Showing papers by "Carl Kesselman published in 2017"

Re)Building a Kidney

Abstract: (Re)Building a Kidney is a National Institute of Diabetes and Digestive and Kidney Diseases-led consortium to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and the integration of these cells into complex structures that replicate human kidney function. The ultimate goals of the consortium are two-fold: to develop and implement strategies for in vitro engineering of replacement kidney tissue, and to devise strategies to stimulate regeneration of nephrons in situ to restore failing kidney function. Projects within the consortium will answer fundamental questions regarding human gene expression in the developing kidney, essential signaling crosstalk between distinct cell types of the developing kidney, how to derive the many cell types of the kidney through directed differentiation of human pluripotent stem cells, which bioengineering or scaffolding strategies have the most potential for kidney tissue formation, and basic parameters of the regenerative response to injury. As these projects progress, the consortium will incorporate systematic investigations in physiologic function of in vitro and in vivo differentiated kidney tissue, strategies for engraftment in experimental animals, and development of therapeutic approaches to activate innate reparative responses.

Experiences with DERIVA: An Asset Management Platform for Accelerating eScience

Abstract: The pace of discovery in eScience is increasingly dependent on a scientist’s ability to acquire, curate, integrate, analyze, and share large and diverse collections of data. It is all too common for investigators to spend inordinate amounts of time developing ad hoc procedures to manage their data. In previous work, we presented DERIVA, a Scientific Asset Management System, designed to accelerate data driven discovery. In this paper, we report on the use of DERIVA in a number of substantial and diverse eScience applications. We describe the lessons we have learned, both from the perspective of the DERIVA technology, as well as the ability and willingness of scientists to incorporate Scientific Asset Management into their daily workflows.

ERMRest: A Collaborative Data Catalog with Fine Grain Access Control

Abstract: Creating and maintaining an accurate description of data assets and the relationships between assets is a critical aspect of making data findable, accessible, interoperable, and reusable (FAIR). Typically, such metadata are created and maintained in a data catalog by a curator as part of data publication. However, allowing metadata to be created and maintained by data producers as the data is generated rather then waiting for publication can have significant advantages in terms of productivity and repeatability. The responsibilities for metadata management need not fall on any one individual, but rather may be delegated to appropriate members of a collaboration, enabling participants to edit or maintain specific attributes, to describe relationships between data elements, or to correct errors. To support such collaborative data editing, we have created ERMrest, a relational data service for the Web that enables the creation, evolution and navigation of complex models used to describe and structure diverse file or relational data objects. A key capability of ERMRest is its ability to control operations down to the level of individual data elements, i.e. fine-grained access control, so that many different modes of data-oriented collaboration can be supported. In this paper we introduce ERMRest and describe its fine-grained access control capabilities that support collaborative editing. ERMrest is in daily use in many data driven collaborations and we describe a sample policy that is based on a common biocuration pattern.