host}=0.11778$ in the SDSS footprint. The burst has a large dispersion
measure ($DM_{FRB}=339.8$ $pc/cm^3$) compared to the expected cosmic average at
its redshift. It also has a large rotation measure ($RM_{FRB}=353$ $rad/m^2$)
and scattering timescale ($\tau=3.3$ $ms$ at $1.28$ $GHz$). Chittidi et al
(2020) perform a detailed analysis of the ultraviolet and optical emission of
the host galaxy and estimate the host DM contribution to be $110\pm 37$
$pc/cm^3$. This work complements theirs and reports the analysis of the optical
data of galaxies in the foreground of FRB 190608 to explore their contributions
to the FRB signal. Together, the two manuscripts delineate an observationally
driven, end-to-end study of matter distribution along an FRB sightline; the
first study of its kind. Combining KCWI observations and public SDSS data, we
estimate the expected cosmic dispersion measure $DM_{cosmic}$ along the
sightline...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9cx8t0wm</guid>
      <pubDate>Sun, 13 Sep 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Simha, Sunil</name>
      </author>
      <author>
        <name>Burchett, Joseph N</name>
      </author>
      <author>
        <name>Prochaska, J Xavier</name>
      </author>
      <author>
        <name>Chittidi, Jay S</name>
      </author>
      <author>
        <name>Elek, Oskar</name>
      </author>
      <author>
        <name>Tejos, Nicolas</name>
      </author>
      <author>
        <name>Jorgenson, Regina</name>
      </author>
      <author>
        <name>Bannister, Keith W</name>
      </author>
      <author>
        <name>Bhandari, Shivani</name>
      </author>
      <author>
        <name>Day, Cherie K</name>
      </author>
      <author>
        <name>Deller, Adam T</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
      <author>
        <name>Macquart, Jean-Pierre</name>
      </author>
      <author>
        <name>Ryder, Stuart D</name>
      </author>
      <author>
        <name>Shannon, Ryan M</name>
      </author>
    </item>
    <item>
      <title>Revealing the Dark Threads of the Cosmic Web</title>
      <link>https://escholarship.org/uc/item/743322t6</link>
      <description>Revealing the Dark Threads of the Cosmic Web</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/743322t6</guid>
      <pubDate>Tue, 26 May 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Burchett, Joseph N</name>
      </author>
      <author>
        <name>Elek, Oskar</name>
      </author>
      <author>
        <name>Tejos, Nicolas</name>
      </author>
      <author>
        <name>Prochaska, J Xavier</name>
      </author>
      <author>
        <name>Tripp, Todd M</name>
      </author>
      <author>
        <name>Bordoloi, Rongmon</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
    </item>
    <item>
      <title>Predicting Biker Density at Bikeshare Station Intersections in San Francisco</title>
      <link>https://escholarship.org/uc/item/6nc512qp</link>
      <description>Predicting Biker Density at Bikeshare Station Intersections in San Francisco</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6nc512qp</guid>
      <pubDate>Tue, 26 May 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Dubey, Mahika</name>
      </author>
      <author>
        <name>Ortiz, Alan Peral</name>
      </author>
      <author>
        <name>Agrawal, Rakshit</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
    </item>
    <item>
      <title>Data Brushes: Interactive Style Transfer for Data Art</title>
      <link>https://escholarship.org/uc/item/8kf7d3w3</link>
      <description>Data Brushes: Interactive Style Transfer for Data Art</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8kf7d3w3</guid>
      <pubDate>Wed, 5 Feb 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Dubey, Mahika</name>
      </author>
      <author>
        <name>Otto, Jasmine</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
    </item>
    <item>
      <title>NeuroCave: A web-based immersive visualization platform for exploring connectome datasets</title>
      <link>https://escholarship.org/uc/item/7fk528sz</link>
      <description>We introduce NeuroCave, a novel immersive visualization system that facilitates the visual inspection of structural and functional connectome datasets. The representation of the human connectome as a graph enables neuroscientists to apply network-theoretic approaches in order to explore its complex characteristics. With NeuroCave, brain researchers can interact with the connectome-either in a standard desktop environment or while wearing portable virtual reality headsets (such as Oculus Rift, Samsung Gear, or Google Daydream VR platforms)-in any coordinate system or topological space, as well as cluster brain regions into different modules on-demand. Furthermore, a default side-by-side layout enables simultaneous, synchronized manipulation in 3D, utilizing modern GPU hardware architecture, and facilitates comparison tasks across different subjects or diagnostic groups or longitudinally within the same subject. Visual clutter is mitigated using a state-of-the-art edge bundling...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7fk528sz</guid>
      <pubDate>Wed, 5 Feb 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Keiriz, Johnson JG</name>
      </author>
      <author>
        <name>Zhan, Liang</name>
      </author>
      <author>
        <name>Ajilore, Olusola</name>
      </author>
      <author>
        <name>Leow, Alex D</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
    </item>
    <item>
      <title>TempoCave: Visualizing Dynamic Connectome Datasets to Support Cognitive Behavioral Therapy</title>
      <link>https://escholarship.org/uc/item/52f5573q</link>
      <description>TempoCave: Visualizing Dynamic Connectome Datasets to Support Cognitive Behavioral Therapy</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/52f5573q</guid>
      <pubDate>Wed, 5 Feb 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Xu, Ran</name>
      </author>
      <author>
        <name>Thomas, Manu Mathew</name>
      </author>
      <author>
        <name>Leow, Alex</name>
      </author>
      <author>
        <name>Ajilore, Olusola A</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
    </item>
    <item>
      <title>RuleVis: Constructing Patterns and Rules for Rule-Based Models</title>
      <link>https://escholarship.org/uc/item/47g8n4zk</link>
      <description>RuleVis: Constructing Patterns and Rules for Rule-Based Models</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/47g8n4zk</guid>
      <pubDate>Wed, 5 Feb 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Abramov, David</name>
      </author>
      <author>
        <name>Otto, Jasmine</name>
      </author>
      <author>
        <name>Dubey, Mahika</name>
      </author>
      <author>
        <name>Artanegara, Cassia</name>
      </author>
      <author>
        <name>Boutillier, Pierre</name>
      </author>
      <author>
        <name>Fontana, Walter</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
    </item>
    <item>
      <title>RuleVis: Constructing Patterns and Rules for Rule-Based Models</title>
      <link>https://escholarship.org/uc/item/9781s0h6</link>
      <description>We introduce RuleVis, a web-based application for defining and editing
"correct-by-construction" executable rules that model biochemical
functionality, which can be used to simulate the behavior of protein-protein
interaction networks and other complex systems. Rule-based models involve
emergent effects based on the interactions between rules, which can vary
considerably with regard to the scale of a model, requiring the user to inspect
and edit individual rules. RuleVis bridges the graph rewriting and systems
biology research communities by providing an external visual representation of
salient patterns that experts can use to determine the appropriate level of
detail for a particular modeling context. We describe the visualization and
interaction features available in RuleVisand provide a detailed example
demonstrating how RuleVis can be used to reason about intracellular
interactions.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9781s0h6</guid>
      <pubDate>Tue, 26 Nov 2019 00:00:00 +0000</pubDate>
      <author>
        <name>Abramov, David</name>
      </author>
      <author>
        <name>Otto, Jasmine</name>
      </author>
      <author>
        <name>Dubey, Mahika</name>
      </author>
      <author>
        <name>Artanegara, Cassia</name>
      </author>
      <author>
        <name>Boutillier, Pierre</name>
      </author>
      <author>
        <name>Fontana, Walter</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
      </author>
    </item>
    <item>
      <title>IGM‐Vis: Analyzing Intergalactic and Circumgalactic Medium Absorption Using Quasar Sightlines in a Cosmic Web Context</title>
      <link>https://escholarship.org/uc/item/9dv1f7bm</link>
      <description>IGM‐Vis: Analyzing Intergalactic and Circumgalactic Medium Absorption Using Quasar Sightlines in a Cosmic Web Context</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9dv1f7bm</guid>
      <pubDate>Tue, 17 Sep 2019 00:00:00 +0000</pubDate>
      <author>
        <name>Burchett, JN</name>
      </author>
      <author>
        <name>Abramov, D</name>
      </author>
      <author>
        <name>Otto, J</name>
      </author>
      <author>
        <name>Artanegara, C</name>
      </author>
      <author>
        <name>Prochaska, JX</name>
      </author>
      <author>
        <name>Forbes, AG</name>
      </author>
    </item>
    <item>
      <title>Phase Angle Spatial Embedding (PhASE)</title>
      <link>https://escholarship.org/uc/item/6fg348w0</link>
      <description>Phase Angle Spatial Embedding (PhASE)</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6fg348w0</guid>
      <pubDate>Tue, 20 Aug 2019 00:00:00 +0000</pubDate>
      <author>
        <name>Morrissey, Zachery</name>
      </author>
      <author>
        <name>Zhan, Liang</name>
      </author>
      <author>
        <name>Lee, Hyekyoung</name>
      </author>
      <author>
        <name>Keiriz, Johnson</name>
      </author>
      <author>
        <name>Forbes, Angus</name>
      </author>
      <author>
        <name>Ajilore, Olusola</name>
      </author>
      <author>
        <name>Leow, Alex</name>
      </author>
      <author>
        <name>Chung, Moo</name>
      </author>
    </item>
    <item>
      <title>From Default Mode Network to the Basal Configuration: Sex Differences in the Resting-State Brain Connectivity as a Function of Age and Their Clinical Correlates</title>
      <link>https://escholarship.org/uc/item/40d153s6</link>
      <description>Connectomics is a framework that models brain structure and function interconnectivity as a network, rather than narrowly focusing on select regions-of-interest. MRI-derived connectomes can be structural, usually based on diffusion-weighted MR imaging, or functional, usually formed by examining fMRI blood-oxygen-level-dependent (BOLD) signal correlations. Recently, we developed a novel method for assessing the hierarchical modularity of functional brain networks-the probability associated community estimation (PACE). PACE uniquely permits a dual formulation, thus yielding equivalent connectome modular structure regardless of whether positive or negative edges are considered. This method was rigorously validated using the 1,000 functional connectomes project data set (F1000, RRID:SCR_005361) (1) and the Human Connectome Project (HCP, RRID:SCR_006942) (2, 3) and we reported novel sex differences in resting-state connectivity not previously reported. (4) This study further examines...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/40d153s6</guid>
      <pubDate>Tue, 11 Sep 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Conrin, Sean D</name>
      </author>
      <author>
        <name>Zhan, Liang</name>
      </author>
      <author>
        <name>Morrissey, Zachery D</name>
      </author>
      <author>
        <name>Xing, Mengqi</name>
      </author>
      <author>
        <name>Forbes, Angus</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
      <author>
        <name>Maki, Pauline</name>
      </author>
      <author>
        <name>Milad, Mohammed R</name>
      </author>
      <author>
        <name>Ajilore, Olusola</name>
      </author>
      <author>
        <name>Langenecker, Scott A</name>
      </author>
      <author>
        <name>Leow, Alex D</name>
      </author>
    </item>
    <item>
      <title>Public Transit Accessibility: Blind Passengers Speak Out</title>
      <link>https://escholarship.org/uc/item/9hq0q8nn</link>
      <description>Riding public transit can be confusing for everyone, especially in an unfamiliar environment. One needs to figure out which transportation lines to take to reach a destination, when and where to catch a bus or a train, when to exit, and how to negotiate transfers. For those with sensorial or cognitive disabilities, these problems become even more daunting. Several technological approaches have been proposed to facilitate use of public transit for everyone. For any assistive technology to be successful, though, it is imperative that it is developed from the ground up with a clear understanding of the intended users’ needs and requirements, and possibly with a direct participation of these users throughout the project lifecycle. In this study, we conduct a focus group with blind participants, designed to highlight the main issues, problems, and limitations with the current transit system in our local area as well as the perception of the participants our proposed RouteMe2 technology...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9hq0q8nn</guid>
      <pubDate>Sat, 21 Jul 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Mirzaei, Fatemeh</name>
      </author>
      <author>
        <name>Manduchi, Roberto</name>
      </author>
      <author>
        <name>Kurniawan, Sri</name>
      </author>
    </item>
    <item>
      <title>Combat in Games</title>
      <link>https://escholarship.org/uc/item/9zj6r5wz</link>
      <description>While the game design and game studies communities have analyzed combat both in specific games and game genres, and while combat is clearly central to many types of games, there is no general account of combat that is portable across diverse games. We provide such an account in the form of criteria which are satisfied by games that players inter- pret as “having combat.” These requirements are eventually fulfilled via operational logics, which tie the game’s observ- able behavior (including its instantial assets) to play expe- riences and cultural knowledge, creating what we refer to as a “combat model.” In addition to establishing a com- prehensive model of combat, making it possible to discuss combat across game genres, this work is the first to describe how complex playable models are constructed from composi- tions of operational logics working in concert; we also define two families of logics which are novel in the literature. This broad model of combat has already proved...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9zj6r5wz</guid>
      <pubDate>Mon, 18 Jun 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Osborn, Joseph C</name>
      </author>
      <author>
        <name>Lederle-Ensign, Dylan</name>
      </author>
      <author>
        <name>Wardrip-Fruin, NG</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
      <author>
        <name>Mateas, Michael</name>
      </author>
    </item>
    <item>
      <title>Defining operational logics</title>
      <link>https://escholarship.org/uc/item/3cv133pn</link>
      <description>Much analysis of games focuses, understandably, on their mechanics and the resulting audience experiences. Similarly, many genres of games are understood at the level of mechanics. But there is also the persistent sense that a deeper level of analysis would be useful, and a number of proposals have been made that attempt to look toward a level that undergirds mechanics. This paper focuses on a particular approach of this sort-operational logics-first proposed by Noah Wardrip-Fruin (2005) and since then discussed by authors such as Michael Mateas (2006) and Ian Bogost (2007). Operational logics connect fundamental abstract operations, which determine the state evolution of a system, with how they are understood at a human level. In this paper we expand on the concept of operational logics, offering a more detailed and rigorous discussion than provided in earlier accounts, setting the stage for more effective future use of logics as an analytical tool. In particular, we clarify...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3cv133pn</guid>
      <pubDate>Mon, 18 Jun 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Mateas, M</name>
      </author>
      <author>
        <name>Wardrip-Fruin, N</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
    </item>
    <item>
      <title>Refining operational logics</title>
      <link>https://escholarship.org/uc/item/2jh5c6k7</link>
      <description>This paper expands on and refines the theoretical framework of operational logics, which simultaneously addresses how games operate at a procedural level and how games communicate these operations to players. In the years since their introduction, operational logics have been applied in domains ranging from game studies to game generation and game modeling languages. To support these uses and to enable new ones, we resolve some standing ambiguities and provide a catalog of key, fundamental operational logics. Concretely, we provide an explicit and detailed definition of operational logics; specify a set of logics which seems fundamental and suffices to interpret a broad variety of games across several genres; give the first detailed explanation of how exactly operational logics combine; and suggest application domains for which operational logics-based analysis and knowledge representation are especially appropriate.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2jh5c6k7</guid>
      <pubDate>Mon, 18 Jun 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Osborn, Joseph C</name>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
      <author>
        <name>Mateas, Michael</name>
      </author>
    </item>
    <item>
      <title>EXPRESSIVE PROCESSING Interpretation and Creation</title>
      <link>https://escholarship.org/uc/item/5453x2sb</link>
      <description>Software Studies approaches use humanities and/or social science methods and engage the specific operations of particular software—for purposes ranging from understanding digital culture to the development of procedural literacy and the creation of novel software. “Expressive processing” names a particular software studies approach that focuses on the (perhaps unconscious) ideas, as well as intellectual and material histories, expressed through how computational processes are designed and operate. Using this approach to examine existing works can reveal something quite different from what software authors state publicly, as this chapter outlines with Abelson and Carroll's “Goldwater Machine.” This approach can also help guide the creation of new works, complementing techniques such as playtesting and arts critique, as this chapter outlines with the social simulation storytelling game Prom Week. Through such work, we can not only better understand the computational media that shapes...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5453x2sb</guid>
      <pubDate>Fri, 18 May 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Wardrip-Fruin, Noah</name>
        <uri>https://orcid.org/0000-0003-1964-7624</uri>
      </author>
    </item>
    <item>
      <title>TimeArcs: Visualizing Fluctuations in Dynamic Networks</title>
      <link>https://escholarship.org/uc/item/5688d0x6</link>
      <description>TimeArcs: Visualizing Fluctuations in Dynamic Networks</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5688d0x6</guid>
      <pubDate>Tue, 16 Jan 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Dang, TN</name>
      </author>
      <author>
        <name>Pendar, N</name>
      </author>
      <author>
        <name>Forbes, AG</name>
      </author>
    </item>
    <item>
      <title>Dynamic Influence Networks for Rule-Based Models</title>
      <link>https://escholarship.org/uc/item/4vm443t3</link>
      <description>We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4vm443t3</guid>
      <pubDate>Tue, 16 Jan 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Forbes, Angus G</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
      <author>
        <name>Burks, Andrew</name>
      </author>
      <author>
        <name>Lee, Kristine</name>
      </author>
      <author>
        <name>Li, Xing</name>
      </author>
      <author>
        <name>Boutillier, Pierre</name>
      </author>
      <author>
        <name>Krivine, Jean</name>
      </author>
      <author>
        <name>Fontana, Walter</name>
      </author>
    </item>
    <item>
      <title>Spectral Landscapes: Visualizing Electromagnetic Interactions</title>
      <link>https://escholarship.org/uc/item/1743m707</link>
      <description>Electromagnetic fields are formed through complex interactions between outer space, the Sun, our Earth, its atmosphere, and the built environment. Our communications technology makes use of them to enable the transmission of information at local, global, and even extraterrestrial scales. This article introduces a series of artworks that explore new creative opportunities made possible both via low-cost sensors and through the use of state-of-the-art receivers. The projects engage with the electromagnetic spectrum as a medium of creative expression that maps the invisible landscapes of what Anthony Dunne has termed "Hertzian space."</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1743m707</guid>
      <pubDate>Tue, 16 Jan 2018 00:00:00 +0000</pubDate>
      <author>
        <name>Balogh, Brett</name>
      </author>
      <author>
        <name>Camci, Anil</name>
      </author>
      <author>
        <name>Murray, Paul</name>
      </author>
      <author>
        <name>Forbes, Angus G</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
    </item>
    <item>
      <title>Implementing Controlled Vocabularies for Computer Game Platforms and Media Formats in SKOS</title>
      <link>https://escholarship.org/uc/item/8k1294z9</link>
      <description>Implementing Controlled Vocabularies for Computer Game Platforms and Media Formats in SKOS</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8k1294z9</guid>
      <pubDate>Tue, 24 Oct 2017 00:00:00 +0000</pubDate>
      <author>
        <name>Kaltman, Eric</name>
      </author>
      <author>
        <name>Wardrip-fruin, Noah</name>
      </author>
      <author>
        <name>Mastroni, Mitch</name>
      </author>
      <author>
        <name>Lowood, Henry</name>
      </author>
      <author>
        <name>De groat, Greta</name>
      </author>
      <author>
        <name>Edwards, Glynn</name>
      </author>
      <author>
        <name>Barrett, Marcia</name>
      </author>
      <author>
        <name>Caldwell, Christy</name>
      </author>
    </item>
    <item>
      <title>Baseline connectome modular abnormalities in the childhood phase of a longitudinal study on individuals with chromosome 22q11.2 deletion syndrome</title>
      <link>https://escholarship.org/uc/item/7gh3t0fp</link>
      <description>Occurring in at least 1 in 3,000 live births, chromosome 22q11.2 deletion syndrome (22q11DS) produces a complex phenotype that includes a constellation of medical complications such as congenital cardiac defects, immune deficiency, velopharyngeal dysfunction, and characteristic facial dysmorphic features. There is also an increased incidence of psychiatric diagnosis, especially intellectual disability and ADHD in childhood, lifelong anxiety, and a strikingly high rate of schizophrenia spectrum disorders, which occur in around 30% of adults with 22q11DS. Using innovative computational connectomics, we studied how 22q11DS affects high-level network signatures of hierarchical modularity and its intrinsic geometry in 55 children with confirmed 22q11DS and 27 Typically Developing (TD) children. Results identified 3 subgroups within our 22q11DS sample using a K-means clustering approach based on several midline structural measures-of-interests. Each subgroup exhibited distinct patterns...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7gh3t0fp</guid>
      <pubDate>Tue, 24 Oct 2017 00:00:00 +0000</pubDate>
      <author>
        <name>Zhan, Liang</name>
      </author>
      <author>
        <name>Jenkins, Lisanne M</name>
      </author>
      <author>
        <name>Zhang, Aifeng</name>
      </author>
      <author>
        <name>Conte, Giorgio</name>
      </author>
      <author>
        <name>Forbes, Angus</name>
        <uri>https://orcid.org/0000-0002-8700-7795</uri>
      </author>
      <author>
        <name>Harvey, Danielle</name>
        <uri>https://orcid.org/0000-0002-5367-0951</uri>
      </author>
      <author>
        <name>Angkustsiri, Kathleen</name>
        <uri>https://orcid.org/0000-0001-9769-6638</uri>
      </author>
      <author>
        <name>Goodrich‐Hunsaker, Naomi J</name>
      </author>
      <author>
        <name>Durdle, Courtney</name>
      </author>
      <author>
        <name>Lee, Aaron</name>
      </author>
      <author>
        <name>Schumann, Cyndi</name>
      </author>
      <author>
        <name>Carmichael, Owen</name>
      </author>
      <author>
        <name>Kalish, Kristopher</name>
      </author>
      <author>
        <name>Leow, Alex D</name>
      </author>
      <author>
        <name>Simon, Tony J</name>
        <uri>https://orcid.org/0000-0002-8987-1966</uri>
      </author>
    </item>
    <item>
      <title>A Secret History of American River People</title>
      <link>https://escholarship.org/uc/item/33r8k3h1</link>
      <description>&lt;p&gt;&lt;em&gt;A Secret History of American River People&lt;/em&gt; is a project to recreate a 1940s shantyboat for a series of epic river voyages in order to build a collection of personal stories of people who live and work on the river. The project is a touring participatory installation, an interactive web documentary, and a research archive—all near-term outcomes of the project.&lt;/p&gt;&lt;p&gt;Using research from fieldwork on the Upper Mississippi River and experiences from a variety of rivers in the Midwest and West Coast, my goal is to create a dialogic and participatory art piece, firmly rooted in a people’s history tradition, that reexamine the issues currently and historically faced by people living or working on the river with particular attention to the invisible stories of native people, working people, people of color, and women, to create a multi-perspective and multi-path take on historical narrative, to explore the importance of a public commons, and to challenge dominant cultural assumptions...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/33r8k3h1</guid>
      <pubDate>Mon, 11 Jan 2016 00:00:00 +0000</pubDate>
      <author>
        <name>Modes, Wesley</name>
      </author>
    </item>
    <item>
      <title>A Unified Approach to Preserving Cultural Software Objects and their Development Histories</title>
      <link>https://escholarship.org/uc/item/0wg4w6b9</link>
      <description>This white paper was made possible with the support of a&amp;nbsp;National Endowment for the Humanities Digital Start-Up GrantHD-51719-13.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0wg4w6b9</guid>
      <pubDate>Mon, 9 Feb 2015 00:00:00 +0000</pubDate>
      <author>
        <name>Kaltman, Eric</name>
      </author>
      <author>
        <name>Wardrip-Fruin, Noah</name>
      </author>
      <author>
        <name>Lowood, Henry</name>
      </author>
      <author>
        <name>Caldwell, Christy</name>
      </author>
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