EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web-Based Transcriptomics Analytics Platform for Diverse Users
Othman Soufan, Jessica Ewald, Guangyan Zhou, Orçun Haçarız, Emily Boulanger, Alper James Alcaraz, Gordon M. Hickey, Steve Maguire, Guillaume Pain, Natacha Hogan, Markus Hecker, Doug Crump, Jessica Head, Niladri Basu, Jianguo Xia
Abstract
The generation and use of transcriptomics data across the life sciences have risen sharply in recent years driven largely by advances in biotechnology and computational biology. Within the field of environmental toxicology, the data being generated from these efforts are providing important insights into stressor‐induced perturbations at the molecular level and helping increase understanding of causal linkages to connect such molecular perturbations with adverse outcomes at the whole‐organism level (Villeneuve et al., 2014). Despite impressive advances in these areas, the scope and pace of adoption of transcriptomics approaches in the practices of chemical risk assessment and environmental management have generally not met the expectations of their proponents (Mondou et al., 2021; Pain et al., 2020). A major challenge with transcriptomics data is that they can be complex and difficult for users to distill and synthesize into clear and actionable insights. Transcriptomics technologies can generate a tremendous amount of data, and accordingly the handling and analysis of these data require powerful computers and comprehensive databases along with bioinformatics and programming know‐how. Even studies of a few dozen genes can prove difficult for many users in terms of data management, analysis, and interpretation. These challenges are compounded for ecological species, which have far fewer and less developed knowledgebases and user‐friendly software tools compared to common model organisms. Further, tools that do exist are generally designed for ‘omics specialists rather than novice users.