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

Leveraging Change: Increasing Access to Arts Education in Rural Areas

In 2015, Massachusetts College of Liberal Arts (MCLA) received funding in the first round of collective impact grants from the National Endowment for the Arts to launch the pilot initiative, Leveraging Change: Improving Access to Arts Education in Rural Areas. The authors conducted research which included a literature review and interviews with arts education leaders in rural areas. Using the research compiled through this process, a pilot convening was held in western Massachusetts' Berkshire County to activate ideas, stimulate the exchange of information, and generate cross-sector collaboration focused on strengthening support for arts education in the region. This working paper is a summary of the research results and insights gleaned from this pilot initiative

The Beginnings and Prospective Ending of “End-to-End”: An Evolutionary Perspective On the Internet’s Architecture

The technology of “the Internet” is not static. Although its “end-to- end” architecture has made this “connection-less” communications system readily “extensible,” and highly encouraging to innovation both in hardware and software applications, there are strong pressures for engineering changes. Some of these are wanted to support novel transport services (e.g. voice telephony, real-time video); others would address drawbacks that appeared with opening of the Internet to public and commercial traffic - e.g., the difficulties of blocking delivery of offensive content, suppressing malicious actions (e.g. “denial of service” attacks), pricing bandwidth usage to reduce congestion. The expected gains from making “improvements” in the core of the network should be weighed against the loss of the social and economic benefits that derive from the “end-to-end” architectural design. Even where technological “fixes” can be placed at the networks’ edges, the option remains to search for alternative, institutional mechanisms of governing conduct in cyberspace.

Penang as a knowledge hub

Malaysian development strategies since independence, again in the 10th Malaysia Plan 2010 have emphasized the development of industrial clusters, like the Penang free trade zone and the MSC. Malaysia has two strong knowledge clusters: the Klang valley with KL and the MSC, Penang State and a number of smaller clusters. A calculation of the density of knowledge institutions and knowledge personnel show the epistemic landscape of Malaysia. A preliminary study of Penang reveals that the epistemic landscape is fragmented. There are several areas with a high density of knowledge institutions and knowledge workers, which however do not necessarily overlap with industrial clusters. These imbalances need to be corrected to ensure a safe passage towards a knowledge-based economy and society.Malaysia; Penang; knowledge clusters; knowledge economy; development strategy