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1. Net.Create: Network Analysis in Collaborative Co-Construction of Historical Context in a Large Undergraduate Classroom

   https://doi.org/https://repository.isls.org//handle/1/6293  

   Craig, Kalani; Danish, Joshua; Humburg, Megan; Szostalo, Maksymilian; McCranie, Ann; Hmelo-Silver, Cindy (January 2020, The Interdisciplinarity of the Learning Sciences, 14th International Conference of the Learning Sciences (ICLS) 2020)

   Gresalfi, M. and (Ed.)

   History educators in large-lecture humanities undergraduate classrooms struggle to support reading comprehension, defined as the ability to simultaneously read a complex text critically, understand the text’s details and context, and vet the text’s claims. Critical reading of historical texts in particular helps bridge the gap between seeing history as memorization-oriented and seeing it as an inquiry-oriented discipline that reconstructs narrative and context. Net.Create is an open-source, network-analysis software tool paired with activities that support intuitive creation and revision of a network data set and accompanying visualization, and through these representational practices, reading comprehension in humanities classrooms. Findings show that as students draw on details in a historical text to collaboratively construct a larger network, they begin to emphasize context reconstruction over memorization. 

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2. CDMAP/CDVIS: context-dependent mutation analysis package and visualization software

   https://doi.org/10.1093/g3journal/jkac299  

   Patton, David L; Cardenas, Thomas; Mele, Perrin; Navarro, Jon; Sung, Way (December 2022, G3 Genes|Genomes|Genetics)

   de los Campos, G (Ed.)

   Abstract The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) is an automated, modular toolkit used for the analysis and visualization of context-dependent mutation patterns (site-specific variation in mutation rate from neighboring-nucleotide effects). The CDMAP computes context-dependent mutation rates using a Variant Call File (VCF), Genbank file, and reference genome and can generate high-resolution figures to analyze variation in mutation rate across spatiotemporal scales. This algorithm has been benchmarked against mutation accumulation data but can also be used to calculate context-dependent mutation rates for polymorphism or closely related species as long as the input requirements are met. Output from CDMAP can be integrated into CDVIS, an interactive database for visualizing mutation patterns across multiple taxa simultaneously. 

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3. Uncertainty in humanities network visualization

   https://doi.org/10.3389/fcomm.2023.1305137  

   Conroy, Melanie; Gillmann, Christina; Harvey, Francis; Mchedlidze, Tamara; Fabrikant, Sara Irina; Windhager, Florian; Scheuermann, Gerik; Tangherlini, Timothy R.; Warren, Christopher N.; Weingart, Scott B.; et al (January 2024, Frontiers in Communication)

   Network visualization is one of the most widely used tools in digital humanities research. The idea of uncertain or “fuzzy” data is also a core notion in digital humanities research. Yet network visualizations in digital humanities do not always prominently represent uncertainty. In this article, we present a mathematical and logical model of uncertainty as a range of values which can be used in network visualizations. We review some of the principles for visualizing uncertainty of different kinds, visual variables that can be used for representing uncertainty, and how these variables have been used to represent different data types in visualizations drawn from a range of non-humanities fields like climate science and bioinformatics. We then provide examples of two diagrams: one in which the variables displaying degrees of uncertainty are integrated/pinto the graph and one in which glyphs are added to represent data certainty and uncertainty. Finally, we discuss how probabilistic data and what-if scenarios could be used to expand the representation of uncertainty in humanities network visualizations. 

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4. L’émergence d’une histoire environnementale interdisciplinaire: Une approche conjointe de l’Holocène tardif

   https://doi.org/10.1017/ahss.2022.114  

   Izdebski, Adam; Bloomfield, Kevin; Eastwood, Warren J.; Fernandes, Ricardo; Fleitmann, Dominik; Guzowski, Piotr; Haldon, John; Ludlow, Francis; Luterbacher, Jürg; Manning, Joseph G.; et al (March 2022, Annales. Histoire, Sciences Sociales)

   Abstract With the efflorescence of palaeoscientific approaches to the past, historians have been confronted with a wealth of new evidence on both human and natural phenomena, from human disease and migration through to landscape change and climate. These new data require a rewriting of our narratives of the past, questioning what constitutes an authoritative historical source and who is entitled to recount history to contemporary societies. Humanities-based historical inquiry must embrace this new evidence, but to do so historians need to engage with it in a critical manner, just as they engage critically with textual and material sources. This article highlights the most vital methodological issues, ranging from the spatiotemporal scales and heterogeneity of the new evidence to the new roles attributed to quantitative methods and the place of scientific data in narrative construction. It considers areas of study where the palaeosciences have “intruded” into fields and subjects previously reserved for historians, especially socioeconomic, climate, and environmental history. The authors argue that active engagement with new approaches is urgently needed if historians want to contribute to our evolving understanding of the challenges of the Anthropocene. 

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5. Building Science Gateways for Humanities

   https://doi.org/10.1145/3311790.3396628  

   Zhou, Jun; Smith, Karen; Wilsbacher, Greg; Sagona, Paul; Reddy, David; Torkian, Ben (July 2020, PEARC '20: Practice and Experience in Advanced Research Computing)

   Building science gateways for humanities content poses new challenges to the science gateway community. Compared with science gateways devoted to scientific content, humanities-related projects usually require 1) processing data in various formats, such as text, image, video, etc., 2) constant public access from a broad audience, and therefore 3) reliable security, ideally with low maintenance. Many traditional science gateways are monolithic in design, which makes them easier to write, but they can be computationally inefficient when integrated with numerous scientific packages for data capture and pipeline processing. Since these packages tend to be single-threaded or nonmodular, they can create traffic bottlenecks when processing large numbers of requests. Moreover, these science gateways are usually challenging to resume development on due to long gaps between funding periods and the aging of the integrated scientific packages. In this paper, we study the problem of building science gateways for humanities projects by developing a service-based architecture, and present two such science gateways: the Moving Image Research Collections (MIRC) – a science gateway focusing on image analysis for digital surrogates of historical motion picture film, and SnowVision - a science gateway for studying pottery fragments in southeastern North America. For each science gateway, we present an overview of the background of the projects, and some unique challenges in their design and implementation. These two science gateways are deployed on XSEDE’s Jetstream academic clouding computing resource and are accessed through web interfaces. Apache Airavata middleware is used to manage the interactions between the web interface and the deep-learning-based (DL) backend service running on the Bridges graphics processing unit (GPU) cluster. 

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