Enables the secure and integrates analysis of data and straightforward access to databases, services and computational resources. MOWServ was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue.
Aims to ease high-throughput sequencing (HTS) data analysis by the using of distributed computation. Eoulsan is a framework able to perform its tasks on distributed computers. The application includes batch analyses, a full automation process managing external file locations and distributed file system. It can be run according three modes: standalone, local cluster or cloud computing on Amazon Elastic MapReduce.
Provides intuitive classes for several tasks of structural bioinformatics research. Biskit is a modular object-oriented library that can assist users in manipulating and analyzing macromolecular structures, protein complexes and molecular dynamics trajectories. The software comes with various scripts (programs) for reproducing published workflows. It was used for automated conformal sampling, protein-protein ensemble docking and quasiharmonic entropy calculations.
Provides programmatic access to major bioinformatics Web Services within a single Python library. BioServices gives access to around twenty Web Services including UniProt, BioModels, ChEMBL, Ensembl, KEGG, MUSCLE, NCBIBlast, and WikiPathway. Web Services available in the software can be used independently but can also be combined. It can be used to complement external and foster the development of new workflows.
Allows to analyze genomic data using Apache Pig and Hadoop. BioPig is built on MapReduce and Hadoop and thus has both the scalability and robustness offered by Apache Hadoop, and the programmability and parallel data flow control offered by Pig. It also has the flexibility to be embedded into other languages to achieve the types of control flows such as loops and branches that are not currently available in the Pig language.
Ables to efficiently integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools. jORCA manages repositories heterogeneity supported by the Modular-API that provides a uniform view of metadata (e.g. GRID-based, WSDL-services, BioMoby and others). jORCA is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users.
Allows binding and deployment of combinations of underutilized cloud computing resources. Aether is a bidding algorithm for cloud computing resources that uses linear programming (LP). The software leverages a linear programming approach to minimize cloud computing cost while being constrained by user needs and cloud capacity. It can be applied to any number of disciplines.
A complete starter kit that allows quick setup of a Hadoop computing environment in a cloud environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern.
Provides a uniform representation of resources available over the Internet, in particular for Web Services. MAPI enhances their interoperability and collaborative use by enabling a uniform and remote access. The framework functionality is organized in modules that can be combined and configured in different ways to fulfil concrete development requirements.
A platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark.
Consists of a platform-independent library of algorithms with the aim of discovering bioinformatics web services and associated data types. Magallanes is a programmatic library that connects available and compatible web services into workflows. It can process data sequentially to reach a desired output given a particular input. Its capabilities can be exploited as an API or directly accessed through a graphic user interface.
Serves for Next Generation Sequencing (NGS) data analysis. miCloud is a bioinformatics platform based on Docker virtual machine containers. It provides built-in functionality for users to run and monitor a set of preconfigured bioinformatics analysis pipelines, in addition to import, export, and management of NGS sequencing data through a visual file explorer.
Ables to efficiently integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools. mORCA manages repositories heterogeneity supported by the Modular-API that provides a uniform view of metadata (e.g. GRID-based, WSDL-services, BioMoby and others), making the integration of bioinformatics Web-Services easier.
Processes and generates large datasets. MapReduce is a programming model and an associated implementation that is amenable to a broad variety of real-world tasks. Users specify the computation in terms of a map and a reduce function, and the underlying runtime system automatically parallelizes the computation across large-scale clusters of machines, handles machine failures, and schedules inter-machine communication to make efficient use of the network and disks. Programmers find the system easy to use: more than ten thousand distinct MapReduce programs have been implemented internally at Google, and an average of one hundred thousand MapReduce jobs are executed on Google’s clusters every day, processing a total of more than twenty petabytes of data per day.
Allows to store, organize, process, and share genomic and other big data. Arvados is a platform designed to make it easier for data scientists to develop analyses, for developers to create genomic web applications and for administers to manage large-scale compute and storage genomic resources. Arvados was created to provide a common solution across a wide range of applications that would be free and open source. The platform is designed to run in the cloud or on any hardware.
Allows next-generation sequence (NGS) analysis and visualization. DNAnexus is a cloud-based solution to manage genomic data. User can create projects, share them with other DNAnexus users at various access levels, run apps and analysis and build a workflow.
Provides an interface for registering, browsing and annotating Web Services to the Life Science community. BioCatalogue allows registration of services that are specific to the Life Sciences and more generic services that are a direct utility in this domain. User can discover services and annotate them. The platform aims to satisfy the needs of service providers, users and experts, bringing them together in a common effort to make Web Services for biology more visible, better documented and easier to use.
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