Collaboration in Metagenomics: Sequence Databases and the Organization of Scientific Work

Abstract

Abstract. In this paper we conduct an ethnographic study of work to explore the interaction between scientific collaboration and computing technologies in the emerging science of metagenomics. In particular, we explore how databases serve to organize scientific collaboration. We find databases existing across scientific communities where scientists have different practices and priorities. We suggest while these databases appear to be boundary objects, they are better understood as boundary negotiating artifacts. Due to rapid scientific and technical innovation the tools, practices, and scientific questions change over the course of merely a few years resulting in challenges for collaboration.

Sociotechnical Studies of Cyberinfrastructure and e-Research: Current Themes and Future Trajectories

“…CI includes a goal to seamlessly integrate the diverse technologies that make up these systems-sensors, databases, processors, operating systems, and visualization tools to name only a few components-and the ways that humans interact with them. The data that populate these systems are also heterogeneous, and each CI endeavor brings with it efforts to account for data's context of production (Faniel and Jacobsen 2010, this issue), context of use (Bietz and Lee 2009), and its means of dissemination across multiple disciplinary communities and often also long periods of time (Karasti et al this issue). For instance, Faniel and Jacobsen discuss the particularities of evaluating trustworthy data in a subfield of Earthquake Engineering, thus pointing at the difficulties of trying to achieve data that is trustworthy across disciplines and highlighting the difficulty of attempting to serve domains with different needs.…”

“…To study standardization is to inspect the ways that local divergence from a desired norm is managed, integrated and/or eradicated; how workarounds and gateways (David and Bunn 1988;Egyedi 2001) can add flexibility to rigid standard implementations; and, how boundary work (Star and Griesemer 1989;Bietz and Lee 2009) can serve to translate and interlink difference while sustaining it. The papers in this issue show how adoption of standards allows participation in a more collective research practice.…”

Research-driven stakeholders in cyberinfrastructure use and development

“…Database systems like CAMERA also provide one route through which research community values and boundaries are established. Bietz and Lee [18] found that sequence databases act as "boundary negotiating artifacts." The design of the system can favor particular scientific questions and approaches, making it easier not only for the scientist to use those approaches, but also to build a community of researchers around a particular set of scientific questions.…”

“…For example, CAMERA exists within a landscape of genomics and metagenomics databases, requiring at least some level of data sharing and compatibility with these other systems [18]. Thus, these other database systems and their users also have an interest in how CAMERA is designed.…”

At the interface of biology and computation

“…Research has focused on the collaborative aspects of scientific (and in some cases biological) tools, often looking to support the sharing of data, analysis and results (e.g. [4,5]). However, the role computation plays in interaction and design has had little if any immediate attention.…”