Experimental Biological Protocols with Formal Semantics

Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from data. However, integration between automated tasks in the process of biological discovery is still lacking, largely due to incompatible or missing formal representations. While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics. This makes it challenging to extract novel understanding by identifying when theory and experimental evidence disagree due to errors in the models or the protocols used to validate them. To address this, we formalize the syntax of a core protocol language, which provides a unified description for the models of biochemical systems being experimented on, together with the discrete events representing the liquid-handling steps of biological protocols. We present both a deterministic and a stochastic semantics to this language, both defined in terms of hybrid processes. In particular, the stochastic semantics captures uncertainties in equipment tolerances, making it a suitable tool for both experimental and computational biologists. We illustrate how the proposed protocol language can be used for automated verification and synthesis of laboratory experiments on case studies from the fields of chemistry and molecular programming

Proposed shunt rounding technique for large-scale security constrained loss minimization

The official published version can be obtained from the link below - Copyright @ 2010 IEEE.Optimal reactive power flow applications often model large numbers of discrete shunt devices as continuous variables, which are rounded to their nearest discrete value at the final iteration. This can degrade optimality. This paper presents novel methods based on probabilistic and adaptive threshold approaches that can extend existing security constrained optimal reactive power flow methods to effectively solve large-scale network problems involving discrete shunt devices. Loss reduction solutions from the proposed techniques were compared to solutions from the mixed integer nonlinear mathematical programming algorithm (MINLP) using modified IEEE standard networks up to 118 buses. The proposed techniques were also applied to practical large-scale network models of Great Britain. The results show that the proposed techniques can achieve improved loss minimization solutions when compared to the standard rounding method.This work was supported in part by the National Grid and in part by the EPSRC. Paper no. TPWRS-00653-2009