SUMMARY: Droplet Digital PCR (ddPCR) is a sensitive platform used to quantify specific nucleic acid molecules amplified by polymerase chain reactions. Its sensitivity makes it particularly useful for the detection of rare mutant molecules, such as those present in a sample of circulating free tumour DNA obtained from cancer patients. ddPCR works by partitioning a sample into individual droplets for which the majority contain only zero or one target molecule. Each droplet then becomes a reaction chamber for PCR, which through the use of fluorochrome labelled probes allows the target molecules to be detected by measuring the fluorescence intensity of each droplet. The technology supports two channels, allowing, for example, mutant and wild type molecules to be detected simultaneously in the same sample. As yet, no open source software is available for the automatic gating of two channel ddPCR experiments in the case where the droplets can be grouped into four clusters. Here, we present an open source R package 'twoddpcr', which uses Poisson statistics to estimate the number of molecules in such two channel ddPCR data. Using the Shiny framework, an accompanying graphical user interface (GUI) is also included for the package, allowing users to adjust parameters and see the results in real-time. AVAILABILITY AND IMPLEMENTATION: twoddpcr is available from Bioconductor (3.5) at https://bioconductor.org/packages/twoddpcr/ . A Shiny-based GUI suitable for non-R users is available as a standalone application from within the package and also as a web application at http://shiny.cruk.manchester.ac.uk/twoddpcr/ . CONTACT: [email protected] or [email protected]. PACKAGE MAINTAINER: [email protected].

Previous studies, e.g., Haritsa et al. (Haritsa, J.R., Livny, M., Carey, M., 1990. Proceedings of Ninth ACM Symposium on Principles of Database systems) have shown that optimistic concurrency control (OCC) generally performs better than lock-based protocols in disk-based real-time database systems (RTDBS). In this paper we compare the two concurrency control protocols in both disk-based and memory-resident multiprocessor RTDBS. Based on simulation, we analyze the intrinsic behaviors of the two protocols. The result of our performance evaluation experiments show that different characteristics of the two environments indeed have great impact on the protocols' performance. We identify such system characteristics and expose the weaknesses of traditional OCC and lock-based protocols. To improve performance, a new protocol, called Two Phase Locking-Lock Write All (2PL-LW), is proposed. We show that 2PL-LW performs better than the traditional protocols in meeting transaction deadlines in both disk-based and memory-resident RTDBS.