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Visualizing Biological Information

Author : Clifford A. Pickover

Publisher : World Scientific

Page : 250 pages

File Size : 45,77 MB

Release : 1995

Category : Science

ISBN : 9789810214272

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Book Description

Biological data of all kinds is proliferating at an incredible rate. If humans attempt to read such data in the form of numbers and letters, they will take in the information at a snail's pace. If the information is rendered graphically, however, human analysts can assimilate it and gain insight at a much faster rate. The emphasis of this book is on the graphic representation of information-containing sequences such as DNA and amino acid sequences in order to help the human analyst find interesting and biologically relevant patterns. The editor's goal is to make this voyage through molecular biology, genetics and computer graphics as accessible to a broad audience as possible, with the inclusion of glossaries at the end of most chapters and program outlines where applicable. The book will be of most interest to biologists and computer scientists and the various large reference lists should be of interest to beginners and advanced students of biology, graphic art and computer science. Contributors have sought to find pattern and meaning in the cacophony of genetic and protein sequence data using unusual computer graphics and musical techniques.



A Primer in Biological Data Analysis and Visualization Using R

Author : Gregg Hartvigsen

Publisher : Columbia University Press

Page : 245 pages

File Size : 28,85 MB

Release : 2014-02-18

Category : Education

ISBN : 0231537042

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Book Description

R is the most widely used open-source statistical and programming environment for the analysis and visualization of biological data. Drawing on Gregg Hartvigsen's extensive experience teaching biostatistics and modeling biological systems, this text is an engaging, practical, and lab-oriented introduction to R for students in the life sciences. Underscoring the importance of R and RStudio in organizing, computing, and visualizing biological statistics and data, Hartvigsen guides readers through the processes of entering data into R, working with data in R, and using R to visualize data using histograms, boxplots, barplots, scatterplots, and other common graph types. He covers testing data for normality, defining and identifying outliers, and working with non-normal data. Students are introduced to common one- and two-sample tests as well as one- and two-way analysis of variance (ANOVA), correlation, and linear and nonlinear regression analyses. This volume also includes a section on advanced procedures and a chapter introducing algorithms and the art of programming using R.



Visualizing Human Biology

Author : Kathleen A. Ireland

Publisher : John Wiley & Sons

Page : 530 pages

File Size : 18,37 MB

Release : 2017-12-19

Category : Science

ISBN : 1119398150

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Book Description

Visualizing Human Biology is a visual exploration of the major concepts of biology using the human body as the context. Students are engaged in scientific exploration and critical thinking in this product specially designed for non-science majors. Topics covered include an overview of human anatomy and physiology, nutrition, immunity and disease, cancer biology, and genetics. The aim of Visualizing Human Biology is a greater understanding, appreciation and working knowledge of biology as well as an enhanced ability to make healthy choices and informed healthcare decisions.



Visualizing Human Biology

Author : Kathleen A. Ireland

Publisher : John Wiley & Sons

Page : 1409 pages

File Size : 26,22 MB

Release : 2010-10-04

Category : Science

ISBN : 0470569190

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Book Description

Medical professionals will be able to connect the science of biology to their own lives through the stunning visuals in Visualizing Human Biology. The important concepts of human biology are presented as they relate to the world we live in. The role of the human in the environment is stressed throughout, ensuring that topics such as evolution, ecology, and chemistry are introduced in a non-threatening and logical fashion. Illustrations and visualization features are help make the concepts easier to understand. Medical professionals will appreciate this visual and concise approach.



A Practical Approach to Microarray Data Analysis

Author : Daniel P. Berrar

Publisher : Springer Science & Business Media

Page : 382 pages

File Size : 35,74 MB

Release : 2007-05-08

Category : Science

ISBN : 0306478153

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Book Description

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.



Membrane Organization and Dynamics

Author : Amitabha Chattopadhyay

Publisher : Springer

Page : 387 pages

File Size : 32,56 MB

Release : 2017-12-06

Category : Science

ISBN : 3319666010

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Book Description

This volume brings together information on membrane organization and dynamics from a variety of spectroscopic, microscopic and simulation approaches, spanning a broad range of time scales. The implication of such dynamic information on membrane function in health and disease is a topic of contemporary interest. The chapters cover various aspects of membrane lipid and protein dynamics, explored using a battery of experimental and theoretical approaches. The synthesis of information and knowledge gained by utilizing multiple approaches will provide the reader with a comprehensive understanding of the underlying membrane dynamics and function, which will help to develop robust dynamic models for the understanding of membrane function in healthy and diseased states. In the last few years, crystal structures of an impressive number of membrane proteins have been reported, thanks to tremendous advances in membrane protein crystallization techniques. Some of these recently solved structures belong to the G protein-coupled receptor (GPCR) family, which are particularly difficult to crystallize due to their intrinsic flexibility. Nonetheless, these static structures do not provide the necessary information to understand the function of membrane proteins in the complex membrane milieu. This volume will address the dynamic nature of membrane proteins within the membrane and will provide the reader with an up-to date overview of the theory and practical approaches that can be used. This volume will be invaluable to researchers working in a wide range of scientific areas, from biochemistry and molecular biology to biophysics and protein science. Students of these fields will also find this volume very useful. This book will also be of great use to those who are interested in the dynamic nature of biological processes.



Ondex

Author : Jan Taubert

Publisher : Sudwestdeutscher Verlag Fur Hochschulschriften AG

Page : 248 pages

File Size : 27,91 MB

Release : 2011-10

Category :

ISBN : 9783838129297

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Book Description

Over the last decade biological research has changed completely. The reductionism approach of studying only a few biological entities at a time in the past is being replaced by the study of the biological system as a whole today. This requires that existing biological knowledge (data) is made readily available. Effective integration of biological knowledge from databases scattered around the internet and other information resources (for example experimental data) is recognized as a pre-requisite for many aspects of biological research. Systems for the integration of biological knowledge have to overcome several challenges: biological data sources may contain similar or overlapping coverage and the user of such systems is faced with the challenge of generating a consensus data set or selecting the "best" data source; different access methods to databases, different data formats, different naming conventions and erroneous or missing data. To address these challenges and enable effective integration of biological knowledge, the ONDEX system was created. ONDEX provides an integrated view across biological data sources to the user. Here the basic principles behind ONDEX are presented.



Visualizing Information in the Biological Sciences

Author :

Publisher :

Page : pages

File Size : 47,90 MB

Release : 2003

Category :

ISBN :

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Book Description

Information visualization is an effective method for displaying large data sets in a pictorial or graphical format. The visualization aids researchers and analysts in understanding data by evaluating the content and grouping documents together around themes and concepts. With the ever-growing amount of information available on the Internet, additional methods are needed to analyze and interpret data. WebTheme allows users to harvest thousands of web pages and automatically organize and visualize their contents. WebTheme is an interactive web-based product that provides a new way to investigate and understand large volumes of HTML text-based information. It has the ability to harvest data from the World Wide Web using search terms and selected search engines or by following URLs chosen by the user. WebTheme enables users to rapidly identify themes and concepts found among thousands of pages of text harvested and provides a suite of tools to further explore and analyze special areas of interest within a data set. WebTheme was developed at Pacific Northwest National Laboratory (PNNL) for NASA as a method for generating meaningful, thematic, and interactive visualizations. Through a collaboration with the Laboratory's Information Science and Engineering (IS & E) group, information specialists are providing demonstrations of WebTheme and assisting researchers in analyzing their results. This paper will provide a brief overview of the WebTheme product, and the ways in which the Hanford Technical Library's information specialists are assisting researchers in using this product.



Practical Protein Bioinformatics

Author : Florencio Pazos

Publisher : Springer

Page : 111 pages

File Size : 20,82 MB

Release : 2014-11-28

Category : Science

ISBN : 3319127276

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Book Description

This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them). It covers a wide range of tools for dealing with different aspects of proteins, from their sequences, to their three-dimensional structures, and the biological networks they are immersed in. The selection of tools is based on the experience of the authors that lead a protein bioinformatics facility in a large research centre, with the additional constraint that the tools should be accessible through standard web browsers without requiring the local installation of specific software, command-line tools, etc. The web tools covered include those aimed to retrieve protein information, look for similar proteins, generate pair-wise and multiple sequence alignments of protein sequences, work with protein domains and motifs, study the phylogeny of a family of proteins, retrieve, manipulate and visualize protein three-dimensional structures, predict protein structural features as well as whole three-dimensional structures, extract biological information from protein structures, summarize large protein sets, study protein interaction and metabolic networks, etc. The book is associated to a dynamic web site that will reflect changes in the web addresses of the tools, updates of these, etc. It also contains QR codes that can be scanned with any device to direct its browser to the tool web site. This monograph will be most valuable for researchers in experimental labs without specific knowledge on bioinformatics or computing.



Data Visualization Tools for Large Biological Data Sets

Author : Jamie Waese

Publisher :

Page : 0 pages

File Size : 22,88 MB

Release : 2017

Category :

ISBN :

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Book Description

Researchers have access to an ever-growing volume of data available at multiple levels of biological analysis. Many visual analytic tools have been developed to display a variety of biological data types but many of these tools are challenging to use and only examine one biological level of analysis at a time. The development and testing of hypotheses is difficult when the information is hard to integrate and laborious to interpret. The application of data visualization principles and user experience design best practices could improve systems biology research workflows by providing visual analytic tools with what is known in the information visualization community as a "transparent" user interface. This thesis consists of four papers that explore two central questions: 1) What is the best way to represent biological information at different levels of analysis? and 2) How do we enable researchers to explore and interact with their data as naturally and intuitively as possible? The first paper describes, ePlant, a tool for visualizing multiple levels of data that was developed using an agile process that included several rounds of user testing. The second paper presents Gene Slider, a tool for visualizing the conservation and entropy of orthologous DNA and protein sequences using a data visualization paradigm that takes better advantage of preattentive visual processing than current methods. The third paper describes Topo-phylogeny, a tool for visualizing phylogenetic relationships using a topographic map visualization paradigm that requires less cognitive processing to interpret than traditional tree diagrams. The final paper demonstrates the importance of user testing when developing a "rapid serial visual presentation" interface for identifying genes of interest using electronic fluorescent pictographs. Together these papers illustrate the complexities and benefits of applying data visualization principles and user experience design best practices to building data visualization tools for the analysis of large biological data sets. Given that hypothesis generation is fundamentally a creative process, any tools or techniques that can help researchers consider their data at a deeper level should be valuable to the scientific community.