Mobyle 1 0_new_features_new_types_of_service
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Mobyle 1.0 introduces new features including workflows, viewers, and improved workspace management. Workflows allow automated chaining of sequential or parallel jobs specified through an XML description. Viewers display specialized output like VARNA diagrams through custom HTML code. Authentication and reporting have also been expanded with OpenID and Google Analytics integration.
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Bosc2011 ntino-krampis-full
Cloud BioLinux provides an open source and fully customizable bioinformatics computing environment on the cloud for genomics research. It allows small labs to perform large-scale genomic analyses independently without dedicated on-site computing resources. The project is a community effort led by Ntino Krampis and developed by a core team, with contributions from bioinformaticians worldwide. Cloud BioLinux builds on existing open source tools by providing pre-configured virtual machines on Amazon Web Services that can be easily deployed through a desktop computer with an internet connection. This allows researchers to share projects, analyses, and computing environments with collaborators through whole-system snapshots.
Bosc talk 7-15-2011x
Cytoscape is a popular open-source software for biological network visualization and analysis. It has a large plugin ecosystem that allows for customization but this has led to issues with backwards compatibility and maintenance over time. Cytoscape 3.0 aims to address these issues by implementing a new architecture based on OSGi, semantic versioning, and Maven to better define dependencies, enforce modularity, and make developing and maintaining plugins easier going forward. This involves rewriting parts of Cytoscape but is intended to improve the sustainability and extensibility of the software long-term.
F02-Cloud-Cloud BioLinux
Cloud BioLinux provides a customizable open source bioinformatics computing environment on cloud platforms for genomics research. As sequencing technologies become more accessible, individual labs will need to perform their own analysis but may lack dedicated infrastructure. Cloud BioLinux addresses this need by offering pre-configured virtual machines with over 100 bioinformatics tools on Amazon EC2, allowing researchers to perform large-scale analysis using only a web browser. Developers can extend Cloud BioLinux by specifying additional software configurations using a framework based on Python fabric scripts. The project aims to expand its community and tool offerings to better support sequencing centers and individual researchers.
B07-GenomeContent-Biomart
BioMart 0.8 offers new features like an integrated tool for building and configuring BioMart servers, support for more database backends, and analysis and visualization plugins. It provides more flexible querying interfaces like diverse web GUIs and programmatic APIs. BioMart hides the complexity of underlying databases and provides a simple conceptual model with concepts like datasets, attributes, and filters. It is used by several large collaborative projects for data management and federation.
B03-GenomeContent-Intermine
The document discusses how InterMine uses RESTful web services for data integration and interoperability between biological databases, providing examples of how the InterMine API can be used to query databases and manage workflows through client libraries and sugar syntax. It also covers lessons learned in developing InterMine including using JSON for data exchange and implementing token-based authentication.
G03-SemanticWeb-OntoCAT
The document discusses several ontology tools and services including the Ontology Lookup Service (OLS) from the European Bioinformatics Institute (EBI) and the National Center for Biomedical Ontology (NCBO) BioPortal. It introduces OntoCAT, an ontology database and browser that provides a REST service for searching and accessing ontology data in a standardized way. OntoCAT aims to facilitate integration across ontologies and has been used to build applications like concept recognizers.
F06-Cloud-Enabling NGS
This document summarizes a presentation about CloudMan, a platform for deploying cloud computing resources and Galaxy instances. CloudMan allows users to setup cloud clusters in minutes without expertise, provides over 700GB of reference genomes and bioinformatics tools, and enables customization and sharing of derived cluster instances. It bridges users, isolated Galaxy instances, and cloud infrastructure. Key features include deployment on AWS, automated configuration, dynamic storage, and elastic scaling of resources.
D03-NextGen-Bio-NGS
This document describes Bio-NGS, a BioRuby plugin for conducting programmable workflows for Next Generation Sequencing (NGS) data. Bio-NGS provides a software development framework, application, and project environment for analyzing NGS data. It integrates third-party bioinformatics tools as wrappers or bindings and allows for modular, reusable plugins. The document outlines features of the Bio-NGS application, software development framework, and project environment.
F07-Cloud-Hadoop-BAM
Hadoop-BAM is a small Java library that allows Binary Alignment Map (BAM) files, a common format for storing aligned DNA sequencing reads, to be directly manipulated and processed on Hadoop. It handles challenges like BAM's binary format and compression by detecting record boundaries and providing access to the files through the Picard SAM API. The library was used to build tools for preprocessing large BAM files for interactive browsing of genome data on Hadoop, demonstrating good scaling on a test of over 50GB of sequencing data from 1000 Genomes Project. Future work involves developing more BAM analysis tools that can leverage Hadoop-BAM.
C03-Visualization-Webapollo
WebApollo is a web-based genome annotation editor that allows multiple users to collaboratively edit annotations in real-time. It uses a client-server model where the web-based client communicates with an annotation editing engine and data server through a framework called Trellis. This allows annotations to be accessed and edited without installing software by running in a web browser.
F01-Cloud-Mygene.info
This document describes MyGene.Info, a gene annotation service that provides gene data through a RESTful API. It discusses how gene data is stored and queried from a CouchDB document-oriented database. Users can search for genes and retrieve full or filtered annotation objects for specific genes in JSON format through HTTP requests to the MyGene.Info website. The service aims to allow quick development of gene-centric websites and applications without needing to maintain a local gene annotation database.
A01-Openness in knowledge-based systems
This document discusses the potential for open source artificial intelligence to help understand molecular biology data. It argues that capturing common sense knowledge computationally has been challenging, but knowledge about molecular biology exists explicitly. An open source AI focused on molecular biology could help explain genomic data by developing a comprehensive knowledge base and using abductive inference. However, explaining biological phenomena is difficult and requires judgment. The document advocates for open source development to gain productivity advantages and build trust through transparency. It outlines challenges and opportunities for facilitating an open source AI community focused on understanding life.
F03-Cloud-Obiwee
OBIWEE is an open source bioinformatics cloud environment for running intensive workflows. It uses SLICEE as a workflow authoring tool and runs jobs on a scalable virtual cluster deployed on private or public clouds using OpenNebula or EC2. Workflows are authored by describing command lines and OBIWEE handles parallelization and job submission to the cluster. It provides tools for deployment, data management, and client access via command line or GUI interfaces like Kepler.
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- 1. Mobyle 1.0: new features, new types of services Hervé Ménager, Bertrand Néron, Vivek Gopalan, Sandrine Larroudé, Julien Maupetit, Adrien Saladin, Pierre Tuffery, Yentram Huyen, Bernard Caudron Bioinformatics Open Source Conference, July 15th, 2011
- 3. Providing an access to bioinformatics resources for biologists ?
- 4. New types of services: Workflows ● Beyond the existing "interactive pipe" functionality ● Automated chaining or sequential/parallel jobs ● base is the same XML description as the other types of services, ● specificity: Execution specified as the coordinated execution of multiple tasks
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- 14. Acknowledgements Institut Pasteur GenOuest Bertrand Néron Olivier Sallou Sandrine Larroudé Anthony Bretaudeau Corinne Maufrais Nicolas Joly NIAID BCBB Bernard Caudron Vivek Gopalan Sophie Créno Yentram Huyen NCSU And many others... Ignazio Carbone Trent Monacell RPBS Julien Maupetit Pierre Tufféry Adrien Saladin LIPM Toulouse Sébastien Carrère