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Cao Y, Tran A, Kim H, Robertson N, Lin Y, Torkel M, Yang P, Patrick E, Ghazanfar S, Yang J. Thinking process templates for constructing data stories with SCDNEY. F1000Res 2023; 12:261. [PMID: 38434622 PMCID: PMC10905113 DOI: 10.12688/f1000research.130623.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 03/05/2024] Open
Abstract
Background Globally, scientists now have the ability to generate a vast amount of high throughput biomedical data that carry critical information for important clinical and public health applications. This data revolution in biology is now creating a plethora of new single-cell datasets. Concurrently, there have been significant methodological advances in single-cell research. Integrating these two resources, creating tailor-made, efficient, and purpose-specific data analysis approaches can assist in accelerating scientific discovery. Methods We developed a series of living workshops for building data stories, using Single-cell data integrative analysis (scdney). scdney is a wrapper package with a collection of single-cell analysis R packages incorporating data integration, cell type annotation, higher order testing and more. Results Here, we illustrate two specific workshops. The first workshop examines how to characterise the identity and/or state of cells and the relationship between them, known as phenotyping. The second workshop focuses on extracting higher-order features from cells to predict disease progression. Conclusions Through these workshops, we not only showcase current solutions, but also highlight critical thinking points. In particular, we highlight the Thinking Process Template that provides a structured framework for the decision-making process behind such single-cell analyses. Furthermore, our workshop will incorporate dynamic contributions from the community in a collaborative learning approach, thus the term 'living'.
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Affiliation(s)
- Yue Cao
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Andy Tran
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Hani Kim
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Nick Robertson
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yingxin Lin
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Marni Torkel
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Pengyi Yang
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Ellis Patrick
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Shila Ghazanfar
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jean Yang
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
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Levenstein D, Alvarez VA, Amarasingham A, Azab H, Chen ZS, Gerkin RC, Hasenstaub A, Iyer R, Jolivet RB, Marzen S, Monaco JD, Prinz AA, Quraishi S, Santamaria F, Shivkumar S, Singh MF, Traub R, Nadim F, Rotstein HG, Redish AD. On the Role of Theory and Modeling in Neuroscience. J Neurosci 2023; 43:1074-1088. [PMID: 36796842 PMCID: PMC9962842 DOI: 10.1523/jneurosci.1179-22.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 02/18/2023] Open
Abstract
In recent years, the field of neuroscience has gone through rapid experimental advances and a significant increase in the use of quantitative and computational methods. This growth has created a need for clearer analyses of the theory and modeling approaches used in the field. This issue is particularly complex in neuroscience because the field studies phenomena that cross a wide range of scales and often require consideration at varying degrees of abstraction, from precise biophysical interactions to the computations they implement. We argue that a pragmatic perspective of science, in which descriptive, mechanistic, and normative models and theories each play a distinct role in defining and bridging levels of abstraction, will facilitate neuroscientific practice. This analysis leads to methodological suggestions, including selecting a level of abstraction that is appropriate for a given problem, identifying transfer functions to connect models and data, and the use of models themselves as a form of experiment.
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Affiliation(s)
- Daniel Levenstein
- Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Veronica A Alvarez
- Laboratory on Neurobiology of Compulsive Behaviors, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20892
| | - Asohan Amarasingham
- Departments of Mathematics and Biology, City College and the Graduate Center, City University of New York, New York, New York 10032
| | - Habiba Azab
- Department of Neuroscience, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota 55455
| | - Zhe S Chen
- Department of Psychiatry, Neuroscience & Physiology, New York University School of Medicine, New York, New York, 10016
| | - Richard C Gerkin
- School of Life Sciences, Arizona State University, Tempe, Arizona 85281
| | - Andrea Hasenstaub
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California 94115
| | | | - Renaud B Jolivet
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Sarah Marzen
- W. M. Keck Science Department, Pitzer, Scripps, and Claremont McKenna Colleges, Claremont, California 91711
| | - Joseph D Monaco
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218
| | - Astrid A Prinz
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Salma Quraishi
- Neuroscience, Developmental and Regnerative Biology Department, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Fidel Santamaria
- Neuroscience, Developmental and Regnerative Biology Department, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Sabyasachi Shivkumar
- Brain and Cognitive Sciences, University of Rochester, Rochester, New York 14627
| | - Matthew F Singh
- Department of Psychological & Brain Sciences, Department of Electrical & Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63112
| | - Roger Traub
- IBM T.J. Watson Research Center, AI Foundations, Yorktown Heights, New York 10598
| | - Farzan Nadim
- Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California 94115
| | - Horacio G Rotstein
- Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California 94115
| | - A David Redish
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455
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Scearce-Levie K, Sanchez PE, Lewcock JW. Leveraging preclinical models for the development of Alzheimer disease therapeutics. Nat Rev Drug Discov 2020; 19:447-462. [PMID: 32612262 DOI: 10.1038/s41573-020-0065-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
A large number of mouse models have been engineered, characterized and used to advance biomedical research in Alzheimer disease (AD). Early models simply damaged the rodent brain through toxins or lesions. Later, the spread of genetic engineering technology enabled investigators to develop models of familial AD by overexpressing human genes such as those encoding amyloid precursor protein (APP) or presenilins (PSEN1 or PSEN2) carrying mutations linked to early-onset AD. Recently, more complex models have sought to explore the impact of multiple genetic risk factors in the context of different biological challenges. Although none of these models has proven to be a fully faithful reproduction of the human disease, models remain essential as tools to improve our understanding of AD biology, conduct thorough pharmacokinetic and pharmacodynamic analyses, discover translatable biomarkers and evaluate specific therapeutic approaches. To realize the full potential of animal models as new technologies and knowledge become available, it is critical to define an optimal strategy for their use. Here, we review progress and challenges in the use of AD mouse models, highlight emerging scientific innovations in model development, and introduce a conceptual framework for use of preclinical models for therapeutic development.
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