No abstract

Tools to systematically reprogram cellular behavior are crucial to address pressing challenges in manufacturing, environment, or healthcare. Recombinases can very efficiently encode Boolean and history-dependent logic in many species, yet current designs are performed on a case-by-case basis, limiting their scalability and requiring time-consuming optimization. Here we present an automated workflow for designing recombinase logic devices executing Boolean functions. Our theoretical framework uses a reduced library of computational devices distributed into different cellular subpopulations, which are then composed in various manners to implement all desired logic functions at the multicellular level. Our design platform called CALIN (Composable Asynchronous Logic using Integrase Networks) is broadly accessible via a web server, taking truth tables as inputs and providing corresponding DNA designs and sequences as outputs (available at ). We anticipate that this automated design workflow will streamline the implementation of Boolean functions in many organisms and for various applications.

We address the issue of Ontology-Based Data Access which consists of exploiting the semantics expressed in ontologies while querying data. Ontologies are represented in the framework of existential rules, also known as Datalog+/-. We focus on the backward chaining paradigm, which involves rewriting the query (assumed to be a conjunctive query, CQ) into a set of CQs (seen as a union of CQs). The proposed algorithm accepts any set of existential rules as input and stops for so-called finite unification sets of rules (fus). The rewriting step relies on a graph notion, called a piece, which allows to identify subsets of atoms from the query that must be processed together. We first show that our rewriting method computes a minimal set of CQs when this set is finite, i.e., the set of rules is a fus. We then focus on optimizing the rewriting step. First experiments are reported.