Automated identification and tracking of cells in Cytometry of Reaction Rate Constant (CRRC).

Cytometry of Reaction Rate Constant (CRRC) is a method for studying cell-population heterogeneity using time-lapse fluorescence microscopy, which allows one to follow reaction kinetics in individual cells. The current and only CRRC workflow utilizes a single fluorescence image to manually identify cell contours which are then used to determine fluorescence intensity of individual cells in the entire time-stack of images. This workflow is only reliable if cells maintain their positions during the time-lapse measurements.

Scalable in-memory processing of omics workflows.

We present a proof of concept implementation of the in-memory computing paradigm that we use to facilitate the analysis of metagenomic sequencing reads. In doing so we compare the performance of POSIX™file systems and key-value storage for omics data, and we show the potential for integrating high-performance computing (HPC) and cloud native technologies. We show that in-memory key-value storage offers possibilities for improved handling of omics data through more flexible and faster data processing.

User-centric genomics infrastructure: trends and technologies.

Genomics is both a data- and compute-intensive discipline. The success of genomics depends on an adequate informatics infrastructure that can address growing data demands and enable a diverse range of resource-intensive computational activities. Designing a suitable infrastructure is a challenging task, and its success largely depends on its adoption by users.