title: Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).
abstract: The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.
authors.affiliation: Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Lyskov
authors.forename: Fang-Chieh
authors.initials: FC
authors.lastname: Chou
authors.forename: Shane Ó
authors.initials: SÓ
authors.lastname: Conchúir
authors.forename: Bryan S
authors.initials: BS
authors.lastname: Der
authors.forename: Kevin
authors.initials: K
authors.lastname: Drew
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kuroda
authors.forename: Jianqing
authors.initials: J
authors.lastname: Xu
authors.forename: Brian D
authors.initials: BD
authors.lastname: Weitzner
authors.forename: P Douglas
authors.initials: PD
authors.lastname: Renfrew
authors.forename: Parin
authors.initials: P
authors.lastname: Sripakdeevong
authors.forename: Benjamin
authors.initials: B
authors.lastname: Borgo
authors.forename: James J
authors.initials: JJ
authors.lastname: Havranek
authors.forename: Brian
authors.initials: B
authors.lastname: Kuhlman
authors.forename: Tanja
authors.initials: T
authors.lastname: Kortemme
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Gray
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
mesh_terms: D020407:Internet; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D012984:Software; D014584:User-Computer Interface