PReServ: Provenance Recording for Services

The importance of understanding the process by which a result was generated in an experiment is fundamental to science. Without such information, other scientists cannot replicate, validate, or duplicate an experiment. We define provenance as the process that led to a result. With large scale in-silico experiments, it becomes increasingly difficult for scientists to record process documentation that can be used to retrieve the provenance of a result. Provenance Recording for Services (PReServ) is a software package that allows developers to integrate process documentation recording into their applications. PReServ has been used by several applications and its performance has been benchmarked.

Transparent Provenance Derivation for User Decisions

It is rare for data's history to include computational processes alone. Even when software generates data, users ultimately decide to execute software procedures, choose their configuration and inputs, reconfigure, halt and restart processes, and so on. Understanding the provenance of data thus involves understanding the reasoning of users behind these decisions, but demanding that users explicitly document decisions could be intrusive if implemented naively, and impractical in some cases. In this paper, therefore, we explore an approach to transparently deriving the provenance of user decisions at query time. The user reasoning is simulated, and if the result of the simulation matches the documented decision, the simulation is taken to approximate the actual reasoning. The plausibility of this approach requires that the simulation mirror human decision -making, so we adopt an automated process explicitly modelled on human psychology. The provenance of the decision is modelled in OPM, allowing it to be queried as part of a larger provenance graph, and an OPM profile is provided to allow consistent querying of provenance across user decisions.

Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.

Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.