A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

User friendly knowledge acquisition system for medical devices actuation

Dissertação para obtenção do Grau de Mestre em Engenharia BiomédicaInternet provides a new environment to develop a variety of applications. Hence, large amounts of data, increasing every day, are stored and transferred through the internet. These data are normally weakly structured making information disperse, uncorrelated, non-transparent and difficult to access and share. Semantic Web, proposed by theWorldWideWeb Consortium (W3C), addresses this problem by promoting semantic structured data, like ontologies, enabling machines to perform more work involved in finding, combining, and acting upon information on theWeb. Pursuing this vision, a Knowledge Acquisition System (KAS) was created, written in JavaScript using JavaScript Object Notation (JSON) as the data structure and JSON Schema to define that structure. It grants new ways to acquire and store knowledge semantically structured and human readable. Plus, structuring data with a Schema generates a software robust and error – free. A novel Human Computer Interaction (HCI) framework was constructed employing this KAS, allowing the end user to configure and control medical devices. To demonstrate the potential of this tool, we present the configuration and control of an electrostimulator. Nowadays, most of the software for Electrostimulation is made with specific purposes, and in some cases they have complicated user interfaces and large, bulky designs that deter usability and acceptability. The HCI concedes the opportunity to configure and control an electrostimulator that surpasses the specific use of several electrostimulator software. In the configuration the user is able to compile different types of electrical impulses (modes) in a temporal session, automating the control, making it simple and user-friendly

Indonesian Culture Learning Application based on Android

Indonesia is a country that has a wealth of diverse cultures spread from Sabang to Merauke. Even though the government has included a lesson about Indonesian culture in terms of some subjects such as Art and Culture, but there are still many people including some students who do not know the forms and names of the tribes, traditional houses, traditional clothing, folk songs, traditional foods, local weapons, and musical instruments regions in Indonesia. Therefore, a learning application is created that utilizes mobile learning technology. Through the use of mobile learning, user can access learning content without any borders so that it can be accessed at any time so that it can be accessed at any time with interesting illustration. Indonesia National Culture Application is made useful to help users in learning the introduction of Indonesian culture that provides the knowledge with illustrations in the form of images, audio, text and video. This application also can be functioned to learn, answer quiz, to view a gallery of images and video and to do puzzle games. The achieved result is an application that can provide knowledge to the users so they can know the culture in Indonesia through the illustrations provided well

EpiJSON: A unified data-format for epidemiology

AbstractEpidemiology relies on data but the divergent ways data are recorded and transferred, both within and between outbreaks, and the expanding range of data-types are creating an increasingly complex problem for the discipline. There is a need for a consistent, interpretable and precise way to transfer data while maintaining its fidelity. We introduce ‘EpiJSON’, a new, flexible, and standards-compliant format for the interchange of epidemiological data using JavaScript Object Notation. This format is designed to enable the widest range of epidemiological data to be unambiguously held and transferred between people, software and institutions. In this paper, we provide a full description of the format and a discussion of the design decisions made. We introduce a schema enabling automatic checks of the validity of data stored as EpiJSON, which can serve as a basis for the development of additional tools. In addition, we also present the R package ‘repijson’ which provides conversion tools between this format, line-list data and pre-existing analysis tools. An example is given to illustrate how EpiJSON can be used to store line list data. EpiJSON, designed around modern standards for interchange of information on the internet, is simple to implement, read and check. As such, it provides an ideal new standard for epidemiological, and other, data transfer to the fast-growing open-source platform for the analysis of disease outbreaks

aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3

Amazon Simple Storage Service (Amazon S3) is a widely used platform for storing large biomedical datasets. Unintended data alterations can occur during data writing and transmission, altering the original content and generating unexpected results. However, no open-source and easy-to-use tool exists to verify end-to-end data integrity. Here, we present aws-s3-integrity-check, a user-friendly, lightweight, and reliable bash tool to verify the integrity of a dataset stored in an Amazon S3 bucket. Using this tool, we only needed ∼114 min to verify the integrity of 1,045 records ranging between 5 bytes and 10 gigabytes and occupying ∼935 gigabytes of the Amazon S3 cloud. Our aws-s3-integrity-check tool also provides file-by-file on-screen and log-file-based information about the status of each integrity check. To our knowledge, this tool is the only open-source one that allows verifying the integrity of a dataset uploaded to the Amazon S3 Storage quickly, reliably, and efficiently. The tool is freely available for download and use at https://github.com/SoniaRuiz/aws-s3-integrity-check and https://hub.docker.com/r/soniaruiz/aws-s3-integrity-check

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)--in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools

Why It's Nice to be Quoted: Quasiquoting for Prolog

Prolog's support for dynamic programming, meta programming and text processing using context free grammars make the language highly suitable for defining domain specific languages (DSL) as well as analysing, refactoring or generating expression states in other (programming) languages. Well known DSLs are the DCG (Definite Clause Grammar) notation and constraint languages such as CHR. These extensions use Prolog operator declarations and the {...} notation to realise a good syntax. When external languages, such as HTML, SQL or JavaScript enter the picture, operators no longer satisfy for embedding snippets of these languages into a Prolog source file. In addition, Prolog has poor support for quoting long text fragments. Haskell introduced quasi quotationsto resolve this problem. In this paper we `ported' the Haskell mechanism for quasi quoting to Prolog. We show that this can be done cleanly and that quasi quoting can solve the above mentioned problems.Comment: Part of WLPE 2013 proceedings (arXiv:1308.2055