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

HTTP Mailbox - Asynchronous RESTful Communication

We describe HTTP Mailbox, a mechanism to enable RESTful HTTP communication in an asynchronous mode with a full range of HTTP methods otherwise unavailable to standard clients and servers. HTTP Mailbox allows for broadcast and multicast semantics via HTTP. We evaluate a reference implementation using ApacheBench (a server stress testing tool) demonstrating high throughput (on 1,000 concurrent requests) and a systemic error rate of 0.01%. Finally, we demonstrate our HTTP Mailbox implementation in a human assisted web preservation application called "Preserve Me".Comment: 13 pages, 6 figures, 8 code blocks, 3 equations, and 3 table

Communication System For Firefighters

Currently firefighters use two-way radios to communicate on the job, and they are forced to write reports based on their memory because there is not an easy way to record the communications between two-way radios. Firefighters need a system to automatically document what happened while they were responding to a call. To save them a significant amount of time when creating reports, our solution is to implement an application that allows firefighters to take pictures, record video and communicate in real time with their team of on-site responders. The proposed system will use a Wireless Local Area Network (WLAN) hosted on the fire truck itself to act as an access point (AP) to which the firefighters can connect. This AP will also save communication between firefighters to a local storage location. Upon return to the fire station, the AP will route all of the information stored locally to a larger database. For now, Wi-Fi will be our communication medium, with a prediction that our technology can eventually be extended to include radio signal

A dataflow platform for applications based on Linked Data

Modern software applications increasingly benefit from accessing the multifarious and heterogeneous Web of Data, thanks to the use of web APIs and Linked Data principles. In previous work, the authors proposed a platform to develop applications consuming Linked Data in a declarative and modular way. This paper describes in detail the functional language the platform gives access to, which is based on SPARQL (the standard query language for Linked Data) and on the dataflow paradigm. The language features interactive and meta-programming capabilities so that complex modules/applications can be developed. By adopting a declarative style, it favours the development of modules that can be reused in various specific execution context

An autonomic delivery framework for HTTP adaptive streaming in multicast-enabled multimedia access networks

The consumption of multimedia services over HTTP-based delivery mechanisms has recently gained popularity due to their increased flexibility and reliability. Traditional broadcast TV channels are now offered over the Internet, in order to support Live TV for a broad range of consumer devices. Moreover, service providers can greatly benefit from offering external live content (e. g., YouTube, Hulu) in a managed way. Recently, HTTP Adaptive Streaming (HAS) techniques have been proposed in which video clients dynamically adapt their requested video quality level based on the current network and device state. Unlike linear TV, traditional HTTP- and HAS-based video streaming services depend on unicast sessions, leading to a network traffic load proportional to the number of multimedia consumers. In this paper we propose a novel HAS-based video delivery architecture, which features intelligent multicasting and caching in order to decrease the required bandwidth considerably in a Live TV scenario. Furthermore we discuss the autonomic selection of multicasted content to support Video on Demand (VoD) sessions. Experiments were conducted on a large scale and realistic emulation environment and compared with a traditional HAS-based media delivery setup using only unicast connections

An Editorial Workflow Approach For Collaborative Ontology Development

The widespread use of ontologies in the last years has raised new challenges for their development and maintenance. Ontology development has transformed from a process normally performed by one ontology engineer into a process performed collaboratively by a team of ontology engineers, who may be geographically distributed and play different roles. For example, editors may propose changes, while authoritative users approve or reject them following a well defined process. This process, however, has only been partially addressed by existing ontology development methods, methodologies, and tool support. Furthermore, in a distributed environment where ontology editors may be working on local copies of the same ontology, strategies should be in place to ensure that changes in one copy are reflected in all of them. In this paper, we propose a workflow-based model for the collaborative development of ontologies in distributed environments and describe the components required to support them. We illustrate our model with a test case in the fishery domain from the United Nations Food and Agriculture Organisation (FAO)