Background: Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.Results: Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). Conclusions:HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito's largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.

Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation. In this article, we define this new field. First, we review the "Grid problem," which we define as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources-what we refer to as virtual organizations. In such settings, we encounter unique authentication, authorization, resource access, resource discovery, and other challenges. It is this class of problem that is addressed by Grid technologies. Next, we present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. We describe requirements that we believe any such mechanisms must satisfy and we discuss the importance of defining a compact set of intergrid protocols to enable interoperability among different Grid systems. Finally, we discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. We maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.

The Globus system is intended to achieve a vertically integrated treatment of application, middleware, and net work. A low-level toolkit provides basic mechanisms such as communication, authentication, network information, and data access. These mechanisms are used to con struct various higher level metacomputing services, such as parallel programming tools and schedulers. The long- term goal is to build an adaptive wide area resource environment (AWARE), an integrated set of higher level services that enable applications to adapt to heteroge neous and dynamically changing metacomputing environ ments. Preliminary versions of Globus components were deployed successfully as part of the I-WAY networking experiment.

Cloud Computing has become another buzzword after Web 2.0. However, there are dozens of different definitions for Cloud Computing and there seems to be no consensus on what a Cloud is. On the other hand, Cloud Computing is not a completely new concept; it has intricate connection to the relatively new but thirteen-year established Grid Computing paradigm, and other relevant technologies such as utility computing, cluster computing, and distributed systems in general. This paper strives to compare and contrast Cloud Computing with Grid Computing from various angles and give insights into the essential characteristics of both.Comment: IEEE Grid Computing Environments (GCE08) 200