Experimental Biological Protocols with Formal Semantics

TL;DR

This paper introduces a formal language for experimental biological protocols with precise semantics, enabling automated verification and synthesis, thus bridging the gap between experimental and computational biology.

Contribution

It formalizes a core protocol language with deterministic and stochastic semantics, facilitating integration and automation in biological discovery processes.

Findings

The language captures uncertainties in equipment tolerances.

It enables automated verification of biological protocols.

Case studies demonstrate practical applications in chemistry and molecular programming.

Abstract

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.