The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools

Model-Based Run-Time Synthesis of Architectural Configurations for Adaptive MILS Systems

In order to be resilient, a system must be adaptable. Trustworthy adaptation requires that a system can be dynamically reconfigured at run-time without compromising the robustness and integrity of the system. Adaptive MILS extends MILS, a successful paradigm for rigorously developed and assured composable static systems, with reconfiguration mechanisms and a framework within which those mechanisms may be safely and securely employed for adaptation. In this paper, we address the problem of synthesizing at run-time reconfigurations that are trustworthy taking into account the entwining of information flows and reconfigurations. The approach is based on a new extension of the Architecture Analysis & Design Language (AADL), already used for specifying MILS policy architectures, which is now enhanced to specify the configuration state space in terms of parameters, the possible reconfigurations, monitoring properties and the related alarms. Supporting tools have been developed for the run-time synthesis of new architectural configurations that preserve safety and security properties formalized in terms of invariants and information flow

Formal Specification and Verification of Dynamic Parametrized Architectures

We propose a novel approach to the formal specification and verification of dynamic architectures that are at the core of adaptive systems such as critical infrastructure protection. Key features include run-time reconfiguration based on adding and removing components and connections, resulting in systems with unbounded number of components. We provide a logic-based specification of a Dynamic Parametrized Architecture (DPA), where parameters represent the infinite-state space of possible configurations, and first-order formulas represent the sets of initial configurations and reconfiguration transitions. We encode information flow properties as reachability problems of such DPAs, define a translation into an array-based transition system, and use a Satisfiability Modulo Theories (SMT)-based model checker to tackle a number of case studies

Molecular Phylogenetics and Chronometrics of Tarsiidae Based on 12S mtDNA Haplotypes: Evidence for Miocene Origins of Crown Tarsiers and Numerous Species within the Sulawesian Clade

10.1007/s10764-010-9457-8International Journal of Primatology3161083-1106IJPR