Bioinformatics workflow management systems | High-throughput sequencing data analysis
Bioinformatics pipelines can be modeled as workflows where each work item is a stage (executable) in the pipeline. Workflow management software allows for the creation and execution of workflows. They are available as both command line controlled software tools that enable users to program and build custom workflows or they can contain a user-interface for predefined use cases. Web based workflow managers provide great flexibility and enable users to access them from any remote location through a browser. These allow researchers to monitor all executing tasks or create new tasks with minimal programming requirements.
Integrates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Galaxy permits users without programming skills to conduct computational analysis through the Web. It builds a succession of tools to perform multistep studies and is able to conserve the complete provenance of each analysis step. This platform offers drag and drop functionalities to ease the construction of workflows.
Offers access to over 180 tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. GenePattern is a genomic analysis platform that provides tools in the form of modules. Users can submit their data and choose suitable settings for performing complex analyses without detailed knowledge of the underlying programming language, algorithms and settings.
A system to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.
Provides an execution environment with a clean and readable specification language to reduce the complexity of creating workflows. Snakemake is a workflow engine inspired by the build system GNU Make. The software interoperates with any installed tool or available web service with well-defined input and output (file) formats. Apart from running on single machines, Snakemake contains a generic mechanism that allows the execution of jobs on a batch system or a compute cluster engine.
A powerful, free bioinformatics workstation platform that can be installed on anything from a laptop to a large server, or run as a virtual machine. Bio-Linux 8 adds more than 250 bioinformatics packages to an Ubuntu Linux 14.04 LTS base, providing around 50 graphical applications and several hundred command line tools. The Galaxy environment for browser-based data analysis and workflow construction is also incorporated in Bio-Linux 8.
Provides an online platform for collecting, managing, analyzing, visualizing and sharing large and complex biomedical data sets. MOLGENIS Research is a life science data solution built on top of the MOLGENIS platform. It integrates apps to inspect, organize, and customize the data. Moreover, it allows the development of various apps for specific tasks, as well as uploading of data models and settings making the platform suitable for specific uses.