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A warehouse delivery problem consists of a set of robots that undertake delivery jobs within a warehouse. Items are moved around the warehouse in response to events. A solution to a warehouse delivery problem is a collision-free schedule of robot movements and actions that ensures that all delivery jobs are completed and each robot is returned to its docking station. While the warehouse delivery problem is related to existing research, such as the study of multi-agent path finding (MAPF), the specific industrial requirements necessitated a novel approach that diverges from these other approaches. For example, our problem description was more suited to formalizing the warehouse in terms of a weighted directed graph rather than the more common grid-based formalization. We formalize and encode the warehouse delivery problem in Answer Set Programming (ASP) extended with difference constraints. We systematically develop and study different encoding variants, with a view to computing good quality solutions in near real-time. In particular, application specific criteria are contrasted against the traditional notion of makespan minimization as a measure of solution quality. The encoding is tested against both crafted and industry data and experiments run using the Hybrid ASP solver clingo[dl]. 

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyze 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical, and gene neighborhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.