BEAST: Bayesian evolutionary analysis by sampling trees

<p>Abstract</p> <p>Background</p> <p>The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.</p> <p>Results</p> <p>BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at <url>http://beast-mcmc.googlecode.com/</url> under the GNU LGPL license.</p> <p>Conclusion</p> <p>BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.</p

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]

Opening new dimensions for e-Tourism

In this paper we describe an e-Tourism environment that takes a community-driven approach to foster a lively society of travelers who exchange travel experiences, recommend tourism destinations or just listen to catch some interesting gossip. Moreover, business transactions such as booking a trip or getting assistance from travel advisors or community members are constituent parts of this environment. All these happen in an integrated, game-like e-Business application where each e-Tourist is impersonated as an avatar. More precisely, we apply 3D Electronic Institutions, a framework developed and employed in the area of multi-agent systems, to the tourism domain. The system interface is realized by means of a 3D game engine that provides sophisticated 3D visualization and enables humans to interact with the environment. We present "itchy feet", a prototype implementing this 3D e-Tourism environment to showcase first visual impressions. This new environment is a perfect research playground for examining heterogeneous societies comprising humans and software agents, and their relationship in e-Tourism. © Springer-Verlag London Limited 2006

Pengembangan Perangkat Lunak Acoustic Descriptor Analyzer (Ada-versi 2004) untuk Identifikasi Kawanan Ikan Pelagis

Pada survei hidroakustik kesalahan identifikasi kelompok spesies akan mempengaruhi akurasi perkiraan distribusi dan biomassa ikan. Tujuan pengembangan perangkat lunak ini adalah untuk mengidentifikasi atau mendeteksi kawanan ikan pelagis di suatu perairan dengan menggunakan deskriptor akustik. Pendekatan program ADA-2004 (Acoustic Descriptor Analyzer) adalah untuk membantu menganalisis berbagai tampilan kawanan ikan pelagis dengan menggunakan teknik pengolahan citra dan mengembangkan algoritma yang dapatmembedakan antar kelompok spesies. Sistem ini menggunakan Window XP atau versi lainnya sebagai dasar untuk mengaplikasi bahasa program Matlab version 6.3. Perangkat lunak ini telah diuji coba untuk pendeteksian kawanan ikan lemuru (Sardinella lemuru Bleeker, 1853) di perairan Selat Bali dan menunjukkan hasil yang memuaskan

"Last-Mile" preparation for a potential disaster

Extreme natural events, like e.g. tsunamis or earthquakes, regularly lead to catastrophes with dramatic consequences. In recent years natural disasters caused hundreds of thousands of deaths, destruction of infrastructure, disruption of economic activity and loss of billions of dollars worth of property and thus revealed considerable deficits hindering their effective management: Needs for stakeholders, decision-makers as well as for persons concerned include systematic risk identification and evaluation, a way to assess countermeasures, awareness raising and decision support systems to be employed before, during and after crisis situations. The overall goal of this study focuses on interdisciplinary integration of various scientific disciplines to contribute to a tsunami early warning information system. In comparison to most studies our focus is on high-end geometric and thematic analysis to meet the requirements of small-scale, heterogeneous and complex coastal urban systems. Data, methods and results from engineering, remote sensing and social sciences are interlinked and provide comprehensive information for disaster risk assessment, management and reduction. In detail, we combine inundation modeling, urban morphology analysis, population assessment, socio-economic analysis of the population and evacuation modeling. The interdisciplinary results eventually lead to recommendations for mitigation strategies in the fields of spatial planning or coping capacity

Models of information systems devoted to medical-imaging labs: an experience in the CNR clinical physiology institute

At the end of the 1990s, the SPERIGEST project, supported by the Italian Health Ministry, and fully developed at the Institute of Clinical Physiology, established an operative integrated clinical and healthcare information system. Continuously evolving and dynamically optimising procedures and protocols solve problems of: harmonisation of instrumentation of different brands; management of multimedia data provided by different medical imaging labs; satisfaction of both clinical and research needs; legal and economical requirements; user-friendship of the system. A ten years experience shows positive approach by medical and healthcare operators, coordinated activity, higher efficiency, simplified procedures, major concentration on medical decision-making

Arsitektur Three Tier (Client Server Programing) pada Aplikasi Perpustakaan Fakultas Teknik Universitas Muhammadiyah Bengkulu

—Perpustakaan Fakultas Teknik Universitas Muhammadiyah Bengkulu adalah salah satu penunjang proses pembelajaran civitas akademika mahasiswa, dosen dan semua yang membutuhkan peningkatan pembelajarannya. Namun kadang kala mahasiswa masih sulit memperoleh informasi buku-buku seperti ketersediaan buku serta letak buku yang di cari pada perpustakaan. Untuk itu perlunya membangun suatu sistem layanan informasi yang dapat diakses oleh banyak orang sekaligus tanpa harus mengantri dan mendatangi pusat pelayanan informasi. Yaitu membangun terdistirbusi. Membangun terdistribusi dengan konsep client server model three tier merupakan inovasi dari model tier sebelum nya, yaitu one tier dan two tier. Konsep client server model three tier adalah model yang membagi fungsionalitas ke dalam lapisan-lapisan, lapisan client, lapisan application server, dan lapisan database server. memusatkan logika pada server application atau middle tier, dapat mendistribusikan beban data pada beberapa mesin, meningkatkan keamanan dan kemampuan menyembunyikan data, cepatnya perawatan dengan tanpa instalasi database server pada setiap client. Dengan demikian pembangunan perpustakaan Fakultas Teknik Universitas Muhammadiyah Bengkulu dengan model arsitektur three tier sangat aman diterapkan pada jaringan yang luas atau pada internet, serta mahasiswa atau masyarakat dapat dengan mudah mencari buku-buku diperpustakaan Fakultas Teknik Universitas Muhammadiyah Bengkulu setelah mendapatkan informasi buku yang dicar