OpenAlea: A visual programming and component-based software platform for plant modeling

International audienceAs illustrated by the approaches presented during the 5th FSPM workshop (Prusinkiewicz and Hanan 2007, and this issue), the development of functional-structural plant models requires an increasing amount of computer modeling. All these models are developed by different teams in various contexts and with different goals. Efficient and flexible computational frameworks are required to augment the interaction between these models, their reusability, and the possibility to compare them on identical datasets. In this paper, we present an open-source platform, OpenAlea, that provides a user-friendly environment for modelers, and advanced deployment methods. OpenAlea allows researchers to build models using a visual programming interface and provides a set of tools and models dedicated to plant modeling. Models and algorithms are embedded in OpenAlea components with well defined input and output interfaces that can be easily interconnected to form more complex models and define more macroscopic components. The system architecture is based on the use of a general purpose, high-level, object-oriented script language, Python, widely used in other scientific areas. We briefly present the rationale that underlies the architectural design of this system and we illustrate the use of the platform to assemble several heterogeneous model components and to rapidly prototype a complex modeling scenario

Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

Image databases: Problems and perspectives

With the increasing number of computer graphics, image processing, and pattern recognition applications, economical storage, efficient representation and manipulation, and powerful and flexible query languages for retrieval of image data are of paramount importance. These and related issues pertinent to image data bases are examined

Modelling the Eddy Pattern in the harbour of Zeebrugge

Hydrodynamic

η\eta Carinae's Dusty Homunculus Nebula from Near-Infrared to Submillimeter Wavelengths: Mass, Composition, and Evidence for Fading Opacity

Infrared observations of the dusty, massive Homunculus Nebula around the luminous blue variable $\eta$ Carinae are crucial to characterize the mass-loss history and help constrain the mechanisms leading to the Great Eruption. We present the 2.4 - 670 $\mu$m spectral energy distribution, constructed from legacy ISO observations and new spectroscopy obtained with the {\em{Herschel Space Observatory}}. Using radiative transfer modeling, we find that the two best-fit dust models yield compositions which are consistent with CNO-processed material, with iron, pyroxene and other metal-rich silicates, corundum, and magnesium-iron sulfide in common. Spherical corundum grains are supported by the good match to a narrow 20.2 $\mu$m feature. Our preferred model contains nitrides AlN and Si$_3$N$_4$ in low abundances. Dust masses range from 0.25 to 0.44 $M_\odot$ but $M_{\rm{tot}} \ge$ 45 $M_\odot$ in both cases due to an expected high Fe gas-to-dust ratio. The bulk of dust is within a 5$"$ $\times$ 7$"$ central region. An additional compact feature is detected at 390 $\mu$m. We obtain $L_{\rm{IR}}$ = 2.96 $\times$ 10$^6$ $L_\odot$, a 25\% decline from an average of mid-IR photometric levels observed in 1971-1977. This indicates a reduction in circumstellar extinction in conjunction with an increase in visual brightness, allowing 25-40\% of optical and UV radiation to escape from the central source. We also present an analysis of $^{12}$CO and $^{13}$CO $J = 5-4$ through $9-8$ lines, showing that the abundances are consistent with expectations for CNO-processed material. The [$^{12}$C~{\sc{ii}}] line is detected in absorption, which we suspect originates in foreground material at very low excitation temperatures.Comment: Accepted in Ap

Visual Techniques for Geological Fieldwork Using Mobile Devices

Visual techniques in general and 3D visualisation in particular have seen considerable adoption within the last 30 years in the geosciences and geology. Techniques such as volume visualisation, for analysing subsurface processes, and photo-coloured LiDAR point-based rendering, to digitally explore rock exposures at the earth’s surface, were applied within geology as one of the first adopting branches of science. A large amount of digital, geological surface- and volume data is nowadays available to desktop-based workflows for geological applications such as hydrocarbon reservoir exploration, groundwater modelling, CO2 sequestration and, in the future, geothermal energy planning. On the other hand, the analysis and data collection during fieldwork has yet to embrace this ”digital revolution”: sedimentary logs, geological maps and stratigraphic sketches are still captured in each geologist’s individual fieldbook, and physical rocks samples are still transported to the lab for subsequent analysis. Is this still necessary, or are there extended digital means of data collection and exploration in the field ? Are modern digital interpretation techniques accurate and intuitive enough to relevantly support fieldwork in geology and other geoscience disciplines ? This dissertation aims to address these questions and, by doing so, close the technological gap between geological fieldwork and office workflows in geology. The emergence of mobile devices and their vast array of physical sensors, combined with touch-based user interfaces, high-resolution screens and digital cameras provide a possible digital platform that can be used by field geologists. Their ubiquitous availability increases the chances to adopt digital workflows in the field without additional, expensive equipment. The use of 3D data on mobile devices in the field is furthered by the availability of 3D digital outcrop models and the increasing ease of their acquisition. This dissertation assesses the prospects of adopting 3D visual techniques and mobile devices within field geology. The research of this dissertation uses previously acquired and processed digital outcrop models in the form of textured surfaces from optical remote sensing and photogrammetry. The scientific papers in this thesis present visual techniques and algorithms to map outcrop photographs in the field directly onto the surface models. Automatic mapping allows the projection of photo interpretations of stratigraphy and sedimentary facies on the 3D textured surface while providing the domain expert with simple-touse, intuitive tools for the photo interpretation itself. The developed visual approach, combining insight from all across the computer sciences dealing with visual information, merits into the mobile device Geological Registration and Interpretation Toolset (GRIT) app, which is assessed on an outcrop analogue study of the Saltwick Formation exposed at Whitby, North Yorkshire, UK. Although being applicable to a diversity of study scenarios within petroleum geology and the geosciences, the particular target application of the visual techniques is to easily provide field-based outcrop interpretations for subsequent construction of training images for multiple point statistics reservoir modelling, as envisaged within the VOM2MPS project. Despite the success and applicability of the visual approach, numerous drawbacks and probable future extensions are discussed in the thesis based on the conducted studies. Apart from elaborating on more obvious limitations originating from the use of mobile devices and their limited computing capabilities and sensor accuracies, a major contribution of this thesis is the careful analysis of conceptual drawbacks of established procedures in modelling, representing, constructing and disseminating the available surface geometry. A more mathematically-accurate geometric description of the underlying algebraic surfaces yields improvements and future applications unaddressed within the literature of geology and the computational geosciences to this date. Also, future extensions to the visual techniques proposed in this thesis allow for expanded analysis, 3D exploration and improved geological subsurface modelling in general.publishedVersio