Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

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

Graphical Programming of Simulation Models in an Object-Oriented Environment

Graphical programming has been used in conjunction with conventional simulation languages via block diagrams or activity networks. Its beneficial effects on programming and modeling in simulation have been accepted by everyone involved in these languages. However, none of these conventional techniques is truely interactive. Given the level of the current hardware and software technology, it is possible to design a very good graphical programming system which supports an interactive incremental programming style in specifications of simulation models. The benefit of such a visual system would go beyond the modeling phase of a simulation study and it might as well be realized in understanding the behavior of complex problems, in being a communication and training medium for the user and developers, and finally in presenting the simulation results. In this study, the graphical programming methodology has been investigated from the perspective of object-oriented simulation. The truely interactive and graphical orientation of some of the object-oriented languages (e.g., Smalltalk-80) has opened up new avenues of research in this very important topic. Today, the nature of this type of research will be not whether it can be done but how the known techniques should be combined to yield the highest benefit