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

Semantic business process management: a vision towards using semantic web services for business process management

Business process management (BPM) is the approach to manage the execution of IT-supported business operations from a business expert's view rather than from a technical perspective. However, the degree of mechanization in BPM is still very limited, creating inertia in the necessary evolution and dynamics of business processes, and BPM does not provide a truly unified view on the process space of an organization. We trace back the problem of mechanization of BPM to an ontological one, i.e. the lack of machine-accessible semantics, and argue that the modeling constructs of semantic Web services frameworks, especially WSMO, are a natural fit to creating such a representation. As a consequence, we propose to combine SWS and BPM and create one consolidated technology, which we call semantic business process management (SBPM

Characterization and Classification of Collaborative Tools

Traditionally, collaboration has been a means for organizations to do their work. However, the context in which they do this work is changing, especially in regards to where the work is done, how the work is organized, who does the work, and with this the characteristics of collaboration. Software development is no exception; it is itself a collaborative effort that is likewise affected by these changes. In the context of both open source software development projects and communities and organizations that develop corporate products, more and more developers need to communicate and liaise with colleagues in geographically distant places about the software product they are conceiving, designing, building, testing, debugging, deploying and maintaining. Thus, work teams face sizeable collaborative challenges, for which they have need of tools that they can use to communicate and coordinate their Work efficiently