We show a simple model of the dynamics of a viral process based, on the determination of the Kaplan-Meier curve P of the virus. Together with the function of the newly infected individuals I, this model allows us to predict the evolution of the resulting epidemic process in terms of the number E of the death patients plus individuals who have overcome the disease. Our model has as a starting point the representation of E as the convolution of I and P. It allows introducing information about latent patients—patients who have already been cured but are still potentially infectious, and re-infected individuals. We also provide three methods for the estimation of P using real data, all of them based on the minimization of the quadratic error: the exact solution using the associated Lagrangian function and Karush-Kuhn-Tucker conditions, a Monte Carlo computational scheme acting on the total set of local minima, and a genetic algorithm for the approximation of the global minima. Although the calculation of the exact solutions of all the linear systems provided by the use of the Lagrangian naturally gives the best optimization result, the huge number of such systems that appear when the time variable increases makes it necessary to use numerical methods. We have chosen the genetic algorithms. Indeed, we show that the results obtained in this way provide good solutions for the model.

Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.

Countries are recording health information on the global spread of COVID-19 using different methods, sometimes changing the rules after a few days. All of them are publishing the number of new individuals infected, recovered and dead individuals, along with some supplementary material. These data are often recorded in a non-uniform manner and do not conform the standard definitions of these variables. In this paper we show that, using data from the first wave of the epidemic (February-June), Kaplan-Meier curves calculated with them could provide useful information on the dynamics of the disease in different countries. We developed our scheme based on the cumulative total number of infected, recovered and dead individuals provided by the countries. We present a robust and simple model to show certain characteristics of the evolution of the dynamic process, showing that the differences in evolution between countries are reflected in the corresponding Kaplan-Meier-type curves. We compare the curves obtained for the most affected countries at that time, with the corresponding interpretation of the properties that distinguish them. The model is revealed as a practical tool for countries in the management of the Healthcare System.

Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.

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