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项目描述

MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.

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2010-07-20 21:51
10-201

内侧副韧带的聚类方案目前由于在相当快的内存管理代码优化。此外，它利用香草矩阵/向量乘法这比稀疏矩阵/矢量乘法更快。速度范围从收益略低于两倍到六倍基于图的大小和边缘密度而定。大速度增加，可能获得的尺寸图高达几百上千个节点。该图形查询程序已经收购了多家边的权重输出和汇总统计选项，和文件是固定的，更新。
标签: Major feature enhancements
The clustering program mcl is now considerably faster due to optimizations in the memory management code. Additionally, it utilises vanilla matrix/vector multiplication where this is faster than sparse matrix/vector multiplication. The speed gains range from slightly below twofold to sixfold depending on graph size and edge density. Large speed increases may be obtained for graphs of sizes up to several hundred thousands of nodes. The graph query program has acquired several edge weight output and summary statistics options, and documentation was fixed and updated.

2010-05-29 06:52
10-148

聚类方案是现在稍快，用于创建从表格数据网络方案已经成为更强大，并支持整个套件的并行计算进行了改进和简化。图变换，现已为许多方案在一个单一的规范语言，并增加了更多的变革。
The clustering program is somewhat faster now, the program for creating networks from tabular data has become more capable, and throughout the suite parallelisation support was improved and streamlined. Graph transformations are now available to many programs in a single specification language, and more transformations have been added.

2009-11-05 01:58
mcl-09-308

此版本增加了一个网络分析程序生成不同的重量分数线边缘的统计数字。该基因表达数据分析程序已被更新，也是一种相互的k -最近邻网络还原选项增加。一些模糊的选项被拆除的不同集群和网络分析程序的集成收紧。
标签: Feature Enhancements
This release adds a network analysis program that generates statistics at different edge weight cutoffs. The gene expression data parser has been updated, and a mutual k-nearest-neighbour network reduction option was added. Some obscure options were removed and integration between the different clustering and network analysis programs was tightened.

2009-09-18 23:15
09-261

此版本改进了阅读和转化表达阵列数据的支持。韧带已经收购了选择sparsify输入图形和分析方式已分裂出去，现在作为机CLM程序模式下可用。在韧带推出甲错误- 09在集群解释程序182已得到修复。该器MCX程序现在可以同时计算节点偏心和介数在多个机器和多线程并行。轻微的改善作出了整个程序的整个套件。
标签: Major
This release improves support for reading and transforming mRNA array
data. MCL has acquired an option to sparsify input graphs, and analysis
modes have been split off and are now available as a mode in the clm
program. A bug introduced in mcl-09-182 in the cluster interpretation
routines has been fixed. The mcx program can now compute both node
eccentricity and betweenness centrality parallelized over multiple
machines and multiple threads. Minor improvements have been made
throughout the entire suite of programs.

2008-06-05 23:05
08-157

该韧带套件是走向一个一般用途的大型图形分析更广泛的关注与重视，除了集群，基本图形和集群的措施和变革。该程序mcxarray现在可以转化为图形输入表格基因表达数据。机CLM实用计算集群系数，直径和偏心率和介数。许多修正和改进了整个。
标签: Major feature enhancements
The mcl suite is moving towards a wider focus on
general purpose large scale graph analysis, with
the emphasis, besides clustering, on basic graph
and clustering measures and transformations. The
program mcxarray can now transform tabular gene
expression data into graph input. The clm utility
computes clustering coefficients, diameter and
eccentricity, and betweenness centrality. Many
fixes and improvements were made throughout.

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