SUMMARY: Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This article introduces BAKIR (Biologically informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community. AVAILABILITY AND IMPLEMENTATION: BAKIR is available at github.com/algo-cancer/bakir.

This paper introduces the PettingZoo library and the accompanying Agent Environment Cycle ("AEC") games model. PettingZoo is a library of diverse sets of multi-agent environments with a universal, elegant Python API. PettingZoo was developed with the goal of accelerating research in Multi-Agent Reinforcement Learning ("MARL"), by making work more interchangeable, accessible and reproducible akin to what OpenAI's Gym library did for single-agent reinforcement learning. PettingZoo's API, while inheriting many features of Gym, is unique amongst MARL APIs in that it's based around the novel AEC games model. We argue, in part through case studies on major problems in popular MARL environments, that the popular game models are poor conceptual models of the games commonly used with MARL, that they promote severe bugs that are hard to detect, and that the AEC games model addresses these problems.