While general usability assessment models for websites have been developed for a wide variety of contexts, research literature on incorporating user feedback in the design of online scientific tools is lacking. In this article, we present an approach that we developed and illustrate how it was used to elicit user feedback of the AnalyzeMyVariant tool, which enables geneticists to use family pedigree data to calculate pathogenicity likelihood ratios for variants of unknown significance. We reviewed existing usability literature and developed a survey instrument emphasizing concepts of importance to online, data-driven, scientific tools. The items on the survey instrument were grouped in four categories: usability, quality, privacy and security, and satisfaction. We performed a two-part evaluation using the survey and a semi-structured interview protocol. The survey instrument was used to collect data about the use experience of AnalyzeMyVariant from 57 genetic experts and trainees who were recruited via email invitations. We also conducted semi-structured interviews with six genetics experts to explore work contexts in which users might use the tool and further delve into issues faced in tool use. Interviews were inductively coded and major themes identified using the constant comparative method. We found that the needs of genetics professionals vary for research- and clinically-focused work. These differences can inform the design of tools to serve their needs. The major contribution of this work is the description of a two-part method to elicit user feedback to inform the design of online, data-driven, scientific tools, which focuses on constructs of particular relevance to these tools such as usability, quality, privacy, security, and satisfaction. The survey instrument that we developed, coupled with contextual interviews, may serve as an example that can be used by others conducting usability studies of similar tools. In addition, our results emphasize the importance of considering contextual factors such as background knowledge, situational factors, and the intended application of results, in the usability evaluation of scientific software. It is our hope that this two-part approach might be adapted to assess the usability of other online scientific tools and facilitate the design of tools to meet the needs of their target audiences.