Browsing by Author "Brown, Joseph W"
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Item Open Access Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.(BMC Bioinformatics, 2013-05-13) Stoltzfus, Arlin; Lapp, Hilmar; Matasci, Naim; Deus, Helena; Sidlauskas, Brian; Zmasek, Christian M; Vaidya, Gaurav; Pontelli, Enrico; Cranston, Karen; Vos, Rutger; Webb, Campbell O; Harmon, Luke J; Pirrung, Megan; O'Meara, Brian; Pennell, Matthew W; Mirarab, Siavash; Rosenberg, Michael S; Balhoff, James P; Bik, Holly M; Heath, Tracy A; Midford, Peter E; Brown, Joseph W; McTavish, Emily Jane; Sukumaran, Jeet; Westneat, Mark; Alfaro, Michael E; Steele, Aaron; Jordan, GregBACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.Item Open Access The Politics of Foreign Military Basing(2020) Brown, Joseph WForeign military bases are anomalies in a world of sovereign states. Why do major powers station their finite military forces to protect other countries and how does the distribution of these bases relate to a country’s grand strategy? Why do host-nations give up their sovereignty and allow foreign forces, capable of existential violence, to deploy within their borders? This dissertation takes a mixed method approach to each of these questions. For the first, I combine descriptive case studies relating the basing postures of five major powers and to their respective grand strategies with a quantitative analysis of the correlates of the US military basing network. To answer the second, I test the role of host-nation security conditions on US military access and then conduct an in-depth process tracing of US-Philippine basing relations. I find that foreign military bases are essential for super-power status and are an arena for great power competition. I conclude that the US foreign basing posture is strongly aligned with American trade relationships and against US enemies. For host-nation motivations, I conclude that security threats to the host-nation matter, but not uniformly. External threats have the greatest influence in increasing foreign military access, but low-intensity revolutionary threats actually tend to decrease a host-nation’s willingness to accommodate foreign forces.