Visualizing Biological Complexity
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Visualizing Biological Complexity
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Author : Anke M. Mulder
language : en
Publisher:
Release Date : 2011-09-09
Visualizing Biological Complexity written by Anke M. Mulder and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-09 with Electron microscopy categories.
The advent of an information age in which cutting edge technologies and important scientific discoveries are accessible to a global audience at an instant's notice has drastically changed the landscape of scientific investigation. The era of advancing scientific knowledge painstakingly and one hypothesis at a time has given way to high-throughput, large scale, discovery based approaches. Discovery-based efforts in genomics, proteomics, and metabolomics have exchanged the old view of single genes that encode single proteins to act in isolation, for an understanding of life as an intricate web of networks of interactions between proteins, RNA, DNA, and small molecules with complex, interrelated feedback loops of information flow. High-throughput efforts in structural genomics are increasingly establishing a role for structural biology in systems level investigations and an understanding of the structural dimension of biological complexity is emerging. Recent advances in automation and computation in single particle electron microscopy (EM), are rapidly pushing this field into the realm of high-throughput structural biology. This thesis strives to illustrate the unique contribution that discovery-based, high-throughput single-particle EM can make toward resolving complex biological interaction networks. First, the design of a discovery-based experiment is illustrated via the discovery-based metabolite profiling (DMP) investigation of the endocannabinoid signaling pathway. Next, the unique ability of single-particle EM data analysis to resolve heterogeneous biological information into homogenous sub-sets is demonstrated via single-particle EM analysis of Kinesin-13 binding to bent microtubule (MT) protofilaments. Finally, a novel discovery-based single particle profiling (DSP) method is developed and used to construct a mechanism for 30S ribosome subunit assembly, thereby illustrating the potential of single particle EM to deconvolute complex biological interaction networks. Future application of DSP to other complex biological networks promises to open exciting new avenues of research, and will establish single particle EM as a formidable contender in the omics-centered nature of the modern scientific landscape.
The Biological Art Drawing Heuristic
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Author : Caryn Babaian
language : en
Publisher:
Release Date : 2021
The Biological Art Drawing Heuristic written by Caryn Babaian and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
ABSTRACTBiology is considered the most visual of the sciences. Historically it has relied on the skill set of observation, experimentation, and (less acknowledged) drawing. Many scientists, who have contributed to the foundations of biology and medicine, were also artists (Smith 2009). The drawing methods employed by these pioneers of biology have been overlooked in history and rarely considered a methodology for research or educational practices related to complex biological topics like evolutionary processes. According to botanist and artist Agnes Arbor, "There is a close association between fingers and brain, that the handing over either the technical or the interpretive side of research to another worker cannot but mean a serious loss of integration" (Arbor 1954). The integrated drawing-experimental methods of the past combined the observational naturalist's skill set with the experimental biologist skill set. As a result, the drawing methods themselves became a complex conceptualization of living systems and illuminated them. Today, biology disciplines are converging on a consensus that living systems are multi-dimensional, networked, dynamic, interdependent, and evolutionary complex webs. Understanding a complex moving web of life for students may require. It may benefit from a non-linear, creative approach for a continued perception of biological phenomena, as it did in the past. Benefits from this historical method may also emerge in the education of future life scientists and physicians. It has been verified that even simple drawing is an activity that increases observational skills, focus, and divergent thinking (Kozbelt 2010). Technology has sped up the discovery process and increased the data output. However, it has had a side-effect of marginalizing those deliberate, mindful, and methodical biology skills, such as observation and drawing from Nature. Alongside the growing technology is a resurgence and a strong need for complementary measured, meditative arts and drawing practice. With this realization, the paradigm of STEAM (science, technology, engineering, art, and math) has become colloquially popular. However, despite the use of "art" in science education and even the presence of artists in laboratories, the historical drawing biology approach has not been revisited, developed further, explored, or practiced in any rigorous way. This is a significant oversight in biological science education, considering that scientists of the past made huge leaps in their iii discoveries using simple technologies and drawing. This genuine unification of biology and drawing is generally not a domain that professional or academic artists or educators can easily address. It requires a deep understanding and intimate relationship with Nature and biological systems. As an authentic merger, it is content-heavy and skill-dependent. Developing a drawing-based model for biology is essential and, perhaps, best undertaken by biology sectors. My interest in this dissertation has been the synthesis that occurs within the learner or researcher of this amalgamated domain. It has not been developed or taught as a model of scientific inquiry today and does not exist in the science or biology curriculum. Yet, it is the core of the visual arts and visual STEAM-based experiences, which assert that they employ the visual arts to enhance biology education. To reveal the potential of the drawing discovery process, I have examined the multidimensional history of drawing for biology and visualizing biological mechanisms. Also, I have developed artistic-narrative methods, retaining the essence of the past and applicable in modern biology courses of today. These efforts address the deficit of a foundational visual skill set, which is the focus of this work.
Biological Data Exploration With Python Pandas And Seaborn
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Author : Martin Jones
language : en
Publisher:
Release Date : 2020-06-03
Biological Data Exploration With Python Pandas And Seaborn written by Martin Jones and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-06-03 with categories.
In biological research, we''re currently in a golden age of data. It''s never been easier to assemble large datasets to probe biological questions. But these large datasets come with their own problems. How to clean and validate data? How to combine datasets from multiple sources? And how to look for patterns in large, complex datasets and display your findings? The solution to these problems comes in the form of Python''s scientific software stack. The combination of a friendly, expressive language and high quality packages makes a fantastic set of tools for data exploration. But the packages themselves can be hard to get to grips with. It''s difficult to know where to get started, or which sets of tools will be most useful. Learning to use Python effectively for data exploration is a superpower that you can learn. With a basic knowledge of Python, pandas (for data manipulation) and seaborn (for data visualization) you''ll be able to understand complex datasets quickly and mine them for biological insight. You''ll be able to make beautiful, informative charts for posters, papers and presentations, and rapidly update them to reflect new data or test new hypotheses. You''ll be able to quickly make sense of datasets from other projects and publications - millions of rows of data will no longer be a scary prospect! In this book, Dr. Jones draws on years of teaching experience to give you the tools you need to answer your research questions. Starting with the basics, you''ll learn how to use Python, pandas, seaborn and matplotlib effectively using biological examples throughout. Rather than overwhelm you with information, the book concentrates on the tools most useful for biological data. Full color illustrations show hundreds of examples covering dozens of different chart types, with complete code samples that you can tweak and use for your own work. This book will help you get over the most common obstacles when getting started with data exploration in Python. You''ll learn about pandas'' data model; how to deal with errors in input files and how to fit large datasets in memory. The chapters on visualization will show you how to make sophisticated charts with minimal code; how to best use color to make clear charts, and how to deal with visualization problems involving large numbers of data points. Chapters include: Getting data into pandas: series and dataframes, CSV and Excel files, missing data, renaming columns Working with series: descriptive statistics, string methods, indexing and broadcasting Filtering and selecting: boolean masks, selecting in a list, complex conditions, aggregation Plotting distributions: histograms, scatterplots, custom columns, using size and color Special scatter plots: using alpha, hexbin plots, regressions, pairwise plots Conditioning on categories: using color, size and marker, small multiples Categorical axes:strip/swarm plots, box and violin plots, bar plots and line charts Styling figures: aspect, labels, styles and contexts, plotting keywords Working with color: choosing palettes, redundancy, highlighting categories Working with groups: groupby, types of categories, filtering and transforming Binning data: creating categories, quantiles, reindexing Long and wide form: tidying input datasets, making summaries, pivoting data Matrix charts: summary tables, heatmaps, scales and normalization, clustering Complex data files: cleaning data, merging and concatenating, reducing memory FacetGrids: laying out multiple charts, custom charts, multiple heat maps Unexpected behaviours: bugs and missing groups, fixing odd scales High performance pandas: vectorization, timing and sampling Further reading: dates and times, alternative syntax
11th International Meeting On Visualizing Biological Data Vizbi 2021
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Author : Sean O’Donoghue
language : en
Publisher: Frontiers Media SA
Release Date : 2022-12-16
11th International Meeting On Visualizing Biological Data Vizbi 2021 written by Sean O’Donoghue and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-12-16 with Science categories.
Complex Fluids In Biological Systems
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Author : Saverio E. Spagnolie
language : en
Publisher: Springer
Release Date : 2014-11-27
Complex Fluids In Biological Systems written by Saverio E. Spagnolie and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-11-27 with Science categories.
This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solutions in the numerical simulation of biologically relevant complex fluid flows This volume will be accessible to advanced undergraduate and beginning graduate students in engineering, mathematics, biology, and the physical sciences, but will appeal to anyone interested in the intricate and beautiful nature of complex fluids in the context of living systems.
Interactive Visualization Of Complex Structures In Modular Models For Systems Biology
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Author : Sebastian Mirschel
language : en
Publisher:
Release Date : 2012-09-06
Interactive Visualization Of Complex Structures In Modular Models For Systems Biology written by Sebastian Mirschel and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-09-06 with categories.
Harnessing Biological Complexity
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Author : Taishin Nomura
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-12-13
Harnessing Biological Complexity written by Taishin Nomura and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-13 with Technology & Engineering categories.
The challenge for the biosciences in the twenty-first century is to integrate genome sequencing information into a better understanding of biology, physiology, and human pathology. Such attempts at integration are moving the world toward a new generation of bioscience and bioengineering, where biological, physiological, and pathological information from humans and other living animals can be quantitatively described in silico across multiple scales of time and size and through diverse hierarchies of organization — from molecules to cells and organs, to individuals. To "harness" such complexity, international communities of integrative bioscientists and bioengineers aim to establish frameworks and information infrastructures for describing biological structures and physiological functions on multiple scales of time and space. This textbook includes a public platform to describe physiological functions using mathematical equations and guides the reader to perform mathematical modeling and computer simulations, to combine existing models as well as to create new models. Accessible to biologists, physiologists, and students of the sciences, with illustrative details provided when necessary, this book seeks to achieve a systematic way of harnessing biological complexity. Sharing the databases among communities worldwide will help to find comprehensive answers to all the important questions.
Biology Life Unit 1 From Atoms To Cells
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Author : Smart Biology Inc.
language : en
Publisher: Smart Biology Inc.
Release Date : 2022-05-01
Biology Life Unit 1 From Atoms To Cells written by Smart Biology Inc. and has been published by Smart Biology Inc. this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-05-01 with Science categories.
BIOLOGY | LIFE | UNIT 1 | From Atoms to Cells focuses on the physical components that make up cells. Embark on one continuous journey to understand and appreciate the interconnections between the subatomic, atomic, molecular, macromolecular, and cellular worlds. We spend time covering the basics so you can understand the complex. Moreover, we explain the underlying why questions so you can truly understand. This downloadable e-book includes access to text, over 350 high-quality, accurate figures, 40 interactive structures, and more, to suit all learners. Note: Access to our online courseware, including our animated video lessons, is not included in this eBook but can be purchased at www.smart-biology.com
Visualizing The Complexity Of The Molecular World
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Author : Jodie Anne Jenkinson
language : en
Publisher:
Release Date : 2012
Visualizing The Complexity Of The Molecular World written by Jodie Anne Jenkinson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Modeling And Visualization Of Complex Systems And Enterprises
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Author : William B. Rouse
language : en
Publisher: John Wiley & Sons
Release Date : 2015-07-27
Modeling And Visualization Of Complex Systems And Enterprises written by William B. Rouse and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-27 with Technology & Engineering categories.
Explains multi-level models of enterprise systems and covers modeling methodology This book addresses the essential phenomena underlying the overall behaviors of complex systems and enterprises. Understanding these phenomena can enable improving these systems. These phenomena range from physical, behavioral, and organizational, to economic and social, all of which involve significant human components. Specific phenomena of interest and how they are represented depend on the questions of interest and the relevant domains or contexts. Modeling and Visualization of Complex Systems and Enterprises examines visualization of phenomena and how understanding the relationships among phenomena can provide the basis for understanding where deeper exploration is warranted. The author also reviews mathematical and computational models, defined very broadly across disciplines, which can enable deeper understanding. Presents a 10 step methodology for addressing questions associated with the design or operation of complex systems and enterprises Examines six archetypal enterprise problems including two from healthcare, two from urban systems, and one each from financial systems and defense systems Provides an introduction to the nature of complex systems, historical perspectives on complexity and complex adaptive systems, and the evolution of systems practice Modeling and Visualization of Complex Systems and Enterprises is written for graduate students studying systems science and engineering and professionals involved in systems science and engineering, those involved in complex systems such as healthcare delivery, urban systems, sustainable energy, financial systems, and national security.
