Poseidon Linux 3.x - The scientific GNU/Linux option

This software review is about the newest version of Poseidon Linux (3.x). The current Poseidon Linux is a remastering from Ubuntu LTS family (Long Term Support), with extra specific software applicable to many areas of scientific research and education. It contains specialist software for GIS/Mapping, bathymetry, numerical modeling, 2D/3D/4D visualization, bioinformatics, chemistry, statistics, as well as tools for creating simple and complex graphics and programming languages. It also includes basic packages as would be expected on a normal desktop, such as a complete office suite, internet browser, e-mail client, instant messaging, chat, multimedia and many other tools. Poseidon Linux can run in two modes, as a live-DVD or installed on the hard disk. There are versions for 32 and 64 bit computers, and support for Brazilian Portuguese, English, Spanish, French, Greek, Italian and German languages. Resumo. Poseidon Linux 3.x – A opção científica GNU/Linux. Esta resenha trata da nova versão do software Poseidon Linux (3.x). A versão atual é uma remasterização a partir do sistema operacional Ubuntu, família LTS (Suporte de Longo Prazo), com pacotes extras para várias áreas da ciência e educação. Contém programas específicos para SIG/mapeamento, batimetria, modelagem numérica, visualização 2D/3D/4D, bioinformática, química, estatística, bem como ferramentas para elaboração de gráficos simples e complexos e linguagem de programação. Inclui também os programas necessários encontrados num sistema operacional desktop, tais como suporte completo para escritório, navegador de internet, programas para envio e recebimento de mensagens instantâneas, multimídia e várias outras ferramentas. O Poseidon Linux pode ser utilizado de duas formas: diretamente do DVD, sem instalá-lo, ou instalando-o no disco rígido do computador. É apresentado nas versões 32 e 64 bits e pode ser totalmente configurado em Português do Brasil, Inglês, Espanhol, Francês, Grego, Italiano e Alemão

Assembling the Tree of Life in Europe (AToLE)

A network of scientists under the umbrella of 'Assembling the Tree of Life in Europe (AToLE)' seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.
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WebLab: a data-centric, knowledge-sharing bioinformatic platform

With the rapid progress of biological research, great demands are proposed for integrative knowledge-sharing systems to efficiently support collaboration of biological researchers from various fields. To fulfill such requirements, we have developed a data-centric knowledge-sharing platform WebLab for biologists to fetch, analyze, manipulate and share data under an intuitive web interface. Dedicated space is provided for users to store their input data and analysis results. Users can upload local data or fetch public data from remote databases, and then perform analysis using more than 260 integrated bioinformatic tools. These tools can be further organized as customized analysis workflows to accomplish complex tasks automatically. In addition to conventional biological data, WebLab also provides rich supports for scientific literatures, such as searching against full text of uploaded literatures and exporting citations into various well-known citation managers such as EndNote and BibTex. To facilitate team work among colleagues, WebLab provides a powerful and flexible sharing mechanism, which allows users to share input data, analysis results, scientific literatures and customized workflows to specified users or groups with sophisticated privilege settings. WebLab is publicly available at http://weblab.cbi.pku.edu.cn, with all source code released as Free Software

Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database

EGI: anOpen e-Infrastructure Ecosystem for the Digital European Research Area

Bringing the digital European Research Area (ERA) online means modernising Europe’s research infrastructure by promoting open science through the availability, accessibility and reuse of scientific data and results, the use of web- based tools that facilitate scientific collaboration and ensuring public access to research. As the European Grid Infrastructure (EGI) is the largest European distributed computing infrastructure providing 24/7 access to large scale computing, storage and data resources through a federation of national resource providers, it allows scientists from all disciplines to make the most out of the latest computing technologies for the benefit of their research. This paper describes the methodology and approach for defining EGI’s role in bringing this digital ERA online. The work presented defines the roles and functions of EGI as an open ICT ecosystem, required service redesign, the added value of EGI for the European research communities and demonstrates the role that EGI plays in contributing to the Europe 2020 strategy for social-economic impact

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

BACKGROUND: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. RESULTS: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. Availability: (interactive), (download). CONCLUSION: From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools