1436574
Scheduling multiple DAGs onto heterogeneous systems
The problem of scheduling a single DAG onto heterogeneous systems has been studied extensively. In this paper, we focus on the problem of scheduling more than one DAG at the same time onto a set of heterogeneous resources. The aim is not only to optimize the overall makespan, but also to achieve fairness, defined on the basis of the slowdown that each DAG would experience as a result of competing for resources with other DAGs. Two policies particularly focussing to deliver fairness are presented and evaluated along with another four policies that can be used to schedule multiple DAGs.
7262387
An Experimental Investigation into the Rank Function of the Heterogeneous Earliest Finish Time Scheduling Algorithm
This paper considers the Heterogeneous Earliest Finish Time (HEFT) algorithm for scheduling the tasks of an application, represented by a directed acyclic graph, onto a bounded number of heterogeneous machines. We focus on the appropriate selection of the weight for the nodes and edges of the graph, and experiment with a number of different schemes for computing these weights. Our findings indicate that the length of the schedule produced may be affected significantly by the scheme used, and suggest that the mean value based approach used by HEFT may not be a particularly good choice.
21716413
Advance Reservation Policies for Workflows
Advance reservation of resources has been suggested as a means to provide a certain level of support that meets user expectations with respect to specific job start times in parallel systems. Those expectations may relate to a single job application or an application that consists of a collection of dependent jobs. In the context of Grid computing, applications consisting of dependent tasks become increasingly important, usually known as workflows. This paper focuses on the problem of planning advance reservations for individual tasks of workflow-type of applications when the user specifies a requirement only for the whole workflow application. Two policies to automate advance reservation planning for individual tasks efficiently are presented and evaluated.
5682481
VitaPad: visualization tools for the analysis of pathway data
MOTIVATION
Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data.


RESULTS
VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance.


AVAILABILITY
http://bioinformatics.med.yale.edu


CONTACTS
matthew.holford@yale.edu; hongyu.zhao@yale.edu.
12416682
Handling multiple testing while interpreting microarrays with the Gene Ontology Database
BackgroundThe development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally.ResultsWe present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database.ConclusionsWe found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.
7867544
A statistical method for identifying differential gene-gene co-expression patterns
MOTIVATION
To understand cancer etiology, it is important to explore molecular changes in cellular processes from normal state to cancerous state. Because genes interact with each other during cellular processes, carcinogenesis related genes may form differential co-expression patterns with other genes in different cell states. In this study, we develop a statistical method for identifying differential gene-gene co-expression patterns in different cell states.


RESULTS
For efficient pattern recognition, we extend the traditional F-statistic and obtain an Expected Conditional F-statistic (ECF-statistic), which incorporates statistical information of location and correlation. We also propose a statistical method for data transformation. Our approach is applied to a microarray gene expression dataset for prostate cancer study. For a gene of interest, our method can select other genes that have differential gene-gene co-expression patterns with this gene in different cell states. The 10 most frequently selected genes, include hepsin, GSTP1 and AMACR, which have recently been proposed to be associated with prostate carcinogenesis. However, genes GSTP1 and AMACR cannot be identified by studying differential gene expression alone. By using tumor suppressor genes TP53, PTEN and RB1, we identify seven genes that also include hepsin, GSTP1 and AMACR. We show that genes associated with cancer may have differential gene-gene expression patterns with many other genes in different cell states. By discovering such patterns, we may be able to identify carcinogenesis related genes.
37263695
A complete solution to a conjecture on chromatic uniqueness of complete tripartite graphs
Let P(G,@l) be the chromatic polynomial of a graph G. A graph G is chromatically unique if for any graph H, P(H,@l)=P(G,@l) implies [email protected]?G. Koh, Teo and Chia conjectured that for any integers n and k with n>=k+2>=4, the complete tripartite graph K(n-k,n,n) is chromatically unique. Let K(n,m,r)-S denote the graph obtained by deleting all edges in S from the complete tripartite K(n,m,r). In this paper, we establish that for any positive integer n>=m>=r>=2, the chromatic equivalence class of K(n,m,r) is contained in the family {K(x,y,z)-S|1==2k and k>=2.
590214
The Chromaticity of Certain Complete Multipartite Graphs
Abstract.In this paper, we first establish a useful inequality on the minimum real roots of the adjoint polynomials of the complete graphs. By using it, we investigate the chromatic uniqueness of certain complete multipartite graphs. An unsolved problem (i.e., Problem 11), posed by Koh and Teo in Graph and Combin. 6(1990) 259–285, is completely solved by giving it a positive answer. Moreover, many existing results on the chromatic uniqueness of complete multipartite graphs are generalized.