GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

BACKGROUND: A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. RESULTS: GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. CONCLUSION: GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at [email protected]. A commercial licence form can be obtained for profit company at [email protected]. See also

An accurate and interpretable model for siRNA efficacy prediction

BACKGROUND: The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. Although considerable progress has been made recently in understanding how the RNAi pathway mediates gene silencing, the design of potent siRNAs remains challenging. RESULTS: We propose a simple linear model combining basic features of siRNA sequences for siRNA efficacy prediction. Trained and tested on a large dataset of siRNA sequences made recently available, it performs as well as more complex state-of-the-art models in terms of potency prediction accuracy, with the advantage of being directly interpretable. The analysis of this linear model allows us to detect and quantify the effect of nucleotide preferences at particular positions, including previously known and new observations. We also detect and quantify a strong propensity of potent siRNAs to contain short asymmetric motifs in their sequence, and show that, surprisingly, these motifs alone contain at least as much relevant information for potency prediction as the nucleotide preferences for particular positions. CONCLUSION: The model proposed for prediction of siRNA potency is as accurate as a state-of-the-art nonlinear model and is easily interpretable in terms of biological features. It is freely available on the web a

Contrôle de surveillance benthique de la Directive Cadre sur l'Eau (2000/60/CE) : Volume I : MacroInvertébrés benthiques de substrats meubles, Année 2016. District Seine-Normandie.

This report presents results of the monitoring actions in 2016 (on benthic invertebrates communities) in the water bodies of the Seine-Normandie water district.Ce rapport présente les résultats des opérations menées lors de l’année 2016 (contrôle de surveillance des invertébrés benthiques) sur l’ensemble des masses d’eau côtières et des sites d’appui rattachées au district Seine-Normandie

Contrôle de surveillance benthique de la Directive Cadre sur l'Eau (2000/60/CE) : Année 2016. District Artois-Picardie.

This report deals with results of monitoring carried out in 2016 for the area concerned by the Artois-Picardie water district.Ce rapport présente les résultats des opérations menées en 2016, sur l’ensemble des masses d’eau côtières et de transition rattachées au district Artois-Picardie

Contrôle de surveillance benthique de la Directive Cadre sur l'Eau (2000/60/CE) : Volume II : Flore autre que phytoplancton, Année 2016. District Seine-Normandie.

This report presents results of the monitoring actions carried out in 2016 (on flora other than phytoplankton) in the water bodies of the Seine-Normandie water district.Ce rapport présente les résultats des opérations menées en 2016 (contrôle de surveillance de la flore autre que phytoplancton) sur l’ensemble des masses d’eau côtières et de transition rattachées au district Seine-Normandie

Disentangling trawling impact from natural variability on benthic communities

Various environmental parameters such as temperature, depth and currents influence the composition and distribution of benthic assemblages. However, the impact of trawling on benthic communities depends on their species composition since not all benthic species are equally sensitive to trawling. Moreover, trawling can have effects on benthic species similar to some natural disturbances, such as a local increase in turbidity. Thus, species adapted to these natural disturbances may be resistant to a certain level of trawling. This study evaluates the joint influence of environmental parameters and trawling pressure on four functional sensitivity indices in three environmentally contrasted areas: the English Channel, the Gulf of Lion and the eastern coast of Corsica, the two latter being located in the Mediterranean Sea. The different environmental parameters influencing the behaviour of these indices were identified in each of the study areas. These parameters were divided into two groups according to the type of influence they have on the benthic community. The first group of variables, used for modeling “Scope for Growth” (SfG), relates to the resilience of species, while the second, “Disturbance” (Dist), concerns their resistance to physical impacts. This work highlighted that the distribution of benthic species in the English Channel is mainly linked to physical disturbances and therefore to their resistance, whereas it is mainly parameters linked to the resilience of communities that influence the distribution of benthic fauna in the Mediterranean. The effect of abrasion could be distinguished from the natural environmental disturbances in the English Channel and Gulf of Lion where trawling was found to have a significant effect on functional sensitivity indices. The composition and distribution of benthic communities in Corsica, did not seem to be influenced by trawling pressure

Contrôle de surveillance benthique de la Directive Cadre sur l'Eau (2000/60/CE) : Année 2015 - District Artois-Picardie

This report shows results of the monitoring actions carried out in 2015 (surveillance monitoring of macrobenthic invertebrates) in the water bodies (coastal and transitional) of the Artois-Picardie water district. Results are compared with those collected during the first management plan (2010-2015).Ce rapport présente les résultats des opérations menées en 2015 (contrôle de surveillance des invertébrés benthiques) sur l’ensemble des masses d’eau côtières et de transition rattachées au district Artois-Picardie. Ces résultats sont comparés à ceux obtenus dans le cadre du premier plan de gestion (2010-2015)

Process-driven and biological characterisation and mapping of seabed habitats sensitive to trawling.

The increase of anthropogenic pressures on the marine environment together with the necessity of a sustainable management of marine living resources have underlined the need to map and model coastal environments, particularly for the purposes of spatial planning and for the implementation of integrated ecosystem-based management approach. The present study compares outputs of a process-driven benthic habitat sensitivity (PDS) model to the structure, composition and distribution of benthic invertebrates in the Eastern English Channel and southern part of the North Sea. Trawl disturbance indicators (TDI) computed from species biological traits and benthic community composition were produced from samples collected with a bottom trawl. The TDI was found to be highly correlated to the PDS further validating the latter's purpose to identify natural process-driven pattern of sensitivity. PDS was found to reflect an environmental potential that may no longer be fully observable in the field and difference with in situ biological observations could be partially explained by the spatial distribution of fishery pressure on the seafloor. The management implication of these findings are discussed and we suggest that, used in conjunction with TDI approaches, PDS may help monitor management effort by evaluating the difference between the current state and the presumed optimal environmental status of marine benthic habitats

Distribution patterns in the benthic diversity of the eastern English Channel

Understanding the distribution of specific diversity is currently an important focus in marine research, and the role of marine biodiversity has been fully recognised as essential for the proper functioning of the biosphere. The objective of this study was to explain the distribution of macrobenthic taxonomic richness (vagile epifauna, endofauna and sessile epifauna) in the eastern part of the English Channel using both classical methods and applying the mid-domain effect (MDE) model. High diversity was encountered in the eastern English Channel (875 taxa), with high-diversity areas often comprising gravelly or pebbly sediments. Sessile epifauna represented 25% of this inventory, revealing the importance of this group. Our results underline the existence of randomness in the observed species richness distribution due to large number of species with restricted ranges