Misplaced Pages

#142857

52-441: UCSF Chimera (or simply Chimera ) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies , sequence alignments, docking results, trajectories, and conformational ensembles . High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use. Chimera

104-407: A simulation to create an image of something so it can be taught about. This is very useful when teaching about a topic that is difficult to otherwise see, for example, atomic structure , because atoms are far too small to be studied easily without expensive and difficult to use scientific equipment. The use of visual representations to transfer knowledge between at least two persons aims to improve

156-532: A 3D scalar field may be implemented using iso-surfaces for field distribution and textures for the gradient of the field. Examples of such visual formats are sketches , diagrams , images , objects, interactive visualizations, information visualization applications, and imaginary visualizations as in stories . While information visualization concentrates on the use of computer-supported tools to derive new insights, knowledge visualization focuses on transferring insights and creating new knowledge in groups . Beyond

208-403: A digital construction of a real object directly from the scientific data. Scientific visualization is usually done with specialized software , though there are a few exceptions, noted below. Some of these specialized programs have been released as open source software, having very often its origins in universities, within an academic environment where sharing software tools and giving access to

260-401: A display are compounded when we go from a static to an animated graphic. Because of their dynamic character, educational animations introduce a further challenge to information extraction beyond those found with static graphics. Certain aspects of a display that changes over time have the potential to capture learner attention. If there is sufficient dynamic contrast between one or more items in

312-407: A form that facilitates human interaction for exploration and understanding. Important aspects of information visualization are dynamics of visual representation and the interactivity. Strong techniques enable the user to modify the visualization in real-time, thus affording unparalleled perception of patterns and structural relations in the abstract data in question. Educational visualization is using

364-418: A larger process of data analysis. Visual analytics has been defined as "the science of analytical reasoning supported by the interactive visual interface". Its focus is on human information discourse (interaction) within massive, dynamically changing information spaces. Visual analytics research concentrates on support for perceptual and cognitive operations that enable users to detect the expected and discover

416-434: A number of content domains . While there have been some findings that show positive effects of animations on learning, other studies have found no effects or even negative effects. Some propose that the efficacy depends on the way the animation characteristics engages the psychological functioning of the learner. In general, it can be concluded that animations are not intrinsically more effective than static graphics. Rather,

468-439: A purely perceptual level, our attention tends to be attracted by some parts of a static display more than by other parts due to their visuospatial properties. For example, an object that is centrally placed, relatively large, unusually shaped, and of a sharply contrasting colour or texture is likely to 'jump out' of the display so that we notice it very easily. Other items in the display may receive correspondingly less attention as

520-663: A result. Well-designed static educational graphics take advantage of these perceptual effects. They manipulate the characteristics of the display in order to direct learner attention to the most relevant information. This helps to ensure that the learner will extract the required information from the display. There is a problem in the design of the animation shown above in this respect. Unfortunately, there are many 'educational' graphics being produced that fail to provide learners with sufficient support of this type. Designers of animation need to take such consideration into account. The correspondence problems due to perceptual characteristics of

572-402: A simulation while it is running in response to a visualization of its current progress. This is called computational steering . More frequently, the representation of the information is changed rather than the information itself. Experiments have shown that a delay of more than 20 ms between when input is provided and a visual representation is updated is noticeable by most people . Thus it

SECTION 10

#1732854680143

624-505: A static graphic but by having it accompany textual explication. Another suggestion for addressing such problems is to provide user control for the learner over how the animation plays. User controllable animations allow learners to vary aspects such as the playing speed and direction, labels and audio commentary to suit themselves. Complexity of the subject matter may not be the only reason for difficulties that learners sometimes have with animations. It seems that problems can also arise from

676-541: A thousand years. Examples from cartography include Ptolemy's Geographia (2nd century AD), a map of China (1137 AD), and Minard 's map (1861) of Napoleon 's invasion of Russia a century and a half ago. Most of the concepts learned in devising these images carry over in a straightforward manner to computer visualization. Edward Tufte has written three critically acclaimed books that explain many of these principles. Computer graphics has from its beginning been used to study scientific problems. However, in its early days

728-522: A visualization application is the field of computer graphics . The invention of computer graphics (and 3D computer graphics ) may be the most important development in visualization since the invention of central perspective in the Renaissance period. The development of animation also helped advance visualization. The use of visualization to present information is not a new phenomenon. It has been used in maps, scientific drawings, and data plots for over

780-453: A visualization to be considered interactive it must satisfy two criteria: One particular type of interactive visualization is virtual reality (VR), where the visual representation of information is presented using an immersive display device such as a stereo projector (see stereoscopy ). VR is also characterized by the use of a spatial metaphor, where some aspect of the information is represented in three dimensions so that humans can explore

832-407: Is a key part of product lifecycle management . Product visualization software typically provides high levels of photorealism so that a product can be viewed before it is actually manufactured. This supports functions ranging from design and styling to sales and marketing. Technical visualization is an important aspect of product development. Originally technical drawings were made by hand, but with

884-628: Is any technique for creating images , diagrams , or animations to communicate a message. Visualization through visual imagery has been an effective way to communicate both abstract and concrete ideas since the dawn of humanity. from history include cave paintings , Egyptian hieroglyphs , Greek geometry , and Leonardo da Vinci 's revolutionary methods of technical drawing for engineering purposes that actively involve scientific requirements. Visualization today has ever-expanding applications in science, education, engineering (e.g., product visualization), interactive multimedia , medicine , etc. Typical of

936-471: Is because their attention is also directed to a considerable extent by their knowledge of which aspects of the subject matter are of most relevance (irrespective of their perceptibility). As a result, their processing of information in the display has a more top-down character. In the pumping system animation example, the air valve would be noticed by those who are already familiar with pumps in general because their existing background knowledge would put them on

988-427: Is desirable for an interactive visualization to provide a rendering based on human input within this time frame. However, when large amounts of data must be processed to create a visualization, this becomes hard or even impossible with current technology. Thus the term "interactive visualization" is usually applied to systems that provide feedback to users within several seconds of input. The term interactive framerate

1040-590: Is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco . Development is partially supported by the National Institutes of Health (NIGMS grant P41-GM103311). The next-generation program is UCSF ChimeraX. Interactive visualization Visualization (or visualisation (see spelling differences )), also known as Graphics Visualization,

1092-620: Is facilitated as animation create positive attitude among the learners, leading to positive learning outcomes. Animations may lack educational effectiveness if target learners can't process the presented information adequately. For example, it seems that when the subject matter is complex, learners may be overwhelmed by animated presentations. This is related to the role of visual perception and cognition in human information processing . Our human perceptual and cognitive systems have limited capacities for processing information. If these limits are exceeded, learning may be compromised. For example,

SECTION 20

#1732854680143

1144-467: Is often used to measure how interactive a visualization is. Framerates measure the frequency with which an image (a frame) can be generated by a visualization system. A framerate of 50 frames per second (frame/s) is considered good while 0.1 frame/s would be considered poor. The use of framerates to characterize interactivity is slightly misleading however, since framerate is a measure of bandwidth while humans are more sensitive to latency . Specifically, it

1196-693: Is possible to achieve a good framerate of 50 frame/s but if the images generated refer to changes to the visualization that a person made more than 1 second ago, it will not feel interactive to a person. The rapid response time required for interactive visualization is a difficult constraint to meet and there are several approaches that have been explored to provide people with rapid visual feedback based on their input. Some include Many conferences occur where interactive visualization academic papers are presented and published. Educational animation The popularity of using animations to help learners understand and remember information has greatly increased since

1248-437: Is the use of interactive, sensory representations, typically visual, of abstract data to reinforce cognition , hypothesis building, and reasoning . Scientific visualization is the transformation, selection, or representation of data from simulations or experiments, with an implicit or explicit geometric structure, to allow the exploration, analysis, and understanding of the data. Scientific visualization focuses and emphasizes

1300-404: Is used when people are physically separated. Using several networked computers, the same visualization can be presented to each person simultaneously. The people then make annotations to the visualization as well as communicate via audio (i.e., telephone), video (i.e., a video-conference), or text (i.e., IRC ) messages. The Programmer's Hierarchical Interactive Graphics System ( PHIGS ) was one of

1352-418: The unique information being represented or the way that the information is presented. When the information being presented is altered, the visualization is usually part of a feedback loop . For example, consider an aircraft avionics system where the pilot inputs roll, pitch, and yaw and the visualization system provides a rendering of the aircraft's new attitude. Another example would be a scientist who changes

1404-409: The advent of powerful graphics-oriented computers. This technology allows animations to be produced much more easily and cheaply than in former years. Previously, traditional animation required specialised labour-intensive techniques that were both time-consuming and expensive. In contrast, software is now available that makes it possible for individual educators to author their own animations without

1456-458: The animated display that are most conspicuous because of their contrast with the rest of the display are not always the best place for learners to direct their attention. In other words, there can be a poor correspondence between the perceptual salience ('noticeability') of a feature and its thematic relevance , and an accompanying text is needed to correct this. This correspondence problem can occur with both static and animated graphics. On

1508-412: The changes involved is available to be read straight from the display without the learner needing to perform mental animation. It's a bit of an exaggeration, but it's more like being kissed instead of reading about a kiss. Research evidence about the educational effectiveness of animations is mixed. Various investigations have compared the educational effectiveness of static and animated displays across

1560-499: The digital animations produced to present meteorological data during weather reports on television , though few can distinguish between those models of reality and the satellite photos that are also shown on such programs. TV also offers scientific visualizations when it shows computer drawn and animated reconstructions of road or airplane accidents. Some of the most popular examples of scientific visualizations are computer-generated images that show real spacecraft in action, out in

1612-444: The display and their surroundings, the effect can be very compelling in a perceptual sense. It seems that a fundamental level, our perceptual system is attuned to detect and follow such changes, irrespective of their importance in terms of the subject matter. As with static displays discussed above, items that are perceptually compelling (in this case because of their dynamic character) may not necessarily be of great thematic relevance to

UCSF Chimera - Misplaced Pages Continue

1664-549: The electric current is invisible. The operation of electric circuits is difficult for students to understand at the beginning. With the aid of computer animations, learning and teaching might become easier, faster and amusing. According to V.M. Williamson and M.R. Abraham, animation helps students learn in two ways. It facilitates the creation of mental representations of concepts, phenomenon, and processes and it also replaces difficult cognitive processes (e.g. abstraction, imagination). There are also studies that revealed that learning

1716-434: The first programmatic efforts at interactive visualization and provided an enumeration of the types of input humans provide. People can: All of these actions require a physical device. Input devices range from the common – keyboards , mice , graphics tablets , trackballs , and touchpads – to the esoteric – wired gloves , boom arms , and even omnidirectional treadmills . These input actions can be used to control both

1768-463: The given learning task. The big orange float in the accompanying animation is far more perceptible than the small grey air valve because of both its visuospatial characteristics, and its high level of dynamic contrast with the rest of the display. The misleading effects of the dynamic contrast are likely to be particularly problematic for learners who lack background knowledge in the content domain depicted in an animation. These learners can be largely in

1820-508: The information as if it were present (where instead it was remote), sized appropriately (where instead it was on a much smaller or larger scale than humans can sense directly), or had shape (where instead it might be completely abstract). Another type of interactive visualization is collaborative visualization, in which multiple people interact with the same computer visualization to communicate their ideas to each other or to explore information cooperatively. Frequently, collaborative visualization

1872-592: The lack of graphics power often limited its usefulness. The recent emphasis on visualization started in 1987 with the publication of Visualization in Scientific Computing, a special issue of Computer Graphics. Since then, there have been several conferences and workshops, co-sponsored by the IEEE Computer Society and ACM SIGGRAPH , devoted to the general topic, and special areas in the field, for example volume visualization. Most people are familiar with

1924-519: The mere transfer of facts , knowledge visualization aims to further transfer insights , experiences , attitudes , values , expectations , perspectives , opinions , and predictions by using various complementary visualizations. See also: picture dictionary , visual dictionary Product visualization involves visualization software technology for the viewing and manipulation of 3D models, technical drawing and other related documentation of manufactured components and large assemblies of products. It

1976-685: The more common. Data visualization is a related subcategory of visualization dealing with statistical graphics and geospatial data (as in thematic cartography ) that is abstracted in schematic form. Information visualization concentrates on the use of computer-supported tools to explore large amount of abstract data. The term "information visualization" was originally coined by the User Interface Research Group at Xerox PARC and included Jock Mackinlay . Practical application of information visualization in computer programs involves selecting, transforming , and representing abstract data in

2028-538: The need for specialist expertise. Teachers are no longer limited to relying on static graphics but can readily convert them into educational animations. Educators are enthusiastically taking up the opportunities that computer animation offers for depicting dynamic content . For example, PowerPoint now has an easy-to-use animation facility that, in the right hands , can produce very effective educational animations. Because animations can explicitly depict changes over time ( temporal changes), they seem ideally suited to

2080-441: The need for these added markings so that displays can be not only simpler and less cluttered, but also more vivid, engaging, and more intuitively comprehended. In addition, the learner does not have to interpret the auxiliary markings and try to infer the changes that they summarise. Such interpretation and inference may demand a level of graphicacy skills that the learner does not possess. With animated depictions, information about

2132-405: The pace at which the animation presents its information may exceed the speed at which the learner can process it effectively. The accompanying animation (part of a pumping system) is problematic for this reason. But the solution is obvious: slow the animation down and accompany it with a written explanation. It is unlikely that superior learning is achieved by thoughtlessly substituting animation for

UCSF Chimera - Misplaced Pages Continue

2184-402: The particular characteristics of individual animations and how they are used to play a key role in the effects that they have on learning. Well-designed animations may help students learn faster and easier. They are also excellent aid to teachers when it comes to explaining difficult subjects. The difficulty of subjects may arise due to the involvement of mathematics or imagination. For instance,

2236-434: The perceptual effects of such presentations. In a poorly designed animation, the information that learners notice most readily in the animation may not be the information that is of greatest importance. Conversely, information that is relatively inconspicuous may be very important. Obviously, perceptibility of information does not necessarily correspond with its actual relevance to the learning task to be performed. Features of

2288-526: The production of 3D content, as large-scale 3D content production can be extremely costly and time-consuming. Visual communication is the communication of ideas through the visual display of information . Primarily associated with two dimensional images , it includes: alphanumerics , art , signs , and electronic resources. Recent research in the field has focused on web design and graphically oriented usability . Visual analytics focuses on human interaction with visualization systems as part of

2340-539: The representation of higher order data using primarily graphics and animation techniques. It is a very important part of visualization and maybe the first one, as the visualization of experiments and phenomena is as old as science itself. Traditional areas of scientific visualization are flow visualization , medical visualization , astrophysical visualization , and chemical visualization . There are several different techniques to visualize scientific data, with isosurface reconstruction and direct volume rendering being

2392-403: The rise of advanced computer graphics the drawing board has been replaced by computer-aided design (CAD). CAD-drawings and models have several advantages over hand-made drawings such as the possibility of 3-D modeling, rapid prototyping , and simulation . 3D product visualization promises more interactive experiences for online shoppers, but also challenges retailers to overcome hurdles in

2444-499: The source code is common. There are also many proprietary software packages of scientific visualization tools. Models and frameworks for building visualizations include the data flow models popularized by systems such as AVS, IRIS Explorer, and VTK toolkit, and data state models in spreadsheet systems such as the Spreadsheet for Visualization and Spreadsheet for Images. As a subject in computer science , scientific visualization

2496-502: The teaching of processes and procedures. When used to present dynamic content, animations can mirror both the changes in position ( translation ), and the changes in form ( transformation ) that are fundamental to learning this type of subject matter. In contrast with static pictures, animations can show temporal change directly (rather than having to indicate it indirectly using auxiliary markings such as arrows and motion lines ). Using animations instead of static graphics removes

2548-525: The thrall of the animation's raw perceptual effects and so tend to process the presented information in a bottom-up manner. For example, their attention within the display is likely to be directed to items that have conspicuous dynamic characteristics. As a result, there is a danger that they will attend to unimportant information merely because it is perceptually compelling. However, learners who already have considerable domain specific background knowledge are likely to be less influenced by perception alone. This

2600-401: The transfer of knowledge by using computer and non-computer-based visualization methods complementarily. Thus properly designed visualization is an important part of not only data analysis but knowledge transfer process, too. Knowledge transfer may be significantly improved using hybrid designs as it enhances information density but may decrease clarity as well. For example, visualization of

2652-506: The unexpected in complex information spaces. Technologies resulting from visual analytics find their application in almost all fields, but are being driven by critical needs (and funding) in biology and national security. Interactive visualization or interactive visualisation is a branch of graphic visualization in computer science that involves studying how humans interact with computers to create graphic illustrations of information and how this process can be made more efficient. For

SECTION 50

#1732854680143

2704-636: The void far beyond Earth, or on other planets . Dynamic forms of visualization, such as educational animation or timelines , have the potential to enhance learning about systems that change over time. Apart from the distinction between interactive visualizations and animation, the most useful categorization is probably between abstract and model-based scientific visualizations. The abstract visualizations show completely conceptual constructs in 2D or 3D. These generated shapes are completely arbitrary. The model-based visualizations either place overlays of data on real or digitally constructed images of reality or make

#142857