This paper introduces a general metacomputing framework for submitting jobs across a variety of distributed computational resources. A first-come, first-served scheduling algorithm distributes the jobs across the computer resources. Because dependencies between jobs are expressed via a dataflow graph, the framework is more than just a uniform interface to the independently running queuing systems and interactive shells on each computer system. Using the dataflow approach extends the concept of sequential batch and interactive processing to running programs across multiple computers and computing sites in cooperation. We present results from a Grand Challenge case study showing that the turnaround time was dramatically reduced by having access to several supercomputers at runtime. The framework is applicable to other complex scientific problems that are coarse grained

A new computational framework is developed for the evolutionary determination of molecular crystal structures using the Shake-and-Bake methodology. Genetic algorithms are performed on the SnB results of known structures in order to optimize critical parameters of the program. The determination of efficient SnB input parameters can significantly reduce the time required to solve unknown molecular structures. Further, the grid-enabled data mining approach that we introduce is able to exploit computational cycles that would otherwise go unused. 1.

Developing and maintaining a large software package is a complex task. Decisions are made early in the design process that affect i) the ability of a user to effectively exploit the package and ii) the ability of a software engineer to maintain it. This case study discusses issues in software development and maintainability of a scientific package called SnB 1 , which is used to determine molecular crystal structures. The design of the user interface is discussed along with software engineering concepts, including modular programming, data encapsulation, and internal code documentation. Issues concerning the integration of Fortran, a language that is still widely used in the scientific community, into a modern scientific application with a C-based user interface are also discussed. Scientific applications benefit from being available on a wide variety of platforms. Due to the demand, SnB is available on a variety of sequential and parallel platforms. Methods used in the design of SnB...

The Shake-and-Bake algorithm is a powerful formulation of direct methods which alternates reciprocal-space phase refinement with filtering in real space to impose constraints. As implemented in SnB version 1.5, the current distributed version of the computer program, Shake-and-Bake combines peak picking in real space with optimization via either parameter-shift reduction of the minimal-function value or tangent-formula refinement. The procedure employs a multisolution approach in which initial trial structures consist of randomly positioned atoms. The SnB program has provided ab initio solutions for protein structures containing as many as 600 independent non-H atoms, provided that goodquality diffraction data are available to 1.1Å resolution. 1 Introduction The successful application of conventional direct methods to the ab initio solution of structures large enough to be regarded as small proteins has been the exclusive province of expert practitioners. Such noteworthy applications t...

The direct-methods program SnB provides an efficient means for solving protein substructures containing many heavy-atom sites (current record: 160).I order to meet the high-throughput requirements of structural genomics projects, substructure determination needs to be tightly integrated with other aspects of the protein-phasing process. This has been accomplished through the design of a common Java interface, BnP, for SnB and components of PHASES, a popular and proven program suite that provides all the tools necessary to proceed from substructure refinement to the computation of an unambiguous protein electron-density map. Therefore, BnP will facilitate a high degree of automation and enable rapid structure determination by bothexperienced and novice crystallographers.

It is now almost 200 years since Gauss, a teenager at the time, formulated his famous principle of least-squares and used it to determine, for the first time, the orbit of one of the asteroids, a problem which had defeated astronomers for years. When applied to the crystallographic phase problem, least-squares leads directly to the formulation of the minimal principle, which effectively replaces the phase problem by one of constrained global minimization. Shake-and-Bake, the computer software package which implements this formulation of the phase problem, provides a completely automatic solution of this problem. Shake-and-Bake requires that diffraction intensities to a resolution of 1.2, at least, be available. Structures having as many as 600 independent nonhydrogen atoms have been routinely solved in this way; the ultimate potential of the method is still not known.

A computational and data grid developed at the Center for Computational Research in Buffalo, New York, will provide a heterogeneous platform to enable scientific and engineering applications to run in a Buffalo-centric grid-based setting. A proof-ofconcept heterogeneous grid has been developed using a critical scientific application in the field of structural biology. The design and functionality of the prototype grid web portal is described, along with plans for a production level grid system based on Globus. Several projects covering a collaborative expansion of this system are also summarized with respect to the core research being investigated. This expansion involves researchers located across the United States who are interested in analyzing and grid-enabling existing software applications and grid technology. Development of Parallel Computing In 1970s, the VAX timeshare resources dominated the computing scene, but these machines required high initial capital expenditures and very expensive annual maintenance costs. These timeshare resources also required very highly skilled users who were capable of dealing with CPU power constraints, restricted memory scenarios, and modest disk storage systems. In the first half of the 1980s, UNIX workstations became available and were more widely deployed than the VAX timeshare resources. However, while these early workstations continued to provide only limited CPU power, memory, and disk storage, they were much more accessible and user friendly than the VAX timeshares of the 1970s.