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This article belongs to the Section Evolutionary Biology., Defining the essential gene components for a system to be considered alive is a crucial step toward the synthesis of artificial life. Fifteen years ago, Gil and coworkers proposed the core of a putative minimal bacterial genome, which would provide the capability to achieve metabolic homeostasis, reproduce, and evolve to a bacterium in an ideally controlled environment. They also proposed a simplified metabolic chart capable of providing energy and basic components for a minimal living cell. For this work, we have identified the components of the minimal metabolic network based on the aforementioned studies, associated them to the KEGG database and, by applying the MetaDAG methodology, determined its Metabolic Building Blocks (MBB) and reconstructed its metabolic Directed Acyclic Graph (m-DAG). The reaction graph of this metabolic network consists of 80 compounds and 98 reactions, while its m-DAG has 36 MBBs. Additionally, we identified 12 essential reactions in the m-DAG that are critical for maintaining the connectivity of this network. In a similar manner, we reconstructed the m-DAG of JCVI-syn3.0, which is an artificially designed and manufactured viable cell whose genome arose by minimizing the one from Mycoplasma mycoides JCVI-syn1.0, and of “Candidatus Nasuia deltocephalinicola”, the bacteria with the smallest natural genome known to date. The comparison of the m-DAGs derived from a theoretical, an artificial, and a natural genome denote slightly different lifestyles, with a consistent core metabolism. The MetaDAG methodology we employ uses homogeneous descriptors and identifiers from the KEGG database, so that comparisons between bacterial strains are not only easy but also suitable for many research fields. The modeling of m-DAGs based on minimal metabolisms can be the first step for the synthesis and manipulation of minimal cells., This research was funded by the Spanish Ministry of Science, Innovation and Universities (MICINN/AEI, projects DPI2015-67082-P and PGC2018-096956-B-C43) the Spanish Ministry of Economy and Competitiveness (projects SAF2015-65878-R and PGC2018-099344-B-I00), Generalitat Valenciana (project Prometeo/2018/A133), and co-financed by the European Regional Development Fund (ERDF). M.R.-P. is a recipient of a grant from the National Board of Science and Technology of México (CONACYT) [grant number 538243].

The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% increase in manually curated content in the database, i.e. bacterial genomes and their associations, with a final count of 2328 bacterial genomes associated to 498 hosts. We describe new querying possibilities for all the modules, as well as new display features for the MetaDAGs module, providing a relevant range of content and utility. This update continues to improve SymGenDB and can help elucidate the mechanisms by which organisms depend on each other., National Board of Science and Technology of México (CONACYT) (538243 to M.R.P.); FPI fellowship from the Ministry of Economy and Competitiveness (BES-2013-063548 to C.V.C.); Spanish Ministry of Science, Innovation and Universities and the European Regional Development Fund through projects DPI2015-67082-P and PGC2018-096956-B-C43 (FEDER/MICINN/AEI) and the Spanish Ministry of Economy and Competitiveness (projects SAF2012-31187, SAF2013-49788-EXP, SAF2015-65878-R and BFU2015-64322-C2-1-R, co-financed by FEDER funds); Carlos III Institute of Health (projects PIE14/00045 and AC15/00022); Generalitat Valenciana (project Prometeo/2018/A/133); Asociación Española contra el Cáncer (project AECC 2017-1485) and co-financed by the European Regional Development Fund (ERDF).

[This corrects the article DOI: 10.1371/journal.pone.0177031.].

In this paper two improvements for the Hypervideo platform, used to represent augmented reality on Interactive TVs thanks to the hypervideo concept, are presented: the introduction of a second-screen application to the platform, enabling the user to obtain the additional information on its handheld device and delivering the video track through the broadcast channel, thanks to the HbbTV capability.

In this paper, an Augmented Reality system for the Interactive and Connected TV is presented through the implementation of a Hypervideo platform. This platform consists of two modules that enable editors and viewers to enjoy an AR experience on current generation Interactive TVs.

In this paper, an Augmented Reality system for the Connected TV is presented through a Hypervideo platform implementation. The Hypervideo platform consists of a backoffice to manage audiovisual content and hot-spots, and an interactive video player based in HbbTV technology. The player lets the user get additional information of the points of interest which are displayed over the images. This project presents a useful platform to audiovisual production teams, letting them mix, in an easy way, these three technological concepts: interactive video, augmented reality and connected television. This paper concludes with some improvement possibilities and extension to other devices.

In order to have a good representation of deformable objects, is clever to have an adequate model to represent them. Since the origins of computer graphics, a large number of representation models have been presented. Not all of them are adequate to represent deformable objects. The way in which the objects can be handled, allowing local changes in their shape, or the possibility of the creation of objects matching with data gathered from one or more datasources, are some of the desirable characteristics in those models. This chapter represents a study of the way in which the deformable objects can be represented. It is possible to classify them into some categories allowing to select the most adequate depending on the use given to the model.

Recently an integrated multiplatform system aiming at offering travel service over several communication channels is under development. A set of cooperating systems in completely different platforms will work together to provide integrated services to the clients anywhere and anytime. The structure, communication environment, some special issues and implementation of the system are discussed in the paper.

There is a lot of development currently being carried out on cooperative visualization via communication networks. User interaction is kept to minimum in this kind of development, such as only making marks on the transmitted images, etc. There is relatively less work being done on complicated cooperative interactions, especially real-time cooperative interaction via networks. The work presented in this paper is a challenge to this type of cooperative work. The objective of the system is to allow multiple users to design a 3D scene cooperatively via communication networks in real time. The paper describes the design and communication model of the system, the design and implementation of the protocol to transmit changes in the 3D scene, the database consistency techniques and the implementation of the 3D editor interface. The current implementation status of the system shows that a real-time, full user interaction in 3D cooperative design via communication networks is achievable by our design strategy.

The paper describes a cooperative design system for a 3D virtual scene. The objective of the system is to allow multiple users to design a 3D scene cooperatively via a communication network. The system is based on a distributed layered architecture. At the application layer, a 3D cooperative design tool is implemented. The basic cooperative design operations include reading and saving a 3D scene, selecting an object from the common 3D scene, modification of the objects by geometrical transformations, modification of the attributes of the global scene or an individual object, such as, object texture, material, illumination parameters, etc. A special protocol (SMI) has been designed and implemented for the communication with the peer cooperative design tool situated on peer hosts. The session control layer and group communication layer form the cooperative support platform for the system. The session control layer is responsible for the tasks required by a cooperative working session such as service multiplexing, data consistency control, member admission etc. The group communication layer provides the point to point or point to multipoint communication. The experimental system is currently implemented on Silicon Graphics hardware platform with a 100 MB/s internal network. Open Inventor has been used for the 3D design tool. The data format is fully VRML compatible.

In this paper we propose a generalized SCODEF deformation method in order to deform NURBS surface. The deformation method propose a wide class of deformation functions applied to a set of select-user constraints and a wide range of influence zones, expanding the used one for the original SCODEF method. Also, we propose the use of several norms and distances in order to define and compute the deformation function and the constraint influence zone, ensuring a wide range of deformed shapes.

A system that integrates 3D virtual scene generation tools and data communication techniques for 3D cooperative design work is presented. The system, named CODI (Sistema Cooperativo de Diseno3D) supports two major functions: 3D cooperative design and multiple client distant access. The system is implemented using Open Inventor Toolkit in C++ with VRML compatibility.