The ability to accurately track cells and particles from images is critical to many biomedical problems. To address this, we developed Lineage Mapper, an open-source tracker for time-lapse images of biological cells, colonies, and particles. Lineage Mapper tracks objects independently of the segmentation method, detects mitosis in confluence, separates cell clumps mistakenly segmented as a sing...

Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available through database updates), less precise homology-based functional transfer is still the default for (meta-)genome annotation. We, therefore, developed eggNOG-mapper...

The mapper(2) Database (http://genome.ufl.edu/mapperdb) is a component of mapper(2), a web-based system for the analysis of transcription factor binding sites in multiple genomes. The database contains predicted binding sites identified in the promoters of all human, mouse and Drosophila genes using 1017 probabilistic models representing over 600 different transcription factors. In this article...

System area networks have been developed to address the needs of computing clusters. Myricom’s Myrinet architecture is one of the predominant technologies in this area. One of the key issues for SANs is faulttolerant routing. Myrinet provides Mapper software to discover and maintain network topology. Myrinet’s Mapper is centralized, susceptible to probe packet deadlock, and does not incorporate...

The Reeb space, which generalizes the notion of a Reeb graph, is one of the few tools in topological data analysis and visualization suitable for the study of multivariate scientific datasets. First introduced by Edelsbrunner et al., it compresses the components of the level sets of a multivariate mapping and obtains a summary representation of their relationships. A related construction called...

Urban vegetations have infinite proven benefits for urban inhabitants including providing shade, improving air quality, and enhancing the look and feel of communities. But creating a complete inventory is a time consuming and resource intensive process. The extraction of urban vegetation is a challenging task, especially to monitor the urban tree heights. In this study we present an efficient e...

We present preliminary results on dynamic self-adaptation of streaming networks of concurrent programs (called boxes) to the underlying hardware platform. The monitoring subsystem gathers on-line measurements on the performance of individual boxes and uses the measurements to construct (and improve) performance models of the boxes. Ideally, the models accurately predict the running time of boxe...