21,479 research outputs found

    The CommUnity Workbench

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    CommUnity is a formal approach to Software Architecture with a strict separation of the computation, coordination, and distribution aspects. The approach is based on a parallel design language with state, which facilitates the specification of computations compared to the process calculi used by other formal approaches, and on category theory, which provides an intuitive yet precise graph-based semantics for the configuration of components and connectors. The CommUnity Workbench is being developed as a proof of concept of the CommUnity framework, providing a graphical integrated development environment to write components, draw configurations, and execute the resulting system. The CommUnity Workbench is being developed as a proof of concept of the CommUnity framework, providing a graphical integrated development environment to write components, draw configurations, and execute the resulting system

    The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

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    RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench

    The RNA workbench: Best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

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    RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis

    Modelling the GSM handover protocol in CommUnity

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    CommUnity is a formal approach to software architecture. It has a precise, yet intuitive mathematical semantics based on category theory. It supports, at the methodological level, a clear separation between computation, coordination, and distribution (including mobility). It provides a simple state-based language for describing component behaviour that is inspired by Unity and Interacting Processes. It also addresses composition as a first class concern and accounts for the emergence of global system properties from interconnections. This paper describes the approach and available tool support by modelling essential aspects of the GSM handover protocol. We also sketch a framework that we are implementing for the distributed execution of such specifications using Klava, a Java library for mobile agent systems based on tuple spaces

    PEMBUATAN WORKBENCH ERGONOMIS UNTUK MENDUKUNG AKTIVITAS PEMILAHAN, PENGEPRESAN, DAN PENGARUNGAN SAMPAH AIR MINUM DALAM KEMASAN DI KELURAHAN WONKUSUMO SURABAYA

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    Kegiatan pengabdian masyarakat ini adalah memberikan workbench untuk kegiatan Bank Sampah di Kelurahan Bulaksari. Para Ibu rumah tangga di beberapa Rukun Tetangga (RT) melakukan pengelolaan sampah Air Minum Dalam Kemasan (AMDK) dengan melakukan sortir, pembersihan sampah dan pengarungan. Namun, didapati kondisi selama proses sortir sampah, tidak ergonomis, dimana para ibu rumah tangga ini melakukan kegiatan tersebut tidak dengan menggunakan alat bantu yang layak dan dengan posisi duduk membungkuk. Implikasi kegiatan pengabdian masyarakat terbagi ke beberapa kegiatan, pertama adalah mengadakan sosialisasi terkait kegiatan pengelolaan sampah dan itikad untuk membantu kegiatan tersebut. Kemudian dilanjutkan dengan pembuatan ergonomic workbench, dimana alat bantu ini dapat memberikan kenyamanan dan keamanan saat bekerja karena didesain dengan mengakomodir prinsip perancangan metode kerja dan produk, Terakhir adalah dengan melakukan trial produk versi pertama untuk mendapatkan masukan dalam pengembangan produk versi kedua. Kata kunci: sampah plastik, air minum dalam kemasan, alat kerja, ergonomis, bank sampah ABSTRACT This community service is to provide a workbench for garbage bank activites in Bulaksari Village. Housewives in several Neighborhood Communities (RT) manage Bottle Drinking Water (AMDK) waste by sorting, cleaning and rafting in a sack. However, it was found that the conditions during the waste sorting process were not ergonomic, where these housewives did not use proper tools and bent sitting position. The implication of community service activities are divided into several activities, first is holding socialization related to waste management activities and the intention to help these activities. Then proceed with the manufacture of an ergonomic workbench, where this tool can provide comfort and safety while working because it is designed to accommodate the principles of ergonomics designing work products. Keywords: plastic waste, bottled mineral drinking water, workbench, ergonomics, waste ban

    myTea: Connecting the Web to Digital Science on the Desktop

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    Bioinformaticians regularly access the hundreds of databases and tools that are available to them on the Web. None of these tools communicate with each other, causing the scientist to copy results manually from a Web site into a spreadsheet or word processor. myGrids' Taverna has made it possible to create templates (workflows) that automatically run searches using these databases and tools, cutting down what previously took days of work into hours, and enabling the automated capture of experimental details. What is still missing in the capture process, however, is the details of work done on that material once it moves from the Web to the desktop: if a scientist runs a process on some data, there is nothing to record why that action was taken; it is likewise not easy to publish a record of this process back to the community on the Web. In this paper, we present a novel interaction framework, built on Semantic Web technologies, and grounded in usability design practice, in particular the Making Tea method. Through this work, we introduce a new model of practice designed specifically to (1) support the scientists' interactions with data from the Web to the desktop, (2) provide automatic annotation of process to capture what has previously been lost and (3) associate provenance services automatically with that data in order to enable meaningful interrogation of the process and controlled sharing of the results
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