AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license

Heterogeneity shapes groups growth in social online communities

Many complex systems are characterized by broad distributions capturing, for example, the size of firms, the population of cities or the degree distribution of complex networks. Typically this feature is explained by means of a preferential growth mechanism. Although heterogeneity is expected to play a role in the evolution it is usually not considered in the modeling probably due to a lack of empirical evidence on how it is distributed. We characterize the intrinsic heterogeneity of groups in an online community and then show that together with a simple linear growth and an inhomogeneous birth rate it explains the broad distribution of group members.Comment: 5 pages, 3 figure panel

The World-Trade Web: Topological Properties, Dynamics, and Evolution

This paper studies the statistical properties of the web of import-export relationships among world countries using a weighted-network approach. We analyze how the distributions of the most important network statistics measuring connectivity, assortativity, clustering and centrality have co-evolved over time. We show that all node-statistic distributions and their correlation structure have remained surprisingly stable in the last 20 years -- and are likely to do so in the future. Conversely, the distribution of (positive) link weights is slowly moving from a log-normal density towards a power law. We also characterize the autoregressive properties of network-statistics dynamics. We find that network-statistics growth rates are well-proxied by fat-tailed densities like the Laplace or the asymmetric exponential-power. Finally, we find that all our results are reasonably robust to a few alternative, economically-meaningful, weighting schemes.Comment: 44 pages, 39 eps figure

Diffusion, peer pressure and tailed distributions

We present a general, physically motivated non-linear and non-local advection equation in which the diffusion of interacting random walkers competes with a local drift arising from a kind of peer pressure. We show, using a mapping to an integrable dynamical system, that on varying a parameter, the steady state behaviour undergoes a transition from the standard diffusive behavior to a localized stationary state characterized by a tailed distribution. Finally, we show that recent empirical laws on economic growth can be explained as a collective phenomenon due to peer pressure interaction.Comment: RevTex: 4 pages + 3 eps-figures. Minor Revision and figure 3 replaced. To appear in Phys. Rev. Letter

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license

Cystamine/cysteamine rescues the dopaminergic system and shows neurorestorative properties in an animal model of Parkinson's disease.

The neuroprotective properties of cystamine identified in pre-clinical studies have fast-tracked this compound to clinical trials in Huntington's disease, showing tolerability and benefits on motor symptoms. We tested whether cystamine could have such properties in a Parkinson's disease murine model and now provide evidence that it can not only prevent the neurodegenerative process but also can reverse motor impairments created by a 6-hydroxydopamine lesion 3weeks post-surgery. Importantly, we report that cystamine has neurorestorative properties 5weeks post-lesion as seen on the number of nigral dopaminergic neurons which is comparable with treatments of cysteamine, the reduced form of cystamine used in the clinic, as well as rasagiline, increasingly prescribed in early parkinsonism. All three compounds induced neurite arborization of the remaining dopaminergic cells which was further confirmed in ex vivo dopaminergic explants derived from Pitx3-GFP mice. The disease-modifying effects displayed by cystamine/cysteamine would encourage clinical testing

Competition and fragmentation: a simple model generating lognormal-like distributions

The current distribution of language size in terms of speaker population is generally described using a lognormal distribution. Analyzing the original real data we show how the double-Pareto lognormal distribution can give an alternative fit that indicates the existence of a power law tail. A simple Monte Carlo model is constructed based on the processes of competition and fragmentation. The results reproduce the power law tails of the real distribution well and give better results for a poorly connected topology of interactions.Comment: 14 pages, 11 figure

Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors

<p>Abstract</p> <p>Background</p> <p>Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices.</p> <p>Results</p> <p>We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices.</p> <p>Conclusions</p> <p>This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.</p

Modelling Hierarchy and Specialization of a System of Cities from an Evolutionary Perspective on Firms' Interactions

Despite their great diversity, most systems of cities show remarkably similar patterns when comparing the size distribution and the economic specialization of their constitutive cities. The universality of these patterns sparked the interest of geographers, economists and physicists. However, until now, no economic model has relied on a micro-based and evolutionary approach to reproduce these regularities. In this chapter, we intend to fill this gap by proposing a model where the micro dynamics of localized firms generate the two macro regularities of size distribution and economic specialization. The model is based on boundedly rational firms’ competition and path dependent innovation. We discuss the possible emergence of macro properties from these micro behaviors of firms