HELM Software for Biopolymers.

Hierarchical Editing Language for Macromolecules (HELM version 2.0) is a molecular line notation similar to SMILEs but specifically for communicating and managing biopolymer structures. The HELM project, part of the Pistoia Alliance nonprofit organization, has been tasked to develop and promote HELM as a global exchange format and recently released version 2.0 of the specification. Here we will describe the specifics of the HELM v2.0 notation along with the large ecosystem of software to support HELM-based structure management. We will highlight a recent open-source software and database for HELM monomers and a new, simpler approach to deploying a large complicated molecular management system.

A novel 'social contract' - An attempt to harmonize a sponsor's exploratory research with a clinical study participant's data rights.

BACKGROUND: Pharmaceutical drug development rarely addresses a study participant's control of their genomic data, how to return individual incidental findings, and how to make use of genomic data more efficiently for exploratory research purposes. Mutually beneficial solutions to these issues are needed, as whole genome sequencing (WGS) is increasingly adopted in human research and as access to such information could provide impactful health-related information for a participant. METHODS: In this paper, we offer a novel framework to align a trial sponsor's need for broad exploratory research of the human genome with the study participant's right to data access and access control. The Exploratory Genetic Research Project (EGRP) aims to gather WGS on all participants of a sponsor's clinical trials. It is set up as a separate umbrella protocol to facilitate the consenting process, as well as the delineation between clinical trial endpoints versus exploratory future research. CONCLUSION: This concept establishes a participant's autonomy regarding access to genomic data and the disclosure of actionable incidental findings. The feasibility of EGRP will be tested and reassessed as it is deployed over the next few years.