1
|
Patel P, Pillai N, Toby I. No-boundary thinking for artificial intelligence in bioinformatics and education. FRONTIERS IN BIOINFORMATICS 2024; 3:1332902. [PMID: 38259432 PMCID: PMC10800434 DOI: 10.3389/fbinf.2023.1332902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
No-boundary thinking enables the scientific community to reflect in a thoughtful manner and discover new opportunities, create innovative solutions, and break through barriers that might have otherwise constrained their progress. This concept encourages thinking without being confined by traditional rules, limitations, or established norms, and a mindset that is not limited by previous work, leading to fresh perspectives and innovative outcomes. So, where do we see the field of artificial intelligence (AI) in bioinformatics going in the next 30 years? That was the theme of a "No-Boundary Thinking" Session as part of the Mid-South Computational Bioinformatics Society's (MCBIOS) 19th annual meeting in Irving, Texas. This session addressed various areas of AI in an open discussion and raised some perspectives on how popular tools like ChatGPT can be integrated into bioinformatics, communicating with scientists in different fields to properly utilize the potential of these algorithms, and how to continue educational outreach to further interest of data science and informatics to the next-generation of scientists.
Collapse
Affiliation(s)
- Prajay Patel
- Chemistry Department, University of Dallas, Irving, TX, United States
| | - Nisha Pillai
- Department of Computer Science, Mississippi State University, Starkville, MS, United States
| | - Inimary Toby
- Biology Department, University of Dallas, Irving, TX, United States
| |
Collapse
|
2
|
Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. Scientists without borders: lessons from Ukraine. Gigascience 2022; 12:giad045. [PMID: 37496156 PMCID: PMC10372202 DOI: 10.1093/gigascience/giad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 07/28/2023] Open
Abstract
Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.
Collapse
Affiliation(s)
- Walter Wolfsberger
- Department of Biological Sciences, Oakland University,
Rochester, MI 48309-4479, USA
| | - Karishma Chhugani
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and
Pharmaceutical Sciences, University of Southern California,
Los Angeles, CA 90033, USA
| | - Khrystyna Shchubelka
- Department of Biological Sciences, Oakland University,
Rochester, MI 48309-4479, USA
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences
of Ukraine, Kyiv Academic University, Kyiv 03143,
Ukraine
| | - Yuriy Salyha
- Institute of Animal Biology, National Academy of Agrarian Sciences (NAAS)
of Ukraine, Lviv 79034, Ukraine
| | - Oksana Zlenko
- National Scientific Center “Institute of Experimental and Clinical
Veterinary Medicine,” Kharkiv 61023, Ukraine
| | - Mykhailo Arych
- Institute of Economics and Management, National University of Food
Technologies (NUFT) of Ukraine, Kyiv 01601,
Ukraine
| | - Dmytro Dziuba
- Department of Anesthesiology and Intensive Care, P.L. Shpyk
NUHC Ukraine, Kyiv 04112, Ukraine
| | - Andrii Parkhomenko
- Department of Finance and Business Economics, Marshall School
of Business, University of Southern California, Los Angeles, CA 90089, USA
| | - Volodymyr Smolanka
- Department of Medicine, Uzhhorod National University,
Uzhhorod 88000, Ukraine
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at
Mount Sinai, New York, NY 10029, USA
| | - Efe Sezgin
- Department of Food Engineering, Izmir Institute of
Technology, Urla, Izmir 35430, Turkey
| | - Alondra Diaz-Lameiro
- Department of Biology, University of Puerto Rico at Mayagüez,
Mayagüez 00681, Puerto
Rico
| | - Viktor R Toth
- Aquatic Botany and Microbial Ecology Research Group, Balaton Limnological
Research Institute, Tihany 8237, Hungary
| | - Megi Maci
- Stritch School of Medicine, Loyola University Chicago,
Maywood, IL 60153, USA
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska,
Anchorage, AK 99508, USA
| | - Fyodor Kondrashov
- Institute of Science and Technology Austria,
Klosterneuburg 3400, Austria
| | - Patricia M Morton
- Department of Sociology, Department of Public Health, Wayne State
University, Detroit, MI 48202, USA
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University,
Kraków 30-348, Poland
| | - Veronika Romero
- Department of Neurobiology, University of Utah, Salt Lake
City, UT 84112, USA
| | - Jakub Hlávka
- Price School of Public Policy, University of Southern
California, Los Angeles, CA 90089-3333, USA
- Masaryk University, Brno 6017, Czech Republic
| | - Serghei Mangul
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and
Pharmaceutical Sciences, University of Southern California,
Los Angeles, CA 90033, USA
- Department of Computational Biology, University of Southern
California, Los Angeles, CA 90033, USA
| | - Taras K Oleksyk
- Department of Biological Sciences, Oakland University,
Rochester, MI 48309-4479, USA
- Department of Biology, Uzhhorod National University, Uzhhorod
88000, Ukraine
| |
Collapse
|
3
|
Keller A, Ankenbrand MJ, Bruelheide H, Dekeyzer S, Enquist BJ, Erfanian MB, Falster DS, Gallagher RV, Hammock J, Kattge J, Leonhardt SD, Madin JS, Maitner B, Neyret M, Onstein RE, Pearse WD, Poelen JH, Salguero‐Gomez R, Schneider FD, Tóth AB, Penone C. Ten (mostly) simple rules to future‐proof trait data in ecological and evolutionary sciences. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Alexander Keller
- Cellular and Organismic Networks, Faculty of Biology Ludwig‐Maximilians‐Universität München Martinsried Germany
| | - Markus J. Ankenbrand
- Center for Computational and Theoretical Biology Julius‐Maximilians‐Universität Würzburg Würzburg Germany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle‐Wittenberg Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | | | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona USA
- The Santa Fe Institute Santa Fe New Mexico USA
| | | | - Daniel S. Falster
- Evolution & Ecology Research Centre University of New South Wales Sydney Sydney New South Wales Australia
| | - Rachael V. Gallagher
- Hawkesbury Institute for the Environment Western Sydney University Richmond New South Wales Australia
| | - Jennifer Hammock
- National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
| | - Jens Kattge
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Max Planck Institute for Biogeochemistry Jena Germany
| | - Sara D. Leonhardt
- Plant‐Insect Interactions, TUM School of Life Science Systems Technical University of Munich Freising Germany
| | - Joshua S. Madin
- Hawai'i Institute of Marine Biology University of Hawai'i at Manoa Kāne'ohe Hawai'i USA
| | - Brian Maitner
- Department of Geography University at Buffalo Buffalo New York USA
- Department of Environment and Sustainability University at Buffalo Buffalo New York USA
| | - Margot Neyret
- Senckenberg Biodiversity and Climate Research Center (SBik‐F) Frankfurt Germany
| | - Renske E. Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Naturalis Biodiversity Center Leiden The Netherlands
| | | | - Jorrit H. Poelen
- Ronin Institute for Independent Scholarship Montclair New Jersey USA
- Cheadle Center for Biodiversity and Ecological Restoration, UC Santa Barbara Santa Barbara California USA
| | | | - Florian D. Schneider
- Senckenberg Biodiversity and Climate Research Center (SBik‐F) Frankfurt Germany
- ISOE ‐ Institute for Social‐Ecological Research Frankfurt am Main Germany
| | - Anikó B. Tóth
- Centre for Ecosystem Science, School of Biological Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | - Caterina Penone
- Institute of Plant Sciences University of Bern Bern Switzerland
| |
Collapse
|
4
|
Diversifying the genomic data science research community. Genome Res 2022; 32:gr.276496.121. [PMID: 35858750 PMCID: PMC9341509 DOI: 10.1101/gr.276496.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Over the past 20 years, the explosion of genomic data collection and the cloud computing revolution have made computational and data science research accessible to anyone with a web browser and an internet connection. However, students at institutions with limited resources have received relatively little exposure to curricula or professional development opportunities that lead to careers in genomic data science. To broaden participation in genomics research, the scientific community needs to support these programs in local education and research at underserved institutions (UIs). These include community colleges, historically Black colleges and universities, Hispanic-serving institutions, and tribal colleges and universities that support ethnically, racially, and socioeconomically underrepresented students in the United States. We have formed the Genomic Data Science Community Network to support students, faculty, and their networks to identify opportunities and broaden access to genomic data science. These opportunities include expanding access to infrastructure and data, providing UI faculty development opportunities, strengthening collaborations among faculty, recognizing UI teaching and research excellence, fostering student awareness, developing modular and open-source resources, expanding course-based undergraduate research experiences (CUREs), building curriculum, supporting student professional development and research, and removing financial barriers through funding programs and collaborator support.
Collapse
|
5
|
Prunuske AJ, Evans-Anderson HJ, Furniss KL, Goller CC, Mirowsky JE, Moore ME, Raut SA, Swamy U, Wick S, Wolyniak MJ. Using personas and the ADKAR framework to evaluate a network designed to facilitate sustained change toward active learning in the undergraduate classroom. DISCOVER EDUCATION 2022; 1:22. [PMID: 36590921 PMCID: PMC9793354 DOI: 10.1007/s44217-022-00023-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022]
Abstract
One promising practice for increasing active learning in undergraduate science education is the use of a mentoring network. The Promoting Active Learning and Mentoring (PALM) Network was launched with practitioners from several professional societies and disciplines to make changes in their teaching based on evidence-based practices and to encourage the members to reflect deeply on their teaching experiences. Members of the Network interviewed seven previous Fellows, 1 to 6 years after completing their fellowship, to better understand the value of the Network and how these interactions impacted their ability to sustain change toward more active teaching practices. The interviews resulted in the creation of three personas that reflect the kinds of educators who engaged with the Network: Neil the Novice, Issa the Isolated, and Etta the Expert. Key themes emerged from the interviews about how interactions with the PALM Network sustained change toward evidence-based teaching practices allowing the members to readily adapt to the online learning environment during the COVID-19 pandemic. Understanding how the personas intersect with the ADKAR model contributes to a better understanding of how mentoring networks facilitate transformative change toward active learning and can inform additional professional development programs. Supplementary Information The online version contains supplementary material available at 10.1007/s44217-022-00023-w.
Collapse
Affiliation(s)
- Amy J. Prunuske
- Department of Microbiology and Immunology, Medical College of Wisconsin-Central Wisconsin, Wausau, WI United States
| | - Heather J. Evans-Anderson
- grid.264307.40000 0000 9688 1551Department of Health Sciences, Stetson University, DeLand, FL United States
| | - Katherine L. Furniss
- grid.17635.360000000419368657Department of Biology Teaching and Learning and Biotechnology Institute, University of Minnesota–Twin Cities, Minneapolis, MN United States
| | - Carlos C. Goller
- grid.40803.3f0000 0001 2173 6074Department of Biological Sciences, North Carolina State University, Raleigh, NC United States
| | - Jaime E. Mirowsky
- grid.264257.00000 0004 0387 8708Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY United States
| | - Michael E. Moore
- grid.265960.e0000 0001 0422 5627STEM Education Center, University of Arkansas at Little Rock, Little Rock, AR United States
| | - Samiksha A. Raut
- grid.265892.20000000106344187Department of Biology, University of Alabama at Birmingham, Birmingham, AL United States
| | - Uma Swamy
- grid.65456.340000 0001 2110 1845Department of Chemistry and Biochemistry, Florida International University, Miami, FL United States
| | - Sue Wick
- grid.17635.360000000419368657Department of Biology Teaching and Learning, University of Minnesota–Twin Cities, Minneapolis, MN United States
| | - Michael J. Wolyniak
- grid.256771.00000 0001 0426 7392Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA United States
| |
Collapse
|
6
|
Drew JC, Grandgenett N, Dinsdale EA, Vázquez Quiñones LE, Galindo S, Morgan WR, Pauley M, Rosenwald A, Triplett EW, Tapprich W, Kleinschmit AJ. There Is More than Multiple Choice: Crowd-Sourced Assessment Tips for Online, Hybrid, and Face-to-Face Environments. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:e00205-21. [PMID: 34970386 PMCID: PMC8673258 DOI: 10.1128/jmbe.00205-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/12/2021] [Indexed: 06/14/2023]
Abstract
Developing effective assessments of student learning is a challenging task for faculty and even more difficult for those in emerging disciplines that lack readily available resources and standards. With the power of technology-enhanced education and accessible digital learning platforms, instructors are also looking for assessments that work in an online format. This article will be useful for all teachers, but especially for entry-level instructors, in addition to more mature instructors who are looking to become more well versed in assessment, who seek a succinct summary of assessment types to springboard the integration of new forms of assessment of student learning into their courses. In this paper, ten assessment types, all appropriate for face-to-face, blended, and online modalities, are discussed. The assessments are mapped to a set of bioinformatics core competencies with examples of how they have been used to assess student learning. Although bioinformatics is used as the focus of the assessment types, the question types are relevant to many disciplines.
Collapse
Affiliation(s)
- Jennifer C. Drew
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Neal Grandgenett
- Department of Teacher Education, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Elizabeth A. Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luis E. Vázquez Quiñones
- Division of Science and Technology, Universidad Ana G. Méndez–Cupey Campus, San Juan, Puerto Rico
| | - Sebastian Galindo
- Department of Agricultural Education and Communication, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | | | - Mark Pauley
- Division of Undergraduate Education, National Science Foundation, Alexandria, Virginia, USA
| | - Anne Rosenwald
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Eric W. Triplett
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - William Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Adam J. Kleinschmit
- Department of Natural and Applied Sciences, University of Dubuque, Dubuque, Iowa, USA
| |
Collapse
|
7
|
Community development, implementation, and assessment of a NIBLSE bioinformatics sequence similarity learning resource. PLoS One 2021; 16:e0257404. [PMID: 34506617 PMCID: PMC8432852 DOI: 10.1371/journal.pone.0257404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022] Open
Abstract
As powerful computational tools and 'big data' transform the biological sciences, bioinformatics training is becoming necessary to prepare the next generation of life scientists. Furthermore, because the tools and resources employed in bioinformatics are constantly evolving, bioinformatics learning materials must be continuously improved. In addition, these learning materials need to move beyond today's typical step-by-step guides to promote deeper conceptual understanding by students. One of the goals of the Network for Integrating Bioinformatics into Life Sciences Education (NIBSLE) is to create, curate, disseminate, and assess appropriate open-access bioinformatics learning resources. Here we describe the evolution, integration, and assessment of a learning resource that explores essential concepts of biological sequence similarity. Pre/post student assessment data from diverse life science courses show significant learning gains. These results indicate that the learning resource is a beneficial educational product for the integration of bioinformatics across curricula.
Collapse
|
8
|
McDonald AR, Roberts R, Koeppe JR, Hall BL. Undergraduate structural biology education: A shift from users to developers of computation and simulation tools. Curr Opin Struct Biol 2021; 72:39-45. [PMID: 34461592 DOI: 10.1016/j.sbi.2021.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/30/2023]
Abstract
The use of theory and simulation in undergraduate education in biochemistry, molecular biology, and structural biology is now common, but the skills students need and the curriculum instructors have to train their students are evolving. The global pandemic and the immediate switch to remote instruction forced instructors to reconsider how they can use computation to teach concepts previously approached with other instructional methods. In this review, we survey some of the curricula, materials, and resources for instructors who want to include theory, simulation, and computation in the undergraduate curriculum. There has been a notable progression from teaching students to use discipline-specific computational tools to developing interactive computational tools that promote active learning to having students write code themselves, such that they view computation as another tool for solving problems. We are moving toward a future where computational skills, including programming, data analysis, visualization, and simulation, will no longer be considered an optional bonus for students but a required skill for the 21st century STEM (Science, Technology, Engineering, and Mathematics) workforce; therefore, all physical and life science students should learn to program in the undergraduate curriculum.
Collapse
Affiliation(s)
- Ashley Ringer McDonald
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93401, USA.
| | - Rebecca Roberts
- Department of Biology, Ursinus College, Collegeville, PA 19426, USA
| | - Julia R Koeppe
- Department of Chemistry, SUNY at Oswego, Oswego, NY 13126, USA
| | - Bonnie L Hall
- Department of Chemistry and Physics, Grand View University, Des Moines, IA 50316, USA
| |
Collapse
|