GRAMM-X public web server for protein-protein docking

This is the publisher's version, also available electronically from "http://nar.oxfordjournals.org".Protein docking software GRAMM-X and its web interface (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx) extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track

Computer-based library or computer-based learning?

Traditionally, libraries have played the role of repository of published information resources and, more recently, gateway to online subscription databases. The library online catalog and digital library interface serve an intermediary function to help users locate information resources available through the library. With competition from Web search engines and Web portals of various kinds available for free, the library has to step up to play a more active role as guide and coach to help users make use of information resources for learning or to accomplish particular tasks. It is no longer sufficient for computer-based library systems to provide just search and access functions. They must provide the functionality and environment to support learning and become computer-based learning systems. This paper examines the kind of learning support that can be incorporated in library online catalogs and digital libraries, including 1) enhanced support for information browsing and synthesis through linking by shared meta-data, references and concepts; 2) visualization of related information; 3) adoption of Library 2.0 and social technologies; 4) adoption of Library 3.0 technologies including intelligent processing and text mining

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer

CernVM Online and Cloud Gateway: a uniform interface for CernVM contextualization and deployment

In a virtualized environment, contextualization is the process of configuring a VM instance for the needs of various deployment use cases. Contextualization in CernVM can be done by passing a handwritten context to the user data field of cloud APIs, when running CernVM on the cloud, or by using CernVM web interface when running the VM locally. CernVM Online is a publicly accessible web interface that unifies these two procedures. A user is able to define, store and share CernVM contexts using CernVM Online and then apply them either in a cloud by using CernVM Cloud Gateway or on a local VM with the single-step pairing mechanism. CernVM Cloud Gateway is a distributed system that provides a single interface to use multiple and different clouds (by location or type, private or public). Cloud gateway has been so far integrated with OpenNebula, CloudStack and EC2 tools interfaces. A user, with access to a number of clouds, can run CernVM cloud agents that will communicate with these clouds using their interfaces, and then use one single interface to deploy and scale CernVM clusters. CernVM clusters are defined in CernVM Online and consist of a set of CernVM instances that are contextualized and can communicate with each other.Comment: Conference paper at the 2013 Computing in High Energy Physics (CHEP) Conference, Amsterda