5,882 research outputs found
Recommended from our members
Kronos: a workflow assembler for genome analytics and informatics.
BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos
Quattor: Tools and Techniques for the Configuration, Installation and Management of Large-Scale Grid Computing Fabrics
This paper describes the quattor tool suite, a new system for the installation, configuration, and management of operating systems and application software for computing fabrics. At present Unix derivatives such as Linux and Solaris are supported. Quattor is a powerful, portable and modular open source solution that has been shown to scale to thousands of computing nodes and offers a significant reduction in management costs for large computing fabrics. The quattor tool suite includes innovations compared to existing solutions which make it very useful for computing fabrics integrated into grid environments. Evaluations of the tool suite in current large scale computing environments are presented
advligorts: The Advanced LIGO Real-Time Digital Control and Data Acquisition System
The Advanced LIGO detectors are sophisticated opto-mechanical devices. At the
core of their operation is feedback control. The Advanced LIGO project
developed a custom digital control and data acquisition system to handle the
unique needs of this new breed of astronomical detector. The advligorts is the
software component of this system. This highly modular and extensible system
has enabled the unprecedented performance of the LIGO instruments, and has been
a vital component in the direct detection of gravitational waves
- …