Gregory R. Madey

VectorBase: A Data Resource for Invertebrate Vector Genomics

VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data.

A Topological Analysis of the Open Souce Software Development Community

The fast growth of OSS has increased the interest in studying the composition of the OSS community and its collaboration mechanisms. Moreover, the success of a project may be related to the underlying social structure of the OSS development community. In this paper, we perform a quantitative analysis of Open Source Software developers by studying the entire development community at SourceForge. Statistics and social network properties are explored to find collaborations and the effects of different members in the OSS development community. Small world phenomenon and scale free behaviors are found in the SourceForge development network. These topological properties may potentially explain the success and efficiency of OSS development practices. We also infer from our analysis that weakly associated but contributing co-developers and active users may be an important factor in OSS development.

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.

VectorBase: a home for invertebrate vectors of human pathogens

VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.

Enhanced Situational Awareness: Application of DDDAS Concepts to Emergency and Disaster Management

We describe a prototype emergency and disaster information system designed and implemented using DDDAS concepts. The system is designed to use real-time cell phone calling data from a geographical region, including calling activity --- who calls whom, call duration, services in use, and cell phone location information --- to provide enhanced situational awareness for managers in emergency operations centers (EOCs) during disaster events. Powered-on cell phones maintain contact with one or more within-range cell towers so as to receive incoming calls. Thus, location data about all phones in an area are available, either directly from GPS equipped phones, or by cell tower, cell sector, distance from tower and triangulation methods. This permits the cell phones of a geographical region to serve as an ad hoc mobile sensor net, measuring the movement and calling patterns of the population. A prototype system, WIPER, serves as a test bed to research open DDDAS design issues, including dynamic validation of simulations, algorithms to interpret high volume data streams, ensembles of simulations, runtime execution, middleware services, and experimentation frameworks [1].

Application of Social Network Analysis to the Study of Open Source Software

Publisher Summary This chapter constructs four social networks for the Open Source Software (OSS) development community at Source Forge. Social network analysis has been used in many research areas to discover the intrinsic mechanisms of social communities by examining the topological properties of the social network formed by relationships between the actors and the groups in those communities. For each social network, number of people are expanded in the network by including the next set of peripheral users as defined by their role in the community, moving from the core project leaders, to the core developers, to the co-developers, and finally out to active users. All the social networks have scale-free properties, and the inclusion of the co-developers and active users triggers the emergence of the small world phenomenon for the social network. The chapter examines how these topological network properties potentially explain the success and efficiency of OSS development practices.

Analysis of Activity in the Open Source Software Development Community

Open source software is computer software for which the source code is publicly open for inspection, modification, and redistribution. While research of a few, large, successful projects have provided insights into the nature and practices of the open source software community; it still leaves open the question about the thousands of other open source projects which are neither large or highly successful. In this paper, we describe a data set of SourceForge.net, the worlds largest open source software development site, which is available for research purposes; we discuss various data mining techniques that can be applied to the data and the type of research questions that can be answered. We apply a few of these techniques and provide analysis of the results

The design and validation of a hybrid information system for the auditor's going concern decision

Decision making in a semistructured environment often involves the use of quantitative, structured analysis along with the qualitative judgment of an expert. Decision support systems and expert systems are often developed to assist in this judgment process. The hybrid information system described in this paper combines a statistical model with a rule-based expert system in order to integrate the quantitative and qualitative aspects of decision making. The GC Advisor hybrid system is designed for use by auditors to assess the ability of the client firm to continue as a going concern. The guidelines for expert system validation given in previous literature are then applied to the validation of GC Advisor.

WIPER: the integrated wireless phone based emergency response system

We describe a prototype emergency response system. This dynamic data driven application system (DDDAS) uses wireless call data, including call volume, who calls whom, call duration, services in use, and cell phone location information. Since all cell phones (that are powered on) maintain contact with one or more local cell towers, location data about each phone is updated periodically and available throughout the cellular phone network. This permits the cell phones of a city to serve as an ad hoc mobile sensor net, measuring the movement and calling patterns of the population. Social network theory and statistical analysis on normal call activity and call locations establish a baseline. A detection and alert system monitors streaming summary cell phone call data. Abnormal call patterns or population movements trigger a simulation and prediction system. Hypotheses about the anomaly are generated by a rule-based system, each initiating an agent-based simulation. Automated dynamic validation of the simulations against incoming streaming data is used to test each hypothesis. A validated simulation is used to predict the evolution of the anomaly and made available to an emergency response decision support system.

A firm-level framework for planning electronic commerce information systems infrastructure

Many firms fail to properly plan their electronic commerce information systems (ECIS) infrastructure before embarking on electronic commerce. Poor planning is often attributed to lack of a framework. Most of the frameworks used for information systems planning were developed before the recent surge of electronic commerce. Each of these frameworks emphasizes one aspect or theme of the business. In the context of E-commerce, a firm-level framework is needed that integrates several themes and recent concepts from the discipline of information systems (IS). The six components are organizational E-commerce strategy, business processes transformation, information technology management, information management, customer management, and organizational knowledge management. The framework emphasizes the significance of framework components and their interrelationships to planning an ECIS infrastructure. The main objective of the framework is to draw management attention to issues and opportunities associated with the six components of the framework. An illustrative approach is outlined to develop a method based on the framework. Firms can use the framework to develop a customized method for their ECIS infrastructure planning.