Federico Ulliana

MyCorporisFabrica: making anatomy easy

Characters with precise internal anatomy are important in film and visual effects, as well as in medical applications. However, setting up detailed anatomical models has been a difficult task, especially for simulation. We demonstrate MyCorporisFabrica [MyCF], the first assistant tool for modeling and simulating anatomical structures such as bones, muscles, viscera and fat tissues. Using a novel ontology-centered knowledge base, it helps selecting anatomical entities based on their type or their contribution to physiological functions. The resulting 3D model can be automatically transfered to an arbitrary humanoid character in a similar pose, only defined by its skin. This allows to quickly generate anatomical models for a large range of target characters, while maintaining anatomical consistency. Finally, the knowledge base also contains mechanical data used to set up a choice of mechanical models of the selected entities, which we export to a simulator. This dramatically eases biomechanical modeling and makes it possible for non-expert users to enter that field. We demonstrate this technology and detail a practical example.

SOCLE : Vers un cadre de préparation des données dans les applications sociales

The web has evolved from a technological platform to a real social milieu thereby be- coming a continuous source of Big Social Data (BSD). BSD is characterized by a combination of factual content such as the coordinates of a restaurant, the content of a webpage or the title of a movie, behavior data such as exchanges between social relationships, as well as subjective data such as users opinions, reviews, and tags. The goal of a social application is to analyze BSD and process it in order to understand it and transform it into valuable content to users. Building social applications requires an essential data preparation step during which raw BSD is sanitized, normalized, enriched, pruned, and transformed making it readily available for fur- ther processing. We argue for the need to formalize data preparation and develop appropriate tools to enable easy prototyping of social applications. We describe SOCLE, our framework for BSD preparation. We provide an architecture inspired from typical social applications, the state of the art of existing languages and algebras for manipulating BSD, and the scientific challenges and opportunities underlying the development of SOCLE. RESUME.Le web, initialement une plateforme technologique, est devenu un veritable eco-systeme socialetunesourcecontinuedeBigDatasociales(BSD).Nousytrouvonsdesdonneesfactuelles et objectives telles que les coordonnees dun restaurant, des donnees comportementales telles que les echanges entre amis et enfin, des donnees subjectives comme les revues, les etiquettes, les notes ou les etoiles. Ces donnees brutes ont besoin detre filtrees et organisees pour en extraire des informations utiles et permettre le developpement dapplications sociales qui ap- portent une valeur ajoutee aux utilisateurs. Dans cet article, nous motivons le besoin de for- maliser letape de preparation des BSD et decrivons SOCLE, notre plateforme pour le faire. Nous presentons une architecture inspiree dapplications sociales types, un etat de lart des langages et algebres existants et les defis scientifiques du developpement de SOCLE.

An Automated Design Framework for Multicellular Recombinase Logic

Tools to systematically reprogram cellular behavior are crucial to address pressing challenges in manufacturing, environment, or healthcare. Recombinases can very efficiently encode Boolean and history-dependent logic in many species, yet current designs are performed on a case-by-case basis, limiting their scalability and requiring time-consuming optimization. Here we present an automated workflow for designing recombinase logic devices executing Boolean functions. Our theoretical framework uses a reduced library of computational devices distributed into different cellular subpopulations, which are then composed in various manners to implement all desired logic functions at the multicellular level. Our design platform called CALIN (Composable Asynchronous Logic using Integrase Networks) is broadly accessible via a web server, taking truth tables as inputs and providing corresponding DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin). We anticipate that this automated design workflow will streamline the implementation of Boolean functions in many organisms and for various applications.

Ontology-Mediated Query Answering for Key-Value Stores

We propose a novel rule-based ontology language for JSON records and investigate its computational properties. After providing a natural translation into first-order logic, we identify relationships to existing ontology languages , which yield decidability of query answering but only rough complexity bounds. By establishing an interesting and non-trivial connection to word rewriting, we are able to pinpoint the exact combined complexity of query answering in our framework and obtain tractability results for data complexity. The upper bounds are proven using a query reformu-lation technique, which can be implemented on top of key-value stores, thereby exploiting their querying facilities.

Datalog Revisited for Reasoning in Linked Data

Linked Data provides access to huge, continuously growing amounts of open data and ontologies in RDF format that describe entities, links and properties on those entities. Equipping Linked Data with inference paves the way to make the Semantic Web a reality. In this survey, we describe a unifying framework for RDF ontologies and databases that we call deductive RDF triplestores. It consists in equipping RDF triplestores with Datalog inference rules. This rule language allows to capture in a uniform manner OWL constraints that are useful in practice, such as property transitivity or symmetry, but also domain-specific rules with practical relevance for users in many domains of interest. The expressivity and the genericity of this framework is illustrated for modeling Linked Data applications and for developing inference algorithms. In particular, we show how it allows to model the problem of data linkage in Linked Data as a reasoning problem on possibly decentralized data. We also explain how it makes possible to efficiently extract expressive modules from Semantic Web ontologies and databases with formal guarantees, whilst effectively controlling their succinctness. Experiments conducted on real-world datasets have demonstrated the feasibility of this approach and its usefulness in practice for data integration and information extraction.

Andromeda: A System for Processing Queries and Updates on Big XML Documents

In this paper we present Andromeda, a system for processing queries and updates on large XML documents. The system is based on the idea of statically and dynamically partitioning the input document, so to distribute the computing load among the machines of a Map/Reduce cluster.

On the k-Boundedness for Existential Rules.

The chase is a fundamental tool for existential rules. Several chase variants are known, which differ on how they handle redundancies possibly caused by the introduction of nulls. Given a chase variant, the halting problem takes as input a set of existential rules and asks if this set of rules ensures the termination of the chase for any factbase. It is well-known that this problem is undecidable for all known chase variants. The related problem of boundedness asks if a given set of existential rules is bounded, i.e., whether there is an upper bound on the depth of the chase, independently from any factbase. This problem is already undecidable in the specific case of datalog rules. However, knowing that a set of rules is bounded for some chase variant does not help much in practice if the bound is unknown. Hence, in this paper, we investigate the decidability of the k-boundedness problem, which asks whether a given set of rules is bounded by an integer k. After introducing a general framework which motivates a breadth-first approach to problems related to chase termination for any chase variant, we prove that k-boundedness is decidable for three chase variants.

From CAD assemblies toward knowledge-based assemblies using an intrinsic knowledge-based assembly model

ABSTRACTCAD assemblies are essentially reduced to a set of components, often solids, and a user-defined tree structure. Given the generation process of CAD assembly models where the user may instan...

Scalable composition frameworks for multicellular logic

A major goal of synthetic biology is to reprogram living organisms to solve pressing challenges in manufacturing, environmental remediation, or healthcare. While many types of genetic logic gates have been engineered, their scalability remains limited. Previous work demonstrated that Distributed Multicellular Computation (DMC) enables the implementation of complex logic within cellular consortia. However, current DMC systems require spatial separation of cellular subpopulation to be scalable to N-inputs, and need cell-cell communication channels to operate. Here we present scalable composition frameworks for the systematic design of multicellular consortia performing recombinase-based Boolean or history-dependent logic, and integrating an arbitrary number of inputs. The theoretical designs for both Boolean and history-dependent logic are based on reduced sets of computational modules implemented into specific cellular subpopulations which can then be combined in various manners to implement all logic functions. Our systems mark a departure from previous DMC architectures as they do not require either cell-cell communication nor spatial separation, greatly facilitating their implementation and making them fully autonomous. Due to their scalability and composability, we anticipate that the design strategies presented here will help researchers and engineers to reprogram cellular behavior for various applications in a streamlined manner. We provide an online tool for automated design of DNA architectures allowing the implementation of multicellular N-inputs logic functions at: http://synbio.cbs.cnrs.fr/calin.