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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.
Enables pipeline development through the adaptation of existing pipelines written in any scripting language. NextFlow is a workflow management system using Docker technology for the multi-scale handling of containerized computation. The software is designed to address numerical instability, efficient parallel execution, error tolerance, execution provenance and traceability. Users can run any current or previous version of a pipeline for any published and properly deposited analyses.
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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.
HIVE / High-performance Integrated Virtual Environment
Stores and allows investigation of next generation sequencing (NGS) and other similarly large datasets. HIVE offers a collaborative environment that is compatible with data from public and private sources. It can manage electronic handshaking protocols, supporting accession and identifier universe. This tool provides parallelization capabilities improving the process of NGS analysis. It can be utilized to translate the DNA sequence into its corresponding protein sequence.
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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.
Manages large-scale workflows that allows formal description of pipelines and partitioning of jobs. COSMOS includes a user-interface for tracking the progress of jobs, abstraction of the job queuing system (to allow interface to multiple queuing systems) and fine-grained control over the workflow. COSMOS runs on cloud-based services such as Amazon Web Services and Google Cloud, as well as traditional high-performance computing (HPC) clusters. COSMOS was developed specifically to support our clinical-time, next-generation sequencing (NGS) variant calling pipeline, but can be used to develop pipelines for any large-scale scientific workflow. It runs our parallelized workflow for optimum and scalable processing of NGS data (currently whole genome and whole exome).
Consists of an extension of the open source platform KNIME by adding the functionality for essential Next Generation Sequencing (NGS) data processing. KNIME4NGS is a comprehensive linux-based toolkit including well-documented modules (nodes) for important steps like read preprocessing, read mapping, variant calling, detection of differential expression and annotation. Complementary to previously existing nodes, this toolbox now facilitates the assembly of basic building blocks into a wide range of customized NGS analysis workflows.
wft4galaxy / WorkFlow Testing 4 Galaxy
Simplifies and automates workflow tests. wft4galaxy is a package to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. It works on based of the unit testing model: a test case is specified as a set of input datasets and parameters, expected output datasets, and the workflow itself; the workflow is run and the actual and expected outputs are compared.
BETSY / Bioinformatics ExperT SYstem
Allows to develop workflows in order to perform analyses. BETSY combines a rich data model with an inference engine tuned to reduce the exponential expansion of the search. Users can specify a desired target and the software proposes a solution, and then enters a dialog with the system to refine the proposed pipeline. It is able to run the pipeline obtained and generate the result. The tool can be used as a black box without an understanding of the workflow developed
A template language for generating qsub files for submission using the Sun Grid Engine system. By using this system, you can separate the logic of your qsub jobs from the specific data of a specific run. qsubsec allows researchers to easily create generic template definitions that encapsulate a particular computational job, effectively separating the process logic from the specific run details. At submission time, the generic template is filled in with specific values. This system provides an intermediate level between simple scripting and complete workflow management tools.
Improves the efficiency and robustness of bioinformatics research. BioQueue provides a web-based workbench and implements an explicit syntax to keep an optimal balance between flexibility and simplicity. This resource implements a greedy algorithm to dispatch jobs with these estimated data to achieve an optimal balance between the efficiency and system resources (CPU, memory and disk). User can export a protocol with a generated model as a plain text file, and then upload the protocol to any forum or our open platform
Allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks allowing software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies.
A data integration framework for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases. Anduril automatically generates thorough summary reports and a website that shows the most relevant features of each gene at a glance, allows sorting of data based on different parameters, and provides direct links to more detailed data on genes, transcripts or genomic regions. Anduril is open-source; all methods and documentation are freely available.
Allows users to publish, integrate and execute command-line applications across platforms. Boutiques focuses on (1) fully-automatic integration of applications, including deployment on heterogeneous computing resources through containers, (2) comprehensive input validation through a strict JSON schema, and (3) flexible application description through a rich JSON schema. The software removes the technological dependency to a particular platform and facilitates application migration.
Maps abstract workflow descriptions onto distributed computing infrastructures. Pegasus has been used for more than twelve years by scientists in a wide variety of domains, including astronomy, seismology, bioinformatics, physics and others. It enables user to represent the workflows at an abstract level without needing to worry about the particulars of the target execution systems. The tool can run workflows across multiple heterogeneous resources distributed in the wide area.
GVL / Genomics Virtual Laboratory
A pipeline implemented as a middleware layer of machine images, cloud management tools, and online services. Genomics Virtual Laboratory enables researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options through the cloud. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required.
Creates portable environments for scientific application. Singularity aims to support existing and traditional high-performance computing (HPC) resources by supplying portable and reproductible containers via a single image file which can be copied, shared and archived. Besides, the software offers to execute a workflow through the image generated as well as redirects IO, pipes, arguments, files, shell redirects and sockets directly to the applications inside the container.
Workflow Conversion
A set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources.
NEAT / NExt generation Analysis Toolbox
Assists users in management of ChIPseq and RNAseq pipelines. NEAT offers several automated modules: unzip, rename, QC, chiprx, map, filter, peakcalling, creation of wig files, etc. The latter can be run through double-clickable icons from any desktop or laptop, an interface that not only facilitates the analysis of next generation sequencing (NGS) data, but that makes it accessible to non-expert users. NEAT includes downstream applications that allow users to effortlessly explore NGS data.
Wings / Workflow INstance Generation and Specialization
Designs and explores computational experiments as workflows. Wings generates vary as the system explores different choices of data sets and parameters. It permits to discover new combination of components or find data sets that users did not know were compatible with a particular experimental design. The tool contains features that incorporate semantic constraints about datasets and workflow components, and are used to create and validate workflows and to generate metadata for new data products.
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