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1. Work in Progress: Development of a Training Program to Prepare Students for an Immersive Bioinformatics Summer Research Experience

   Chapman, MA ( July 2021 , 2021 American Society for Engineering Education Virtual Annual Conference)

   null (Ed.)

   The publication of the first human genome in 2001 transformed biomedical research. Since then, an explosion of new sequencing technologies has required engineers and computer scientists to invent computational methods to analyze and interpret the ever-growing data. Now, large-scale biological data encompasses many types of ‘omics’ datasets, including genomes, transcriptomes, proteomes and metabolomes, and each of these new datasets has created a new set of analytical challenges. To meet this need, the field of bioinformatics has expanded significantly, but there is still a large need for engineers and scientists to work in this inherently interdisciplinary field. Properly trained bioinformaticians have expertise in computer science/engineering and understand the biological and medical context underlying their work. Therefore, the development of robust bioinformatics training programs is critical to educate the next generation of bioinformaticians. Although undergraduate degree programs in bioinformatics exist, providing students with hands-on bioinformatics skills through immersive research experiences is necessary to prepare students for graduate work. Thus, this work describes a recently funded NSF – International Research Experience for Students (IRES) site: US-Sweden Clinical Bioinformatics Research Training Program targeted at training students from diverse educational backgrounds to prepare them for authentic bioinformatics research experiences. Given the inherent interdisciplinary nature of bioinformatics, it is extremely difficult to design a training program that prepares students from different backgrounds (computer science, bioengineering, computational biology, biology) to be successful in a bioinformatics research group. Therefore, this ‘Work-in-Progress’ describes the pre-departure training program developed for this IRES site and the initial lessons learned. 

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2. Current and future directions in network biology

   https://doi.org/10.1093/bioadv/vbae099  

   Zitnik, Marinka ; Li, Michelle_M ; Wells, Aydin ; Glass, Kimberly ; Morselli_Gysi, Deisy ; Krishnan, Arjun ; Murali, T_M ; Radivojac, Predrag ; Roy, Sushmita ; Baudot, Anaïs ; et al ( August 2024 , Bioinformatics Advances)

   Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

   Not applicable.

    

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3. Molecular storytelling: a conceptual framework for teaching and learning with molecular case studies

   https://doi.org/10.3389/feduc.2024.1379515  

   Trujillo, Caleb M ; Dutta, Shuchismita ( June 2024 , Frontiers in Education)

   Molecular case studies (MCSs) provide educational opportunities to explore biomolecular structure and function using data from public bioinformatics resources. The conceptual basis for the design of MCSs has yet to be fully discussed in the literature, so we present molecular storytelling as a conceptual framework for teaching with case studies. Whether the case study aims to understand the biology of a specific disease and design its treatments or track the evolution of a biosynthetic pathway, vast amounts of structural and functional data, freely available in public bioinformatics resources, can facilitate rich explorations in atomic detail. To help biology and chemistry educators use these resources for instruction, a community of scholars collaborated to create the Molecular CaseNet. This community uses storytelling to explore biomolecular structure and function while teaching biology and chemistry. In this article, we define the structure of an MCS and present an example. Then, we articulate the evolution of a conceptual framework for developing and using MCSs. Finally, we related our framework to the development of technological, pedagogical, and content knowledge (TPCK) for educators in the Molecular CaseNet. The report conceptualizes an interdisciplinary framework for teaching about the molecular world and informs lesson design and education research.

    

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4. Promoting Inclusivity in Computing (PINC) via Computing Application Minor

   Yoon, I ; Pennings, P. ; Kulkarni, A. ; Okada, K ; Domingo, C. ( January 2018 , 2018 CoNECD - The Collaborative Network for Engineering and Computing Diversity Conference)

   We aimed to build a new educational pathway that would provide basic training in computer science for women and students from underrepresented (UR) groups who otherwise may not take computer science classes in college. Specifically, this on-going project focused on creating a 2-year Computer Science (CS) program consisting of exciting new courses aimed at biology majors. Biology traditionally attracts large numbers of women, a significant number of students from UR groups, and has compelling needs for CS technology. The interdisciplinary program is training the next generation of innovators in the biological sciences who will be prepared to cross disciplinary boundaries. The program consists of the following: (1) computer science courses with content related to biology, (2) cohorts of students that progress through the program together, and (3) a small group peer mentoring environment, and (4) facilitated interdisciplinary research projects. Graduates from this program, referred to as "PINC" - Promoting INclusivity in Computing - will receive a “Minor in Computing Applications” in addition to their primary science degree in Biology. The program is now in its second year and thus far 60 students have participated. Among them, 73% are women and 51% are underrepresented minorities (URM). The majority of students in the PINC program stated that they would not have taken CS courses without the structured support of the PINC program. Here we present the data collected during this two year period as well as details about the Computing Application minor and programmatic components that are having a positive impact on student outcomes. 

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5. Design of an Evaluative Rubric for CT Integrated Curriculum in the Elementary Grades Authors

   https://doi.org/10.34641/ctestem.2022.475  

   Florence R. Sullivan, Lian Duan ( July 2022 , CTE-STEM 2022 Conference.)

   Despite the recent proliferation of research concerning integrating computational thinking (CT) into K-5th grade curriculum, there is little literature concerning how to evaluate the quality of CT integrated curricula, especially curricula integrating CT into language arts and social studies content areas. In this paper, we present a theoretically derived rubric for the evaluation of CT integrated curricula for grades K-5 across the curriculum (math, science, language arts, social studies). Our rubric is divided into two sections. The first section provides guidelines for identifying the integration type (disciplinary, multidisciplinary, interdisciplinary, or transdisciplinary). The second section presents six categories of evaluation that further subsume nine sub-categories. The principal categories of evaluation include the following: conceptual coherence, role of computational technology, assessment, use of multiple representations, play, and equity. We include the play category as an aspect of developmental appropriateness. Play is an important pedagogical approach for learning in the early grades. Our work takes place in the context of the Computer Science (CS) for All initiative in the United States which emphasizes the goal of improving racial and gender diversity in CS participation. Therefore, creating integrated lessons that address equity is important. Our paper describes rubric development from the theoretical perspectives that underlie the inclusion of each type, category, and sub-category. Our evaluative rubric can guide future efforts to integrate CT/CS into the elementary curricula. Researchers can utilize our rubric to evaluate and analyze CT-integrated curricula, and educators can benefit from using this rubric as a guideline for curriculum development. 

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