explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots.

explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots

Agent-based model with asymmetric trading and herding for complex financial systems

Background: For complex financial systems, the negative and positive return-volatility correlations, i.e., the so-called leverage and anti-leverage effects, are particularly important for the understanding of the price dynamics. However, the microscopic origination of the leverage and anti-leverage effects is still not understood, and how to produce these effects in agent-based modeling remains open. On the other hand, in constructing microscopic models, it is a promising conception to determine model parameters from empirical data rather than from statistical fitting of the results. Methods: To study the microscopic origination of the return-volatility correlation in financial systems, we take into account the individual and collective behaviors of investors in real markets, and construct an agent-based model. The agents are linked with each other and trade in groups, and particularly, two novel microscopic mechanisms, i.e., investors' asymmetric trading and herding in bull and bear markets, are introduced. Further, we propose effective methods to determine the key parameters in our model from historical market data. Results: With the model parameters determined for six representative stock-market indices in the world respectively, we obtain the corresponding leverage or anti-leverage effect from the simulation, and the effect is in agreement with the empirical one on amplitude and duration. At the same time, our model produces other features of the real markets, such as the fat-tail distribution of returns and the long-term correlation of volatilities. Conclusions: We reveal that for the leverage and anti-leverage effects, both the investors' asymmetric trading and herding are essential generation mechanisms. These two microscopic mechanisms and the methods for the determination of the key parameters can be applied to other complex systems with similar asymmetries.Comment: 17 pages, 6 figure

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

QB2OLAP : enabling OLAP on statistical linked open data

Publication and sharing of multidimensional (MD) data on the Semantic Web (SW) opens new opportunities for the use of On-Line Analytical Processing (OLAP). The RDF Data Cube (QB) vocabulary, the current standard for statistical data publishing, however, lacks key MD concepts such as dimension hierarchies and aggregate functions. QB4OLAP was proposed to remedy this. However, QB4OLAP requires extensive manual annotation and users must still write queries in SPARQL, the standard query language for RDF, which typical OLAP users are not familiar with. In this demo, we present QB2OLAP, a tool for enabling OLAP on existing QB data. Without requiring any RDF, QB(4OLAP), or SPARQL skills, it allows semi-automatic transformation of a QB data set into a QB4OLAP one via enrichment with QB4OLAP semantics, exploration of the enriched schema, and querying with the high-level OLAP language QL that exploits the QB4OLAP semantics and is automatically translated to SPARQL.Peer ReviewedPostprint (author's final draft

Km4City Ontology Building vs Data Harvesting and Cleaning for Smart-city Services

Presently, a very large number of public and private data sets are available from local governments. In most cases, they are not semantically interoperable and a huge human effort would be needed to create integrated ontologies and knowledge base for smart city. Smart City ontology is not yet standardized, and a lot of research work is needed to identify models that can easily support the data reconciliation, the management of the complexity, to allow the data reasoning. In this paper, a system for data ingestion and reconciliation of smart cities related aspects as road graph, services available on the roads, traffic sensors etc., is proposed. The system allows managing a big data volume of data coming from a variety of sources considering both static and dynamic data. These data are mapped to a smart-city ontology, called KM4City (Knowledge Model for City), and stored into an RDF-Store where they are available for applications via SPARQL queries to provide new services to the users via specific applications of public administration and enterprises. The paper presents the process adopted to produce the ontology and the big data architecture for the knowledge base feeding on the basis of open and private data, and the mechanisms adopted for the data verification, reconciliation and validation. Some examples about the possible usage of the coherent big data knowledge base produced are also offered and are accessible from the RDF-Store and related services. The article also presented the work performed about reconciliation algorithms and their comparative assessment and selection