PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here, we present PEPATAC, an ATAC-seq pipeline that is easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also demonstrate the advantage of aligning to the mitochondrial genome serially, which improves the accuracy of alignment statistics and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project. BSD2-licensed code and documentation are available at https://pepatac.databio.org.

A Game Theoretic Mechanism for Management of IoT Resources in a Smart City

IoT is emerging in all the dimensions of the physical world, and smart city is one of the most promising among them. This article focuses on the efficient utilisation of resources in an IoT system. IoT resources have been identified and classified in context to a smart city. The number and type of resources may grow dynamically in a smart city, and user's demand may also vary dynamically. Therefore, to maximise the throughput of the system, the resources must be deployed, managed, and used efficiently. This manuscript has identified the concept, role, and composition of the resource manager with respect to an IoT system and presents a game theoretic approach to manage the resources from provider point of view. Using a complete and dynamic use case, including the multiple resources, it illustrates the usability of the proposed approach. The major focus is on the efficient use of IoT resources in a smart city.

Exploring the resource manager role in a project-based organization

PurposeThe author aims to explore and provide new insights on the resource manager role in a matrix-like project-based organization. What is the content of this role and the challenges as perceived by role incumbents?Design/methodology/approachThis a case study of a large project department in an industrial organization. The main source of data is interviews with 12 respondents.FindingsThe author describes and analyzes several mechanisms related to the key tasks of resource allocation, competence development and performance appraisals. Key challenges are the magnitude of stakeholders, especially the relationship with the project manager. To cope with these challenges, resource managers engage in extensive networking and recurrent dialog with the project manager. In addition, system knowledge and a sociable personality are perceived to enhance coping.Research limitations/implicationsOne case. 12 interviews were conducted at one point in time. The resource manager is a specific type of line manager, complementing a task (project) manager. Hypotheses and research questions based on empirical findings are identified.Practical implicationsOrganizational structure and the content of managerial roles are important in order to understand HRM challenges and activities in project-based organizations. Networking, relation maintenance and system knowledge and sociable and creative mindsets are key success factors for resource managers in large matrix-like project-based organizations.Originality/valueOne of the few in-depth studies of the resource manager in a project-based organization. A novel organizational context for the study of roles in HRM. A number of suggestions for further research.

Negotiating Ethos: An Army Corps of Engineers Resource Manager Persuades a Community to Protect a Recreational Lake Area

This article presents an observational case study of a U.S. Army Corps of Engineers Resource Manager working with community members through a contested project. Using the Aristotelian concepts of ethos, credibility, and character development, I examine ethos appeals the Resource Manager used to align Corps’s sustainability values with the community’s values. Transcribed interviews with community members reveal this alignment evolved through a coconstructed ethos negotiation process between the Resource Manager and the community. The article concludes with rhetorical and pedagogical insights gained from the case study that apply to conflict resolution in organizational communication.