8 research outputs found

    The ribosome builder: A software project to simulate the ribosome

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    CELLmicrocosmos - Integrative cell modeling at the  molecular, mesoscopic and functional level

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    Sommer B. CELLmicrocosmos - Integrative cell modeling at the  molecular, mesoscopic and functional level. Bielefeld: Bielefeld University; 2012.The modeling of cells is an important application area of Systems Biology. In the context of this work, three cytological levels are defined: the mesoscopic, the molecular and the functional level. A number of related approaches which are quite diverse will be introduced during this work which can be categorized into these disciplines. But none of these approaches covers all areas. In this work, the combination of all three aforementioned cytological levels is presented, realized by the CELLmicrocosmos project, combining and extending different Bioinformatics-related methods. The mesoscopic level is covered by CellEditor which is a simple tool to generate eukaryotic or prokaryotic cell models. These are based on cell components represented by three-dimensional shapes. Different methods to generate these shapes are discussed by using partly external tools such as Amira, 3ds Max and/or Blender; abstract, interpretative, 3D-microscopy-based and molecular-structure-based cell component modeling. To communicate with these tools, CellEditor provides import as well as export capabilities based on the VRML97 format. In addition, different cytological coloring methods are discussed which can be applied to the cell models. MembraneEditor operates at the molecular level. This tool solves heterogeneous Membrane Packing Problems by distributing lipids on rectangular areas using collision detection. It provides fast and intuitive methods supporting a wide range of different application areas based on the PDB format. Moreover, a plugin interface enables the use of custom algorithms. In the context of this work, a high-density-generating lipid packing algorithm is evaluated; The Wanderer. The semi-automatic integration of proteins into the membrane is enabled by using data from the OPM and PDBTM database. Contrasting with the aforementioned structural levels, the third level covers the functional aspects of the cell. Here, protein-related networks or data sets can be imported and mapped into the previously generated cell models using the PathwayIntegration. For this purpose, data integration methods are applied, represented by the data warehouse DAWIS-M.D. which includes a number of established databases. This information is enriched by the text-mining data acquired from the ANDCell database. The localization of proteins is supported by different tools like the interactive Localization Table and the Localization Charts. The correlation of partly multi-layered cell components with protein-related networks is covered by the Network Mapping Problem. A special implementation of the ISOM layout is used for this purpose. Finally, a first approach to combine all these interrelated levels is represented; CellExplorer which integrates CellEditor as well as PathwayIntegration and imports structures generated with MembraneEditor. For this purpose, the shape-based cell components can be correlated with networks as well as molecular membrane structures using Membrane Mapping. It is shown that the tools discussed here can be applied to scientific as well as educational tasks: educational cell visualization, initial membrane modeling for molecular simulations, analysis of interrelated protein sets, cytological disease mapping. These are supported by the user-friendly combination of Java, Java 3D and Web Start technology. In the last part of this thesis the future of Integrative Cell Modeling is discussed. While the approaches discussed here represent basically three-dimensional snapshots of the cell, prospective approaches have to be extended into the fourth dimension; time

    Intuitive visualization of surface properties of biomolecules

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    In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as Electrostatic Potential (EP) and hydropathy expressed as Molecular Lipophilic Potential (MLP). The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by phisicochemical programs and visualized as range of colours that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of colour to encode both characteristics makes the simultaneous visualization almost impossible. This is why most of the times EP and MLP are presented in two different images. In this thesis, we describe a novel and intuitive code for the simultaneous visualization of these properties. For our purpose we use Blender, an open-source, free, cross-platform 3D application used for modelling, animation, gaming and rendering. On the basis of Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins motion with the simultaneous visualization of their chemical and physical features. Blender's Game Engine, equipped with specific physico-chemical rules is used to elaborate the motion of proteins, interpolating between different conformations (NMR collections or different X-rays of the same protein). We obtain a physically plausible sequence of intermediate conformations which are the basis for the subsequent visual elaboration. A new visual code is introduced for MLP visualization: a range of optical features that goes from dull-rough surfaces for the most hydrophilic areas to shiny-smooth surfaces for the most lipophilic ones. This kind of representation permits a photorealistic rendering of the smooth spatial distribution of the values of MLP on the surface of the protein. EP is represented as animated line particles that flow along field lines, from positive to negative, proportional to the total charge of the protein. Our system permits EP and MLP simultaneous visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Moreover, this representation contributes to gain insight into the molecules function by drawing viewer's attention to the most active regions of the protein

    Interactive web-based visualization

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    The visualization of large amounts of data, which cannot be easily copied for processing on a user’s local machine, is not yet a fully solved problem. Remote visualization represents one possible solution approach to the problem, and has long been an important research topic. Depending on the device used, modern hardware, such as high-performance GPUs, is sometimes not available. This is another reason for the use of remote visualization. Additionally, due to the growing global networking and collaboration among research groups, collaborative remote visualization solutions are becoming more important. The additional use of collaborative visualization solutions is eventually due to the growing global networking and collaboration among research groups. The attractiveness of web-based remote visualization is greatly increased by the wide availability of web browsers on almost all devices; these are available today on all systems - from desktop computers to smartphones. In order to ensure interactivity, network bandwidth and latency are the biggest challenges that web-based visualization algorithms have to solve. Despite the steady improvements in available bandwidth, these improvements are still significantly slower than, for example, processor performance, resulting in increasing the impact of this bottleneck. For example, visualization of large dynamic data in low-bandwidth environments can be challenging because it requires continuous data transfer. However, bandwidth improvement alone cannot improve the latency because it is also affected by factors such as the distance between server and client and network utilization. To overcome these challenges, a combination of techniques is needed to customize the individual processing steps of the visualization pipeline, from efficient data representation to hardware-accelerated rendering on the client side. This thesis first deals with related work in the field of remote visualization with a particular focus on interactive web-based visualization and then presents techniques for interactive visualization in the browser using modern web standards such as WebGL and HTML5. These techniques enable the visualization of dynamic molecular data sets with more than one million atoms at interactive frame rates using GPU-based ray casting. Due to the limitations which exist in a browser-based environment, the concrete implementation of the GPU-based ray casting had to be customized. Evaluation of the resulting performance shows that GPU-based techniques enable the interactive rendering of large data sets and achieve higher image quality compared to polygon-based techniques. In order to reduce data transfer times and network latency, and improve rendering speed, efficient approaches for data representation and transmission are used. Furthermore, this thesis introduces a GPU-based volume-ray marching technique based on WebGL 2.0, which uses progressive brick-wise data transfer, as well as multiple levels of detail in order to achieve interactive volume rendering of datasets stored on a server. The concepts and results presented in this thesis contribute to the further spread of interactive web-based visualization. The algorithmic and technological advances that have been achieved form a basis for further development of interactive browser-based visualization applications. At the same time, this approach has the potential for enabling future collaborative visualization in the cloud.Die Visualisierung großer Datenmengen, welche nicht ohne Weiteres zur Verarbeitung auf den lokalen Rechner des Anwenders kopiert werden können, ist ein bisher nicht zufriedenstellend gelöstes Problem. Remote-Visualisierung stellt einen möglichen Lösungsansatz dar und ist deshalb seit langem ein relevantes Forschungsthema. Abhängig vom verwendeten Endgerät ist moderne Hardware, wie etwa performante GPUs, teilweise nicht verfügbar. Dies ist ein weiterer Grund für den Einsatz von Remote-Visualisierung. Durch die zunehmende globale Vernetzung und Kollaboration von Forschungsgruppen gewinnt kollaborative Remote-Visualisierung zusätzlich an Bedeutung. Die Attraktivität web-basierter Remote-Visualisierung wird durch die weitreichende Verfügbarkeit von Web-Browsern auf nahezu allen Endgeräten enorm gesteigert; diese sind heutzutage auf allen Systemen - vom Desktop-Computer bis zum Smartphone - vorhanden. Bei der Gewährleistung der Interaktivität sind Bandbreite und Latenz der Netzwerkverbindung die größten Herausforderungen, welche von web-basierten Visualisierungs-Algorithmen gelöst werden müssen. Trotz der stetigen Verbesserungen hinsichtlich der verfügbaren Bandbreite steigt diese signifikant langsamer als beispielsweise die Prozessorleistung, wodurch sich die Auswirkung dieses Flaschenhalses immer weiter verstärkt. So kann beispielsweise die Visualisierung großer dynamischer Daten in Umgebungen mit geringer Bandbreite eine Herausforderung darstellen, da kontinuierlicher Datentransfer benötigt wird. Dennoch kann die alleinige Verbesserung der Bandbreite keine entsprechende Verbesserung der Latenz bewirken, da diese zudem von Faktoren wie der Distanz zwischen Server und Client sowie der Netzwerkauslastung beeinflusst wird. Um diese Herausforderungen zu bewältigen, wird eine Kombination verschiedener Techniken für die Anpassung der einzelnen Verarbeitungsschritte der Visualisierungspipeline benötigt, angefangen bei effizienter Datenrepräsentation bis hin zu hardware-beschleunigtem Rendering auf der Client-Seite. Diese Doktorarbeit befasst sich zunächst mit verwandten Arbeiten auf dem Gebiet der Remote-Visualisierung mit besonderem Fokus auf interaktiver web-basierter Visualisierung und präsentiert danach Techniken für die interaktive Visualisierung im Browser mit Hilfe moderner Web-Standards wie WebGL und HTML5. Diese Techniken ermöglichen die Visualisierung dynamischer molekularer Datensätze mit mehr als einer Million Atomen bei interaktiven Frameraten durch die Verwendung GPU-basierten Raycastings. Aufgrund der Einschränkungen, welche in einer Browser-basierten Umgebung vorliegen, musste die konkrete Implementierung des GPU-basierten Raycastings angepasst werden. Die Evaluation der daraus resultierenden Performanz zeigt, dass GPU-basierte Techniken das interaktive Rendering von großen Datensätzen ermöglichen und eine im Vergleich zu Polygon-basierten Techniken höhere Bildqualität erreichen. Zur Verringerung der Übertragungszeiten, Reduktion der Latenz und Verbesserung der Darstellungsgeschwindigkeit werden effiziente Ansätze zur Datenrepräsentation und übertragung verwendet. Des Weiteren wird in dieser Doktorarbeit eine GPU-basierte Volumen-Ray-Marching-Technik auf Basis von WebGL 2.0 eingeführt, welche progressive blockweise Datenübertragung verwendet, sowie verschiedene Detailgrade, um ein interaktives Volumenrendering von auf dem Server gespeicherten Datensätzen zu erreichen. Die in dieser Doktorarbeit präsentierten Konzepte und Resultate tragen zur weiteren Verbreitung von interaktiver web-basierter Visualisierung bei. Die erzielten algorithmischen und technologischen Fortschritte bilden eine Grundlage für weiterführende Entwicklungen von interaktiven Visualisierungsanwendungen auf Browser-Basis. Gleichzeitig hat dieser Ansatz das Potential, zukünftig kollaborative Visualisierung in der Cloud zu ermöglichen

    Telepresence and Transgenic Art

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    ImMApp: An immersive database of sound art

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    The ImMApp (Immersive Mapping Application) thesis addresses contemporary and historical sound art from a position informed by, on one hand, post-structural critical theory, and on the other, a practice-based exploration of contemporary digital technologies (MySQL, XML, XSLT, X3D). It proposes a critical ontological schema derived from Michel Foucault's Archaeology of Knowledge (1972) and applies this to pre-existing information resources dealing with sound art. Firstly an analysis of print-based discourses (Sound by Artists. Lander and Lexier (1990), Noise, Water, Meat. Kahn (2001) and Background Noise: Perspectives on Sound Art. LaBelle (2006» is carried out according to Foucauldian notions of genealogy, subject positions, the statement, institutional affordances and the productive nature of discursive formation. The discursive field (the archive) presented by these major canonical texts is then contrasted with a formulation derived from Giles Deleuze and Felix Guattari: that of a 'minor' history of sound art practices. This is then extended by media theory (McLuhan, Kittler, Manovich) into a critique of two digital sound art resources (The Australian Sound Design Project (Bandt and Paine (2005) and soundtoys.net Stanza (1998). The divergences between the two forms of information technologies (print vs. digital) are discussed. The means by which such digitised methodologies may enhance Foucauldian discourse analysis points onwards towards the two practice-based elements of the thesis. Surface, the first iterative part, is a web-browser based database built on an Apache/MySQIlXML architecture. It is the most extensive mapping of sound art undertaken to date and extends the theoretical framework discussed above into the digital domain. Immersion, the second part, is a re-presentation of this material in an immersive digital environment, following the transformation of the source material via XSL-T into X3D. Immersion is a real-time, large format video, surround sound (5.ln.l) installation and the thesis concludes with a discussion of how this outcome has articulated Foucauldian archaeological method and unframed pre-existing notions of the nature of sound art

    Seventh Biennial Report : June 2003 - March 2005

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