Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case

A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation stage the cell is going through and may be regarded as the first versions of a transcriptogram. This method is useful for extracting information from cell stimuli/responses experiments, and may be applied with diagnostic purposes to different organisms

SatNOGS: Satellite Networked Open Ground Station

Abstract—The SatNOGS, or Satellite Network Open Ground Stations, project promotes and supports free and open space applications. It seeks to solve the problem of connecting many satellite users/observers to many ground station operators. Modern open software, web, and hardware techniques are used in implementing the Network, Database, Client, and Ground Station sub- projects. Modularity in all the systems promotes the dual-use of ground stations by not interfering with local operation while utilizing the great amount of time a civilian, non-commercial ground station would otherwise sit idle

Developing and applying an integrated modular design methodology within a SME

Modularity within a product can bring advantages to the design process by facilitating enhanced design reuse, reduced lead times, decreased cost and higher levels of quality. While the benefits of modularity are becoming increasingly better known, at present it is usually left to the designers themselves to introduce modularity into products. Studies into modularity have shown that byimplementing 'formal' methods, further benefits can be made in terms of time, cost, quality and performance. Current approaches that have been proposed for the formal development of modular design methodologies fail to accurately represent knowledge that is inherently produced during design projects and fail to consider design from the different viewpoints of the development process. This work, built on previous work on modularity and design for reuse, aims to develop an integrated design methodology that will optimise the modules created through the design process and allow for modularity to be 'built-in' to product development from the initial stages. The methodology andassociated tools have been developed to provide an easy-to-use approach to modularity that has support for design rationales and company knowledge that aid in effective design decision making. The methodology, named GeMoCURE, provides an integrated total solution to modular design based on reuse of proven physical and knowledge modules. Its incremental nature allows for the optimalstructure to be maintained as the design progresses. A special focus has been on the application of this approach for Small to Medium Enterprises (SMEs), which are typically challenged by a lack of design human resources and expertise

Static and Dynamic Aspects of Scientific Collaboration Networks

Collaboration networks arise when we map the connections between scientists which are formed through joint publications. These networks thus display the social structure of academia, and also allow conclusions about the structure of scientific knowledge. Using the computer science publication database DBLP, we compile relations between authors and publications as graphs and proceed with examining and quantifying collaborative relations with graph-based methods. We review standard properties of the network and rank authors and publications by centrality. Additionally, we detect communities with modularity-based clustering and compare the resulting clusters to a ground-truth based on conferences and thus topical similarity. In a second part, we are the first to combine DBLP network data with data from the Dagstuhl Seminars: We investigate whether seminars of this kind, as social and academic events designed to connect researchers, leave a visible track in the structure of the collaboration network. Our results suggest that such single events are not influential enough to change the network structure significantly. However, the network structure seems to influence a participant's decision to accept or decline an invitation.Comment: ASONAM 2012: IEEE/ACM International Conference on Advances in Social Networks Analysis and Minin

A statistical network analysis of the HIV/AIDS epidemics in Cuba

The Cuban contact-tracing detection system set up in 1986 allowed the reconstruction and analysis of the sexual network underlying the epidemic (5,389 vertices and 4,073 edges, giant component of 2,386 nodes and 3,168 edges), shedding light onto the spread of HIV and the role of contact-tracing. Clustering based on modularity optimization provides a better visualization and understanding of the network, in combination with the study of covariates. The graph has a globally low but heterogeneous density, with clusters of high intraconnectivity but low interconnectivity. Though descriptive, our results pave the way for incorporating structure when studying stochastic SIR epidemics spreading on social networks

IMDB network revisited: unveiling fractal and modular properties from a typical small-world network

We study a subset of the movie collaboration network, imdb.com, where only adult movies are included. We show that there are many benefits in using such a network, which can serve as a prototype for studying social interactions. We find that the strength of links, i.e., how many times two actors have collaborated with each other, is an important factor that can significantly influence the network topology. We see that when we link all actors in the same movie with each other, the network becomes small-world, lacking a proper modular structure. On the other hand, by imposing a threshold on the minimum number of links two actors should have to be in our studied subset, the network topology becomes naturally fractal. This occurs due to a large number of meaningless links, namely, links connecting actors that did not actually interact. We focus our analysis on the fractal and modular properties of this resulting network, and show that the renormalization group analysis can characterize the self-similar structure of these networks.Comment: 12 pages, 9 figures, accepted for publication in PLOS ON