CG3DR: Coordination of icosahedral virus reconstruction using Condensed Graphs

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• 作者：Chenqi Wang^a ; ^b ; ^{c.wang@cs.ucc.ie"" rel=""nofollow} ; Neil Cafferkey^a ; ^{n.cafferkey@cs.ucc.ie"" rel=""nofollow} ; James Kennedy^a ; ^{j.kennedy@cs.ucc.ie"" rel=""nofollow} ; John P. Morrison^a ; ^{j.morrison@cs.ucc.ie"" rel=""nofollow}
• 关键词：High performance computing ; Workflow ; Process coordination ; WebCom ; Condensed Graphs ; 3D reconstruction ; Virus structure
• 刊名：Parallel Computing
• 出版年：2011
• 出版时间：August 2011
• 年：2011
• 卷：37
• 期：8
• 页码：451-465
• 全文大小：880 K

文摘

We present a visual executable workflow for the three-dimensional reconstruction of icosahedral virus structure using the Traditional Model (TM) method. This workflow is implemented using WebCom, a metacomputer platform based on the Condensed Graph (CG) model. The CG model allows the application to be constructed with a structure that closely mirrors an abstract description of the workflow. By utilising WebCom’s Integrated Development Environment, we also create a workbench environment that facilitates construction of related workflows through the reuse of components developed for the TM workflow. As an example of this component reuse, we outline the construction of a workflow for the alternative Unbiased Model reconstruction method. In addition, we demonstrate that using a separate machine for the coordination of such workflows results in improved execution times.