Supporting curation communities and collecting technical dividends.

Scientific research is inherently a collaborative task; for curation of genome annotations, this means a dialog within and between communities of researchers to reach a shared understanding of the biology underlying the sequences. Here we describe our experience developing software to support an increasing number of genome curation communities, emphasizing the collection of technical contributions as unexpected dividends in the process. Annotation tools help improve curation quality, and in many research groups, they constitute a means to introducing human curation to the annotation process for the first time. To facilitate the dialog between and within communities of curators, our team has developed a number of web-based tools, among them Apollo, a widely-adopted genome annotation editor designed to support structural curation of gene models in a collaborative, real-time fashion. Apollo, built on top JBrowse ( http://jbrowse.org/ ), presents a set of tooling for data extraction and integration that allows users to generate analysis-ready data and progress reports; it also offers a secure web-service API to programmatically perform annotations, to integrate Apollo with workflow tools (e.g. Galaxy https://galaxyproject.org/ , via Docker https://www.docker.com/ ), etc. We have dedicated considerable efforts to spread the word about Apollo (i.e. talks and workshops to train the community on installation and use), and to continuously make improvements to support the needs of the growing research community that forms our user base. It is currently used in more than one hundred genome annotation projects around the world and across the tree of life. Recently, these improvements have included technical contributions from developers outside our core group, ranging from productive discussions, to organizing public hackathons, to welcoming code contributions to Apollo’s main development branch. This means that a portion of our target communities both have an interest in creating an ideal curation environment for their research objectives using Apollo, and are choosing to prioritize investing their resources to achieve it. It is also evidence that our efforts to support curators with an open-source, community-based bioinformatics tool have been so far successful. And as a result, we are receiving extensive technical contributions from these communities, an unexpected return on these efforts that both supports our mission and improves the workflow for our community of users. Project Website: http://genomearchitect.org/ Source Code: https://github.com/GMOD/Apollo    License: Berkeley Software Distribution (BSD-3) .