Node-Oriented Workflow (NOW): A Command Template Workflow Management Tool for High Throughput Data Analysis Pipelines

Next generation sequencing (NGS) systems produce vast quantities of data that require substantial computational resources for typical analysis tasks. In addition, data that are generated by different NGS systems are not homogeneous. Moreover, there are an overwhelming number of tools available for performing typical tasks. Managing NGS workflows involves writing custom scripts that quickly grow in complexity, often resulting in unwieldy workflows that underutilize typical high performance compute resources, and increase the demands of the staff managing these workflows. We present Node-Oriented Workflow (NOW), a dynamic command template workflow engine for high performance distributed computing (HPC) systems. Our system provides a simple-to-use browser-based front end for designing and managing complex workflows. Workflows are configured using a simple browser interface, and are managed by the integrated job engine, which initializes nodes, monitors node status, and processes results of individual jobs across nodes in an HPC configuration. We reduce excessive messaging across nodes by placing the burden on nodes to start tasks in a workflow when dependencies are met, i.e., node oriented workflow. Our system was designed for NGS processing in the clinical research setting, emphasizing user simplicity, tool scalability, minimization of redundancy in workflows, while maximizing throughput in an HPC environment. Furthermore, NOW is not restricted to NGS pipeline management, but can used to manage any computational pipeline

Blockade of CD40-CD154 interferes with human T cell engraftment in scid mice

Antibodies to the ligand for CD40 (CD154) have been shown to exert profound effects on the development of cell-mediated immune responses in mice. The present study shows that an antibody to human CD154 (hCD40L) inhibits in vivo Tetanus toxoid (TT) specific secondary antibody responses in hu-PBL-scid mice, as well as the expansion of xenoreactive human T cells in the scid mice. A possible cause for the reduced expansion of xenoreactive, human T cells, was the decreased expression of murine B7.1 and B7.2 caused by the administration of anti-hCD40L. Therefore, it may be that defective maturation of murine antigen-presenting cells impeded the priming and expansion of human xenoreactive T cells