CRS4 Articolo

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A conceptual framework for multi-modal interactive virtual workspaces
(2001-11) Aspin, Rob; Da Dalto, Laurent; Fernando, Terrence; Gobbetti, Enrico; Marache, Mathieu; Shelbourn, Mark; Soubra, Souheil
Construction projects involve a large number of both direct stakeholders (clients, professional teams, contractors, etc.) and indirect stakeholders (local authorities, residents, workers, etc.). Current methods of communicating building design information can lead to several types of difficulties (e.g. incomplete understanding of the planned construction, functional inefficiencies, inaccurate initial work or clashes between components, etc.). Integrated software solutions based on VR technologies can bring significant value improvement and cost reduction to the Construction Industry. The aim of this paper is to present research being carried out in the frame of the DIVERCITY project (Distributed Virtual Workspace for Enhancing Communication within the Construction Industry - IST project n°13365), funded under the European IST programme (Information Society Technologies). DIVERCITY's goal is to develop a Virtual Workspace that addresses three key building construction phases: (1) Client briefing (with detailed interaction between clients and architects); (2) Design Review (which requires detailed input from multidisciplinary teams - architects, engineers, facility managers, etc.); (3) Construction (aiming to fabricate or refurbish the building).Using a distributed architecture, the DIVERCITY system aims to support and enhance concurrent engineering practices for these three phases allowing teams based in different geographic locations to collaboratively design, test and validate shared virtual projects. The global DIVERCITY project will be presented in terms of objectives and the software architecture will be detailed.
A generalizable definition of chemical similarity for read-across
(BioMed Central, 2014-10-18) Floris, Matteo; Manganaro, Alberto; Nicolotti, Orazio; Medda, Ricardo; Mangiatordi, Giuseppe Felice; Benfenati, Emilio
Background: Methods that provide a measure of chemical similarity are strongly relevant in several fields of chemoinformatics as they allow to predict the molecular behavior and fate of structurally close compounds. One common application of chemical similarity measurements, based on the principle that similar molecules have similar properties, is the read-across approach, where an estimation of a specific endpoint for a chemical is provided using experimental data available from highly similar compounds. Results: This paper reports the comparison of multiple combinations of binary fingerprints and similarity metrics for computing the chemical similarity in the context of two different applications of the read-across technique. Conclusions: Our analysis demonstrates that the classical similarity measurements can be improved with a generalizable model of similarity. The proposed approach has already been used to build similarity indices in two open-source software tools (CAESAR and VEGA) that make several QSAR models available. In these tools, the similarity index plays a key role for the assessment of the applicability domain.
A GPU framework for parallel segmentation of volumetric images using discrete deformable models
(Springer, 2011-02) Schmid, Jerome; Iglesias Guitián, José Antonio; Gobbetti, Enrico; Magnenat-Thalmann, Nadia
Despite the ability of current GPU processors to treat heavy parallel computation tasks, its use for solving medical image segmentation problems is still not fully exploited and remains challenging. A lot of difficulties may arise related to, for example, the different image modalities, noise and artifacts of source images, or the shape and appearance variability of the structures to segment. Motivated by practical problems of image segmentation in the medical field, we present in this paper a GPU framework based on explicit discrete deformable models, implemented over the NVidia CUDA architecture, aimed for the segmentation of volumetric images. The framework supports the segmentation in parallel of different volumetric structures as well as interaction during the segmentation process and real-time visualization of the intermediate results. Promising results in terms of accuracy and speed on a real segmentation experiment have demonstrated the usability of the system.
A multiprocessor decoupled system for the simulation of temporal bone surgery
(Springer, 2002-07) Agus, Marco; Giachetti, Andrea; Gobbetti, Enrico; Zanetti, Gianluigi; Zorcolo, Antonio
A training system for simulating temporal bone surgery is presented. The system is based on patient-specific volumetric object models derived from 3D CT and MR imaging data. Real-time feedback is provided to the trainees via real-time volume rendering and haptic feedback. The performance constraints dictated by the human perceptual system are met by exploiting parallelism via a decoupled simulation approach on a multi-processor PC platform. In this paper, system components are detailed and the current state of the integrated system is presented.
Adaptive tetrapuzzles: efficient out-of-core construction and visualization of gigantic multiresolution polygonal models
(ACM, 2004-08) Cignoni, Paolo; Ganovelli, Fabio; Gobbetti, Enrico; Marton, Fabio; Ponchio, Federico; Scopigno, Roberto
We describe an efficient technique for out-of-core construction and accurate view-dependent visualization of very large surface models. The method uses a regular conformal hierarchy of tetrahedra to spatially partition the model. Each tetrahedral cell contains a precomputed simplified version of the original model, represented using cache coherent indexed strips for fast rendering. The representation is constructed during a fine-to-coarse simplification of the surface contained in diamonds (sets of tetrahedral cells sharing their longest edge). The construction preprocess operates out-of-core and parallelizes nicely. Appropriate boundary constraints are introduced in the simplification to ensure that all conforming selective subdivisions of the tetrahedron hierarchy lead to correctly matching surface patches. For each frame at runtime, the hierarchy is traversed coarse-to-fine to select diamonds of the appropriate resolution given the view parameters. The resulting system can interatively render high quality views of out-of-core models of hundreds of millions of triangles at over 40Hz (or 70M triangles/s) on current commodity graphics platforms.
An energy preserving upscaling technique for enhanced volume rendering of medical data
(2010) Giachetti, Andrea; Iglesias Guitián, José Antonio; Gobbetti, Enrico
In this paper we describe an edge-directed optimization-based method for volumetric data supersampling. Our method faces the problem of partial volume effect by upscaling the volumetric data, subdividing voxels in smaller parts and performing an optimization step keeping constant the energy of each original subdivided voxel while enhancing edge continuity. Experimental tests show the good quality of the results obtained with our approach. Furthermore, we show how offline 3D upscaling of volumes can be coupled with recent techniques to perform high quality volume rendering of large datsets, obtaining a better inspection of medical volumetric data.
An interactive 3D medical visualization system based on a light field display
(Springer-Verlag, 2009-09-01) Agus, Marco; Bettio, Fabio; Giachetti, Andrea; Gobbetti, Enrico; Iglesias Guitián, José Antonio; Marton, Fabio; Nilsson, Jonas; Pintore, Giovanni; CRS4
We present a prototype medical data visualization system exploiting a light field display and custom direct volume rendering techniques to enhance understanding of massive volumetric data, such as CT, MRI, and PET scans. The system can be integrated with standard medical image archives and extends the capabilities of current radiology workstations by supporting real-time rendering of volumes of potentially unlimited size on light field displays generating dynamic observer-independent light fields. The system allows multiple untracked naked-eye users in a sufficiently large interaction area to coherently perceive rendered volumes as real objects, with stereo and motion parallax cues. In this way, an effective collaborative analysis of volumetric data can be achieved. Evaluation tests demonstrate the usefulness of the generated depth cues and the improved performance in understanding complex spatial structures with respect to standard techniques.
An interactive 3D medical visualization system based on a light ﬁeld display
(Springer, 2009-09) Agus, Marco; Bettio, Fabio; Giachetti, Andrea; Gobbetti, Enrico; Iglesias Guitián, José Antonio; Marton, Fabio; Nilsson, Jonas; Pintore, Giovanni
This paper presents a prototype medical data visualization system exploiting a light field display and custom direct volume rendering techniques to enhance understanding of massive volumetric data, such as CT, MRI, and PET scans. The system can be integrated with standard medical image archives and extends the capabilities of current radiology workstations by supporting real-time rendering of volumes of potentially unlimited size on light field displays generating dynamic observer-independent light fields. The system allows multiple untracked naked-eye users in a sufficiently large interaction area to coherently perceive rendered volumes as real objects, with stereo and motion parallax cues. In this way, an effective collaborative analysis of volumetric data can be achieved. Evaluation tests demonstrate the usefulness of the generated depth cues and the improved performance in understanding complex spatial structures with respect to standard techniques.
Animating Spaceland
(IEEE, 1996-08-29) Balaguer, Jean-Francis; Gobbetti, Enrico
Modern 3D animation systems let a growing number of people generate increasingly sophisticated animated movies, frequently for tutorials or multimedia documents. However, although these tasks are inherently three dimensional, these systems' user interfaces are still predominantly two dimensional. This makes it difficult to interactively input complex animated 3D movements. We have developed Virtual Studio, an inexpensive and easy-to-use 3D animation environment in which animators can perform all interaction directly in three dimensions. Animators can use 3D devices to specify complex 3D motions. Virtual tools are visible mediators that provide interaction metaphors to control application objects. An underlying constraint solver lets animators tightly couple application and interface objects. Users define animation by recording the effect of their manipulations on models. Virtual Studio applies data-reduction techniques to generate editable representations of each animated element that is manipulated.
Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism
(BioMed Central, 2008-07-11) Mentzen, Wieslawa I; Peng, Jianling; Ransom, Nick; Nikolau, Basil J.; Wurtele, Eve Syrkin
Elucidating metabolic network structures and functions in multicellular organisms is an emerging goal of functional genomics. We describe the co-expression network of three core metabolic processes in the genetic model plant Arabidopsis thaliana: fatty acid biosynthesis, starch metabolism and amino acid (leucine) catabolism. These co-expression networks form modules populated by genes coding for enzymes that represent the reactions generally considered to define each pathway. However, the modules also incorporate a wider set of genes that encode transporters, cofactor biosynthetic enzymes, precursor-producing enzymes, and regulatory molecules. We tested experimentally the hypothesis that one of the genes tightly co-expressed with starch metabolism module, a putative kinase AtPERK10, will have a role in this process. Indeed, knockout lines of AtPERK10 have an altered starch accumulation. In addition, the co-expression data define a novel hierarchical transcript-level structure associated with catabolism, in which genes performing smaller, more specific tasks appear to be recruited into higher-order modules with a broader catabolic function. Each of these core metabolic pathways is structured as a module of co-expressed transcripts that co-accumulate over a wide range of environmental and genetic perturbations and developmental stages, and represent an expanded set of macromolecules associated with the common task of supporting the functionality of each metabolic pathway. As experimentally demonstrated, co-expression analysis can provide a rich approach towards understanding gene function.
Assessment of fission fragments enhancement for nuclear thermal propulsion
(American Institute of Aeronautics and Astronautics, 2006-06) Di Piazza, Ivan; Mulas, Marco
A novel concept of Nuclear Thermal Rocket (NTR) propulsion is presented. It is based onthe direct conversion of the kinetic energy of the Fission Fragments (FFs) into the propellantenthalpy. The FFs can escape from an extremely thin layer of ﬁssionable material: a sufﬁciently large surface coated with few micrometers of Americium 242m, conﬁned by a neutron diffuser, may become a critical reactor. The novel FF NTR propulsion concept may allow the propellant to achieve temperatures higher than the nuclear fuel, thus overcoming the limit in the speciﬁc enthalpy achievable by the propellant in the conventional solid-core NTR propulsion. Such a limit comes from the need to keep the temperature of the fuel material within a safe interval by using conventional convective heat transfer mechanism. A preliminary assessment of the FF NTR concept’s propulsion characteristics has been carried out using an in-house developed software system which integrates a Computational Fluid Dynamic code, a neutronic code and a Monte Carlo code. The assessment shows the potential to reach speciﬁc impulses of about 15,000 m/s and thrust levels in the range 4,000 to 6,000 N, with a trhust to weight ratio of a few percent of the acceleration of gravity. Such performances may make the FF propulsion a candidate for human missions to the planet Mars.
Automated and traceable processing for large-scale high-throughput sequencing facilities
(2013) Pireddu, Luca; Cuccuru, Gianmauro; Lianas, Luca; Vocale, Matteo; Fotia, Giorgio; Zanetti, Gianluigi
Scaling up production in medium and large high-throughput sequencing facilities presents a number of challenges. As the rate of samples to process increases, manually performing and tracking the center’s operations becomes increasingly difficult, costly and error prone, while processing the massive amounts of data poses significant computational challenges. We present our ongoing work to automate and track all data-related procedures at the CRS4 Sequencing and Genotyping Platform, while integrating state-of-the-art processing technologies such as Hadoop, OMERO, iRODS, and Galaxy into our automated workflows. Currently, the core system is in its testing phase and it is on schedule to be in production use at CRS4 by May 2013. The results thus far obtained are encouraging and the authors are confident that the CRS4 Platform will increase its efficiency and capacity thanks to this system. In the near future, the integration components will be released as as open source software.
BlaSTorage: a fast package to parse, manage and store BLAST results
(BioMed Central, 2013-01-30) Orsini, Massimiliano; Carcangiu, Simone
Background: Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them. Findings: We implemented BlaSTorage, a Python package that parses multi BLAST results and returns them in a purpose-built object-database format. Unlike other BLAST parsers, BlaSTorage retains and stores all parts of BLAST results, including alignments, without loss of information; a complete API allows access to all the data components. Conclusions: BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.
Calcolo del bilancio idrico della regione Sardegna con il modello idrologico SWAT
(Associazione Idrotecnica Italiana, 2005-09) Cau, Pierluigi; Cadeddu, Alessandro; Lecca, Giuditta; Gallo, Claudio; Marrocu, Marino
Una diminuzione del 20% delle precipitazioni nell’ultimo trentennio e perdite del 40% nella rete di distribuzione hanno causato un sensibile abbassamento dei livelli idrici medi nei laghi e negli invasi artificiali della Sardegna, con la conseguenza che negli ultimi anni le municipalità, il comparto agricolo e quello industriale hanno subito le impopolari misure di razionamento. Fino ad oggi, gli enti regionali preposti alla gestione delle acque si sono serviti di modelli a scatola chiusa di tipo black box. Tuttavia da un lato appare incerta l’applicabilità di tali modelli in aree prive di misure e dall’altro tale approccio si dimostra carente nel tenere in conto le trasformazione di uso del territorio e le variazioni climatiche. Questo studio presenta l’applicazione del modello idrologico distribuito e fisicamente basato SWAT per la stima del bilancio idrologico della regione Sardegna. La procedura di caratterizzazione del tipo e della copertura del suolo ha seguito un approccio regionale, utilizzando e valorizzando al massimo le frammentarie informazioni disponibili. Per compensare la mancanza di dati di pioggia a passo giornaliero, necessari al modello idrologico, è stato sviluppato un generatore di tempo basato sull’analisi statistica di dati climatici registrati. In base alla distribuzione spaziale delle grandezze statistiche, le stazioni pluviometriche sono state raggruppate in due gruppi. Lo studio ha prodotto una serie di archivi informatici a scala regionale, creati secondo i formati di input del modello SWAT. L’applicazione del modello ai bacini idrologici della Sardegna ha tenuto conto della qualità dell’informazione descrittiva del territorio come, ad esempio, la risoluzione spaziale delle carte di base, la densità delle reti climatiche e la qualità del dato di pioggia, al fine di garantire la massima verosimiglianza del modello concettuale con le singole realtà in studio. Il sistema informatico è stato progettato ed implementato per supportare studi ed analisi mirati alla pianificazione della gestione della risorsa idrica regionale, all’individuazione di aree soggette a stress idrico e allo studio di fenomeni legati al ciclo dell’acqua, quali il ciclo dei sedimenti e dei nutrienti.
CRS Seismic Data Imaging: A Case Study for Basin Reevaluation
(Sociedade Brasileira de Geofısica, 2007-09) Leite, Lourenildo Williame Barbosa; Heilmann, Bjorn Zeno; Gomes, Anderson Batista
This paper summarizes practical results of a consistent attention to the seismic processing and interpretation of some land data lines from a set of the Tacutu graben (Brazil), where was applied the fundamental steps of the WIT imaging system grounded on the data-driven CRS (Common Reflection Surface) stack.As a major result, we expect to establish a work-flow for seismic reevaluation of sedimentary basins. Founded on the recovered wave front attributes of the CRS stack, a smooth macro-velocity model was obtained via tomographic inversion. Using this macro-model, pre- and post-stack depth migration was carried out. Besides that, other CRS-stack based processing techniques were performed in parallel as residual static correction and limited-aperture migration based on estimated projected Fresnel zone. A geological interpretation was attempted on the stacked and migrated sections. From visual details of the panels, we could interpret discontinuities, thinning, a principal faulted anticline where plays of horsts, grabens and rollovers are present. Also, part of the selected line needs more detailed processing to make better evident any present structures in the subsurface.
Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor
(BioMed Central, 2009-12-13) Mentzen, Wieslawa I; Floris, Matteo; de la Fuente, Alberto
Background: Elucidating the sequence of molecular events underlying breast cancer formation is of enormous value for understanding this disease and for design of an effective treatment. Gene expression measurements have enabled the study of transcriptome-wide changes involved in tumorigenesis. This usually occurs through identification of differentially expressed genes or pathways. Results: We propose a novel approach that is able to delineate new cancer-related cellular processes and the nature of their involvement in tumorigenesis. First, we define modules as densely interconnected and functionally enriched areas of a Protein Interaction Network. Second, 'differential expression' and 'differential co-expression' analyses are applied to the genes in these network modules, allowing for identification of processes that are up- or down-regulated, as well as processes disrupted (low co-expression) or invoked (high co-expression) in different tumor stages. Finally, we propose a strategy to identify regulatory miRNAs potentially responsible for the observed changes in module activities. We demonstrate the potential of this analysis on expression data from a mouse model of mammary gland tumor, monitored over three stages of tumorigenesis. Network modules enriched in adhesion and metabolic processes were found to be inactivated in tumor cells through the combination of dysregulation and down-regulation, whereas the activation of the integrin complex and immune system response modules is achieved through increased co-regulation and up-regulation. Additionally, we confirmed a known miRNA involved in mammary gland tumorigenesis, and present several new candidates for this function. Conclusions: Understanding complex diseases requires studying them by integrative approaches that combine data sources and different analysis methods. The integration of methods and data sources proposed here yields a sensitive tool, able to pinpoint new processes with a role in cancer, dissect modulation of their activity and detect the varying assignments of genes to functional modules over the course of a disease.
Duplication of the dystroglycan gene in most branches of teleost fish
(BioMed Central, 2007-05-17) Pavoni, Ernesto; Cacchiarelli, Davide; Tittarelli, Roberta; Orsini, Massimiliano; Galtieri, Antonio; Giardina, Bruno; Brancaccio, Andrea
The dystroglycan (DG) complex is a major non-integrin cell adhesion system whose multiple biological roles involve, among others, skeletal muscle stability, embryonic development and synapse maturation. DG is composed of two subunits: alpha-DG, extracellular and highly glycosylated, and the transmembrane beta-DG, linking the cytoskeleton to the surrounding basement membrane in a wide variety of tissues. A single copy of the DG gene (DAG1) has been identified so far in humans and other mammals, encoding for a precursor protein which is post-translationally cleaved to liberate the two DG subunits. Similarly, D. rerio (zebrafish) seems to have a single copy of DAG1, whose removal was shown to cause a severe dystrophic phenotype in adult animals, although it is known that during evolution, due to a whole genome duplication (WGD) event, many teleost fish acquired multiple copies of several genes (paralogues). RESULTS: Data mining of pufferfish (T. nigroviridis and T. rubripes) and other teleost fish (O. latipes and G. aculeatus) available nucleotide sequences revealed the presence of two functional paralogous DG sequences. RT-PCR analysis proved that both the DG sequences are transcribed in T. nigroviridis. One of the two DG sequences harbours an additional mini-intronic sequence, 137 bp long, interrupting the uncomplicated exon-intron-exon pattern displayed by DAG1 in mammals and D. rerio. A similar scenario emerged also in D. labrax (sea bass), from whose genome we have cloned and sequenced a new DG sequence that also harbours a shorter additional intronic sequence of 116 bp. Western blot analysis confirmed the presence of DG protein products in all the species analysed including two teleost Antarctic species (T. bernacchii and C. hamatus). CONCLUSION: Our evolutionary analysis has shown that the whole-genome duplication event in the Class Actinopterygii (ray-finned fish) involved also DAG1. We unravelled new important molecular genetic details about fish orthologous DGs, which might help to increase the current knowledge on DG expression, maturation and targeting and on its physiopathological role in higher organisms.
Experiences with workflows for automating data-intensive bioinformatics
(BioMed Central, 2015-08-19) Spjuth, Ola; Bongcam-Rudlof, Erik; Carrasco Hernández, Guillermo; Forer, Lucas; Giovacchini, Mario; Valls Guimera, Roman; Kallio, Aleksi; Korpelainen, Eija; Kanduła, Maciej M; Krachunov, Milko; Kreil, David P.; Kulev, Ognyan; Łabaj, Pavel P.; Lampa, Samuel; Pireddu, Luca; Schönherr, Sebastian; Siretskiy, Alexey; Vassilev, Dimitar
High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.
Exploring virtual prototypes using time-critical rendering techniques
(ERCIM EEIG, 2001-01) Gobbetti, Enrico; Scateni, Riccardo
Scientists at CRS4, the Center for Advanced Studies, Research and Development in Cagliari, Sardinia, Italy, have developed a time-critical rendering algorithm that relies upon a scene description in which objects are represented as multiresolution meshes. In collaboration with other European partners, this technique has been applied to the visual and collaborative exploration of large digital mock-ups.
Far Voxels: A Multiresolution Framework for Interactive Rendering of Huge Complex 3D Models on Commodity Graphics Platforms
(ACM, 2005-08) Gobbetti, Enrico; Marton, Fabio
We present an efficient approach for end-to-end out-of-core construction and interactive inspection of very large arbitrary surface models. The method tightly integrates visibility culling and out-of-core data management with a level-of-detail framework. At preprocessing time, we generate a coarse volume hierarchy by binary space partitioning the input triangle soup. Leaf nodes partition the original data into chunks of a fixed maximum number of triangles, while inner nodes are discretized into a fixed number of cubical voxels. Each voxel contains a compact direction dependent approximation of the appearance of the associated volumetric subpart of the model when viewed from a distance. The approximation is constructed by a visibility aware algorithm that fits parametric shaders to samples obtained by casting rays against the full resolution dataset. At rendering time, the volumetric structure, maintained off-core, is refined and rendered in front-to-back order, exploiting vertex programs for GPU evaluation of view-dependent voxel representations, hardware occlusion queries for culling occluded subtrees, and asynchronous I/O for detecting and avoiding data access latencies. Since the granularity of the multiresolution structure is coarse, data management, traversal and occlusion culling cost is amortized over many graphics primitives. The efficiency and generality of the approach is demonstrated with the interactive rendering of extremely complex heterogeneous surface models on current commodity graphics platforms.

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