Integrating BDI agents with Agent-based simulation platforms

Agent-Based Models (ABMs) is increasingly being used for exploring and supporting decision making about social science scenarios involving modelling of human agents. However existing agent-based simulation platforms (e.g., SWARM, Repast) provide limited support for the simulation of more complex cognitive agents required by such scenarios. We present a framework that allows Belief-Desire Intention (BDI) cognitive agents to be embedded in an ABM system. Architecturally, this means that the "brains" of an agent can be modelled in the BDI system in the usual way, while the "body" exists in the ABM system. The architecture is exible in that the ABM can still have non-BDI agents in the simulation, and the BDI-side can have agents that do not have a physical counterpart (such as an organisation). The framework addresses a key integration challenge of coupling event-based BDI systems, with time-stepped ABM systems. Our framework is modular and supports integration off-the-shelf BDI systems with off-the-shelf ABM systems. The framework is Open Source, and all integrations and applications are available for use by the modelling community

Dicer recognizes the 5′ end of RNA for efficient and accurate processing

A hallmark of RNA silencing is a class of approximately 22-nucleotide RNAs that are processed from double-stranded RNA precursors by Dicer. Accurate processing by Dicer is crucial for the functionality of microRNAs (miRNAs). The current model posits that Dicer selects cleavage sites by measuring a set distance from the 3′ overhang of the double-stranded RNA terminus. Here we report that human Dicer anchors not only the 3′ end but also the 5′ end, with the cleavage site determined mainly by the distance (~22 nucleotides) from the 5′ end (5′ counting rule). This cleavage requires a 5′-terminal phosphate group. Further, we identify a novel basic motif (5′ pocket) in human Dicer that recognizes the 5′-phosphorylated end. The 5′ counting rule and the 5′ anchoring residues are conserved in Drosophila Dicer-1, but not in Giardia Dicer. Mutations in the 5′ pocket reduce processing efficiency and alter cleavage sites in vitro. Consistently, miRNA biogenesis is perturbed in vivo when Dicer-null embryonic stem cells are replenished with the 5′-pocket mutant. Thus, 5′-end recognition by Dicer is important for precise and effective biogenesis of miRNAs. Insights from this study should also afford practical benefits to the design of small hairpin RNAs