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Rittenbruch M, Vella K, Brereton M, Hogan JM, Johnson D, Heinrich J, O'Donoghue S. Collaborative Sense-Making in Genomic Research: The Role of Visualisation. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2022; 28:4477-4489. [PMID: 34156943 DOI: 10.1109/tvcg.2021.3090746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genomic research emerges from collaborative work within and across different scientific disciplines. A diverse range of visualisation techniques has been employed to aid this research, yet relatively little is known as to how these techniques facilitate collaboration. We conducted a case study of collaborative research within a biomedical institute to learn more about the role visualisation plays in genomic mapping. Interviews were conducted with molecular biologists (N = 5) and bioinformaticians (N = 6). We found that genomic research comprises a variety of distinct disciplines engaged in complex analytic tasks that each resist simplification, and their complexity influences how visualisations were used. Visualisation use was impacted by group-specific interactions and temporal work patterns. Visualisations were also crucial to the scientific workflow, used for both question formation and confirmation of hypotheses, and acted as an anchor for the communication of ideas and discussion. In the latter case, two approaches were taken: providing collaborators with either interactive or static imagery representing a viewpoint. The use of generic software for simplified visualisations, and quick production and curation was also noted. We discuss these findings with reference to group-specific interactions and present recommendations for improving collaborative practices through visual analytics.
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Blanco E, González-Ramírez M, Di Croce L. Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. Sci Rep 2021; 11:19545. [PMID: 34599234 PMCID: PMC8486768 DOI: 10.1038/s41598-021-98889-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu, and the source code is freely distributed at https://github.com/eblancoga/seqcode.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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Ing-Simmons E, Vaquerizas JM. Visualising three-dimensional genome organisation in two dimensions. Development 2019; 146:146/19/dev177162. [PMID: 31558569 DOI: 10.1242/dev.177162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The three-dimensional organisation of the genome plays a crucial role in developmental gene regulation. In recent years, techniques to investigate this organisation have become more accessible to labs worldwide due to improvements in protocols and decreases in the cost of high-throughput sequencing. However, the resulting datasets are complex and can be challenging to analyse and interpret. Here, we provide a guide to visualisation approaches that can aid the interpretation of such datasets and the communication of biological results.
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Affiliation(s)
- Elizabeth Ing-Simmons
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, DE-48149 Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, DE-48149 Muenster, Germany
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Qian M, Cheng Y, Wang X. The methodology study of three-dimensional (3D) genome research. Semin Cell Dev Biol 2019; 90:12-18. [DOI: 10.1016/j.semcdb.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022]
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Nusrat S, Harbig T, Gehlenborg N. Tasks, Techniques, and Tools for Genomic Data Visualization. COMPUTER GRAPHICS FORUM : JOURNAL OF THE EUROPEAN ASSOCIATION FOR COMPUTER GRAPHICS 2019; 38:781-805. [PMID: 31768085 PMCID: PMC6876635 DOI: 10.1111/cgf.13727] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this need has become crucial in genomics, as biomedical research is increasingly data-driven and many studies lack well-defined hypotheses. A key challenge in data-driven research is to discover unexpected patterns and to formulate hypotheses in an unbiased manner in vast amounts of genomic and other associated data. Over the past two decades, this has driven the development of numerous data visualization techniques and tools for visualizing genomic data. Based on a comprehensive literature survey, we propose taxonomies for data, visualization, and tasks involved in genomic data visualization. Furthermore, we provide a comprehensive review of published genomic visualization tools in the context of the proposed taxonomies.
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Affiliation(s)
- S Nusrat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - T Harbig
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - N Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Goodstadt MN, Marti-Renom MA. Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning. J Mol Biol 2018; 431:1071-1087. [PMID: 30419242 DOI: 10.1016/j.jmb.2018.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023]
Abstract
Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.
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Affiliation(s)
- Mike N Goodstadt
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet 2018; 50:1352-1358. [PMID: 30262815 DOI: 10.1038/s41588-018-0236-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 07/19/2018] [Indexed: 11/09/2022]
Abstract
Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand that the linear genome is folded in ways that may modulate how genes are expressed during the basic functioning of cells. Importantly, it is now possible to build 3D models of how the genome folds within the nucleus and changes over time (4D). Because genome folding influences its function, this opens exciting new possibilities to broaden our understanding of the mechanisms that determine cell fate. However, the rapid evolution of methods and the increasing complexity of data can result in ambiguity and reproducibility challenges, which may hamper the progress of this field. Here, we describe such challenges ahead and provide guidelines to think about strategies for shared standardized validation of experimental 4D nucleome data sets and models.
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Waldispühl J, Zhang E, Butyaev A, Nazarova E, Cyr Y. Storage, visualization, and navigation of 3D genomics data. Methods 2018; 142:74-80. [PMID: 29792917 DOI: 10.1016/j.ymeth.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/27/2023] Open
Abstract
The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art computing technology, as well as the solutions adopted by the platforms currently available.
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Affiliation(s)
| | - Eric Zhang
- School of Computer Science, McGill University, Montréal, Canada
| | | | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, Canada
| | - Yan Cyr
- Beam Me Up Labs, Montréal, Canada
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Just W. Jerusalem Special Issue. FEBS Lett 2018; 591:2503-2504. [PMID: 28876461 DOI: 10.1002/1873-3468.12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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