LAPIS is a fast web API for massive open virus sequencing data.

BACKGROUND: Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories around the globe generated new sequences at unprecedented speed and volume and bioinformaticians developed new tools and dashboards to analyze this wealth of data. However, a major challenge that remains is the lack of simple and efficient approaches for accessing and processing sequencing data. RESULTS: The Lightweight API for Sequences (LAPIS) facilitates rapid retrieval and analysis of genomic sequencing data through a REST API. It supports complex mutation- and metadata-based queries and can perform aggregation operations on massive datasets. LAPIS is optimized for typical questions relevant to genomic epidemiology. Using a newly-developed in-memory database engine, it has a high speed and throughput: between 25 January and 4 February 2023, the SARS-CoV-2 instance of LAPIS, which contains 14.5 million sequences, processed over 20 million requests with a mean response time of 411 ms and a median response time of 1 ms. LAPIS is the core engine behind our dashboards on genspectrum.org and we currently maintain public LAPIS instances for SARS-CoV-2 and mpox. CONCLUSIONS: Powered by an optimized database engine and available through a web API, LAPIS enhances the accessibility of genomic sequencing data. It is designed to serve as a common backend for dashboards and analyses with the potential to be integrated into common database platforms such as GenBank.

Comparison of various excitation and detection schemes for dye-doped polymeric whispering gallery mode micro-lasers.

We compare different excitation and collection configurations based on free-space optics and evanescently coupled tapered fibers for both lasing and fluorescence emission from dye-doped doped polymeric whispering gallery mode (WGM) micro-disk lasers. The focus of the comparison is on the lasing threshold and efficiency of light collection. With the aid of optical fibers, we localize the pump energy to the cavity-mode volume and reduce the necessary pump energy to achieve lasing by two orders of magnitude. When using fibers for detection, the collection efficiency is enhanced by four orders of magnitude compared to a free-space read-out perpendicular to the resonator plane. By enhancing the collection efficiency we are able to record a pronounced modulation of the dye fluorescence under continuous wave (cw) pumping conditions evoked by coupling to the WGMs. Alternatively to fibers as a collection tool, we present a read-out technique based on the detection of in-plane radiated light. We show that this method is especially beneficial in an aqueous environment as well as for size-reduced micro-lasers where radiation is strongly pronounced. Furthermore, we show that this technique allows for the assignment of transverse electric (TE) and transverse magnetic (TM) polarization to the observed fundamental modes in a water environment by performing polarization-dependent photoluminescence (PL) spectroscopy. We emphasize the importance of the polarization determination for sensing applications and verify expected differences in the bulk refractive index sensitivity for TE and TM WGMs experimentally.