A framework for building distributed social network websites

Las redes son la esencia de comunidades y sociedades humanas; constituyen el entramado en el que nos relacionamos y determinan cómo lo hacemos, cómo se disemina la información o incluso cómo las cosas se llevan a cabo. Pero el protagonismo de las redes va más allá del que adquiere en las redes sociales. Se encuentran en el seno de múltiples estructuras que conocemos, desde las interaciones entre las proteínas dentro de una célula hasta la interconexión de los routers de internet. Las redes sociales están presentes en internet desde sus principios, en el correo electrónico por tomar un ejemplo. Dentro de cada cliente de correo se manejan listas contactos que agregadas constituyen una red social. Sin embargo, ha sido con la aparición de los sitios web de redes sociales cuando este tipo de aplicaciones web han llegado a la conciencia general. Las redes sociales se han situado entre los sitios más populares y con más tráfico de la web. Páginas como Facebook o Twitter manejan cifras asombrosas en cuanto a número de usuarios activos, de tráfico o de tiempo invertido en el sitio. Pero las funcionalidades de red social no están restringidas a las redes sociales orientadas a contactos, aquellas enfocadas a construir tu lista de contactos e interactuar con ellos. Existen otros ejemplos de sitios que aprovechan las redes sociales para aumentar la actividad de los usuarios y su involucración alrededor de algún tipo de contenido. Estos ejemplos van desde una de las redes sociales más antiguas, Flickr, orientada al intercambio de fotografías, hasta Github, la red social de código libre más popular hoy en día. No es una casualidad que la popularidad de estos sitios web venga de la mano de sus funcionalidades de red social. El escenario es más rico aún, ya que los sitios de redes sociales interaccionan entre ellos, compartiendo y exportando listas de contactos, servicios de autenticación y proporcionando un valioso canal para publicitar la actividad de los usuarios en otros sitios web. Esta funcionalidad es reciente y aún les queda un paso hasta que las redes sociales superen su condición de bunkers y lleguen a un estado de verdadera interoperabilidad entre ellas, tal como funcionan hoy en día el correo electrónico o la mensajería instantánea. Este trabajo muestra una tecnología que permite construir sitios web con características de red social distribuída. En primer lugar, se presenta una tecnología para la construcción de un componente intermedio que permite proporcionar cualquier característica de gestión de contenidos al popular marco de desarrollo web modelo-vista-controlador (MVC) Ruby on Rails. Esta técnica constituye una herramienta para desarrolladores que les permita abstraerse de las complejidades de la gestión de contenidos y enfocarse en las particularidades de los propios contenidos. Esta técnica se usará también para proporcionar las características de red social. Se describe una nueva métrica de reusabilidad de código para demostrar la validez del componente intermedio en marcos MVC. En segundo lugar, se analizan las características de los sitios web de redes sociales más populares, con el objetivo de encontrar los patrones comunes que aparecen en ellos. Este análisis servirá como base para definir los requisitos que debe cumplir un marco para construir redes sociales. A continuación se propone una arquitectura de referencia que proporcione este tipo de características. Dicha arquitectura ha sido implementada en un componente, Social Stream, y probada en varias redes sociales, tanto orientadas a contactos como a contenido, en el contexto de una asociación vecinal tanto como en proyectos de investigación financiados por la UE. Ha sido la base de varios proyectos fin de carrera. Además, ha sido publicado como código libre, obteniendo una comunidad creciente y está siendo usado más allá del ámbito de este trabajo. Dicha arquitectura ha permitido la definición de un nuevo modelo de control de acceso social que supera varias limitaciones presentes en los modelos de control de acceso para redes sociales. Más aún, se han analizado casos de estudio de sitios de red social distribuídos, reuniendo un conjunto de caraterísticas que debe cumplir un marco para construir redes sociales distribuídas. Por último, se ha extendido la arquitectura del marco para dar cabida a las características de redes sociales distribuídas. Su implementación ha sido validada en proyectos de investigación financiados por la UE. Abstract Networks are the substance of human communities and societies; they constitute the structural framework on which we relate to each other and determine the way we do it, the way information is diseminated or even the way people get things done. But network prominence goes beyond the importance it acquires in social networks. Networks are found within numerous known structures, from protein interactions inside a cell to router connections on the internet. Social networks are present on the internet since its beginnings, in emails for example. Inside every email client, there are contact lists that added together constitute a social network. However, it has been with the emergence of social network sites (SNS) when these kinds of web applications have reached general awareness. SNS are now among the most popular sites in the web and with the higher traffic. Sites such as Facebook and Twitter hold astonishing figures of active users, traffic and time invested into the sites. Nevertheless, SNS functionalities are not restricted to contact-oriented social networks, those that are focused on building your own list of contacts and interacting with them. There are other examples of sites that leverage social networking to foster user activity and engagement around other types of content. Examples go from early SNS such as Flickr, the photography related networking site, to Github, the most popular social network repository nowadays. It is not an accident that the popularity of these websites comes hand-in-hand with their social network capabilities The scenario is even richer, due to the fact that SNS interact with each other, sharing and exporting contact lists and authentication as well as providing a valuable channel to publize user activity in other sites. These interactions are very recent and they are still finding their way to the point where SNS overcome their condition of data silos to a stage of full interoperability between sites, in the same way email and instant messaging networks work today. This work introduces a technology that allows to rapidly build any kind of distributed social network website. It first introduces a new technique to create middleware that can provide any kind of content management feature to a popular model-view-controller (MVC) web development framework, Ruby on Rails. It provides developers with tools that allow them to abstract from the complexities related with content management and focus on the development of specific content. This same technique is also used to provide the framework with social network features. Additionally, it describes a new metric of code reuse to assert the validity of the kind of middleware that is emerging in MVC frameworks. Secondly, the characteristics of top popular SNS are analysed in order to find the common patterns shown in them. This analysis is the ground for defining the requirements of a framework for building social network websites. Next, a reference architecture for supporting the features found in the analysis is proposed. This architecture has been implemented in a software component, called Social Stream, and tested in several social networks, both contact- and content-oriented, in local neighbourhood associations and EU-founded research projects. It has also been the ground for several Master’s theses. It has been released as a free and open source software that has obtained a growing community and that is now being used beyond the scope of this work. The social architecture has enabled the definition of a new social-based access control model that overcomes some of the limitations currenly present in access control models for social networks. Furthermore, paradigms and case studies in distributed SNS have been analysed, gathering a set of features for distributed social networking. Finally the architecture of the framework has been extended to support distributed SNS capabilities. Its implementation has also been validated in EU-founded research projects.

Transcription factors of the bzip factors of the BZIP family affecting arabidopsis thaliana germination sensu stricto

During seed germination, the endosperm cell walls (CWs) suffer an important weakening process mainly driven by hydrolytic enzymes, such are endo-?- mannanases (MAN; EC. 3.2.1.78) that catalyze the cleavage of ?1?4 bonds in the mannan-polymers. In Arabidopsis thaliana seeds, endo-?-mannanase activity increases during seed imbibition, decreasing after radicle emergence1. AtMAN7 is the most highly expressed MAN gene in seeds upon germination and their transcripts are restricted to the micropylar endosperm and to the radicle tip just before radicle emergence. Mutants with a T-DNA insertion in this gene (K.O. MAN7) have a slower germination rate than the wild type (t50=34 h versus t50=25 h). To gain insight into the transcriptional regulation of the AtMAN7 gene, a bioinformatic search for conserved non-coding cis-elements (phylogenetic shadowing) within the Brassicaceae orthologous MAN7 gene promoters has been done and these conserved motives have been used as baits to look for their interacting transcription factors (TFs), using as a prey an arrayed yeast library of circa 1,200 TFs from A. thaliana. The basic leucine zipper AtbZIP44, but not its closely related ortholog AtbZIP11, has been thus identified and its regulatory function upon AtMAN7 during seed germination validated by different molecular and physiological techniques, such are RT-qPCR analyses, mRNA Fluorescence in situ Hybridization (FISH) experiments, and by the establishment of the germination kinetics of both over-expression (oex) lines and TDNA insertion mutants in AtbZIP44. The transcriptional combinatorial network through which AtbZIP44 regulates AtMAN7 gene expression during seed germination has been further explored through protein-protein interactions between AtbZIP44 and other bZIP members. In such a way, AtbZIP9 has been identified by yeast two-hybrid experiments and its physiological implication in the control of AtMAN7 expression similarly established.

Unveiling Protein Functions through the Dynamics of the Interaction Network

Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes

Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.

Modeling iron-catecholates binding to NGAL protein

Neutrophil gelatinase associated lipocalin (NGAL) protein is attracting a great interest because of its antibacterial properties played upon modulating iron content in competition against iron acquisition processes developed by pathogenic bacteria that bind selective ferric iron chelators (siderophores). Besides its known high affinity to enterobactin, the most important siderophore, it has been recently shown that NGAL is able to bind Fe(III) coordinated by catechols. The selective binding of Fe(III)-catechol ligands to NGAL is here studied by using iron coordination structures with one, two, and three catecholate ligands. By means of a computational approach that consists of B3LYP/6-311G(d,p) quantum calculations for geometries, electron properties and electrostatic potentials of ligands, protein–ligand flexible docking calculations, analyses of protein–ligand interfaces, and Poisson–Boltzmann electrostatic potentials for proteins, we study the binding of iron catecholate ligands to NGAL as a central member of the lipocalin family of proteins. This approach provides a modeling basis for exploring in silico the selective binding of iron catecholates ligands giving a detailed picture of their interactions in terms of electrostatic effects and a network of hydrogen bonds in the protein binding pocket.