Representing and analysing molecular and cellular function in the computer

Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era. The complexity of biological systems is such that this cannot be envisaged without the help of powerful computer systems capable of representing and analysing the intricate networks of physical and functional interactions between the different cellular components. In this review we try to provide the reader with an appreciation of where we stand in this regard. We discuss some of the inherent problems in describing the different facets of biological function, give an overview of how information on function is currently represented in the major biological databases, and describe different systems for organising and categorising the functions of gene products. In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner. The model is capable of representing a large variety of biochemical processes, including metabolic pathways, regulation of gene expression and signal transduction. It also incorporates taxonomies for categorising molecular entities, interactions and processes, and it offers means of viewing the information at different levels of resolution, and dealing with incomplete knowledge. The data model has been implemented in the database on protein function and cellular processes 'aMAZE' (http://www.ebi.ac.uk/research/pfbp/), which presently covers metabolic pathways and their regulation. Several tools for querying, displaying, and performing analyses on such pathways are briefly described in order to illustrate the practical applications enabled by the model

Seismic Risk Analysis of Revenue Losses, Gross Regional Product and transportation systems.

Natural threats like earthquakes, hurricanes or tsunamis have shown seri- ous impacts on communities. In the past, major earthquakes in the United States like Loma Prieta 1989, Northridge 1994, or recent events in Italy like L’Aquila 2009 or Emilia 2012 earthquake emphasized the importance of pre- paredness and awareness to reduce social impacts. Earthquakes impacted businesses and dramatically reduced the gross regional product. Seismic Hazard is traditionally assessed using Probabilistic Seismic Hazard Anal- ysis (PSHA). PSHA well represents the hazard at a specific location, but it’s unsatisfactory for spatially distributed systems. Scenario earthquakes overcome the problem representing the actual distribution of shaking over a spatially distributed system. The performance of distributed productive systems during the recovery process needs to be explored. Scenario earthquakes have been used to assess the risk in bridge networks and the social losses in terms of gross regional product reduction. The proposed method for scenario earthquakes has been applied to a real case study: Treviso, a city in the North East of Italy. The proposed method for scenario earthquakes requires three models: one representation of the sources (Italian Seismogenic Zonation 9), one attenuation relationship (Sa- betta and Pugliese 1996) and a model of the occurrence rate of magnitudes (Gutenberg Richter). A methodology has been proposed to reduce thou- sands of scenarios to a subset consistent with the hazard at each location. Earthquake scenarios, along with Mote Carlo method, have been used to simulate business damage. The response of business facilities to earthquake has been obtained from fragility curves for precast industrial building. Fur- thermore, from business damage the reduction of productivity has been simulated using economic data from the National statistical service and a proposed piecewise “loss of functionality model”. To simulate the economic process in the time domain, an innovative businesses recovery function has been proposed. The proposed method has been applied to generate scenarios earthquakes at the location of bridges and business areas. The proposed selection method- ology has been applied to reduce 8000 scenarios to a subset of 60. Subse- quently, these scenario earthquakes have been used to calculate three system performance parameters: the risk in transportation networks, the risk in terms of business damage and the losses of gross regional product. A novel model for business recovery process has been tested. The proposed model has been used to represent the business recovery process and simulate the effects of government aids allocated for reconstruction. The proposed method has efficiently modeled the seismic hazard using scenario earthquakes. The scenario earthquakes presented have been used to assess possible consequences of earthquakes in seismic prone zones and to increase the preparedness. Scenario earthquakes have been used to sim- ulate the effects to economy of the impacted area; a significant Gross Regional Product reduction has been shown, up to 77% with an earthquake with 0.0003 probability of occurrence. The results showed that limited funds available after the disaster can be distributed in a more efficient way

Self-Organizing Innovation Networks: When do Small Worlds Emerge?

In this paper, we present a model of 'collective innovation' built upon the network formation formalism. In our model, agents localized on a circle benefit from knowledge flows from other agents with whom they are directly or indirectly connected. They support costs for direct connections which are linearly increasing with geographic distance. The dynamic process of network formation exhibits prefeRential meeting for close agents (in the relational network and in the geographic metrics). We show how the set of stochastically stable networks selected in the long run is affected by the degree of knowledge transferability. We find critical values of this parameter for which stable \"small world\" networks are dynamically selected.Network Formation, Stochastic Stability, Preferential Meeting, Self-Organization,

The Structure of Information Networks

We develop a model of information acquisition in a network where agents pay for all the information they acquire including those through indirect links. The cost of information depends on the value of information itself and the distance it traverses in the network. We find that when the costs of information increase with distance, the complete network is the only Nash network. When costs of information decrease with distance capturing delay, all equilibrium information networks are minimally connected, though not all trees are Nash. We analyze the popular star and chain networks and identify strict Nash networks. We show that there is almost no divergence between efficient and equilibrium information networks. We explore the implications of a spatial model and information decay and discuss the relationship with experimental evidence.Nash networks, information networks, efficient networks