Jiro Sumitomo

Biomashups: the new world of exploratory bioinformatics?

Bioinformatics is dominated by online databases and sophisticated web‐accessible tools. As such, it is ideally placed to benefit from the rapid, purpose specific combination of services achievable via web mashups. The recent introduction of a number of sophisticated frameworks has greatly simplified the mashup creation process, making them accessible to scientists with limited programming expertise. In this paper we investigate the feasibility of mashups as a new approach to bioinformatic experimentation, focusing on an exploratory niche between interactive web usage and robust workflows, and attempting to identify the range of computations for which mashups may be employed. While we treat each of the major frameworks, we illustrate the ideas with a series of examples developed under the Popfly framework ‡ . Copyright

BioMashups: The New World of Exploratory Bioinformatics?

Bioinformatics is dominated by on-line databases and sophisticated web-accessible tools. As such, it is ideally placed to benefit from the rapid, purpose specific combination of services and tools achievable via web mashups. The recent introduction of a number of sophisticated frameworks has greatly simplified the mashup creation process, making them accessible to scientists with limited programming expertise. We investigate the feasibility of mashups as a new approach to bioinformatic experimentation, focusing on an exploratory niche between interactive web usage and robust workflows and attempting to identify the range of computations for which mashups may be employed. While we treat each of the major frameworks, we illustrate the ideas with a series of examples developed under the Popfly framework.

A Unified Model of Batch and Interactive Scientific Workflow and Its Implementation Using Windows Workflow

Workflow is a key technology for eScience. It enables scientific tools to be composed and the resulting workflows to be managed. Workflow and most other computing tools typically distinguish batch from interactive operation. This distinction is ill-suited to scientific experimentation which typically starts interactively and then may progress to batch operation for larger or repeated runs of experiments. In this paper we present a scientific workflow model which unifies batch and interactive operation. This supports seamless experimentation by scientists. The model is implemented in a web based environment through the Microsoft Windows Workflow system and features a novel model for workflow components.

Comparative Studies Simplified in GPFlow

We present a novel, web-accessible scientific workflow system which makes large-scale comparative studies accessible without programming or excessive configuration requirements. GPFlow allows a workflow defined on single input values to be automatically lifted to operate over collections of input values and supports the formation and processing of collections of values without the need for explicit iteration constructs. We introduce a new model for collection processing based on key aggregation and slicing which guarantees processing integrity and facilitates automatic association of inputs, allowing scientific users to manage the combinatorial explosion of data values inherent in large scale comparative studies. The approach is demonstrated using a core task from comparative genomics, and builds upon our previous work in supporting combined interactive and batch operation, through a lightweight web-based user interface.

Comparative Studies Made Simple in GPFlow

This work describes recent extensions to the GPFlow scientific workflow system in development at MQUTeR (www.mquter.qut.edu.au), which facilitate interactive experimentation, automatic lifting of computations from single-case to collection-oriented computation and automatic correlation and synthesis of collections. A GPFlow workflow presents as an acyclic data flow graph, yet provides powerful iteration and collection formation capabilities.