AllegroMCODE

Fast CPU & GPU MCODE Cluster Finder for Large Networks.
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### Introduction AllegroMCODE Plugin is a high-performance MCODE cluster finder **supporting both of CPU and GPU clustering**. Clusters in a protein interaction network can be considered as protein complexes and functional modules, which can be identified as highly interconnected subgraphs. It finds the same clusters as the MCODE plugin does, but **to process large complex networks, it is totally redesigned for fast analysis, low memory consumption, and interactive cluster exploring without creating a network view or subnetwork.** * For more details about MCODE algorithm, please see our awesome video presentation: http://allegroviva.com/allegromcode/mcode-algorithm/. * AllegroMCODE Video Tutorial: http://youtu.be/emAL9xVDDdQ ### Features * **Nvidia GPU Acceleration** * It includes our proprietary highly parallel algorithm based on the original sequential MCODE algorithm and can exploits GPU computing. Its GPU analysis is more than 100x faster and usually takes less than a second to find clusters in a large complex network. * Performance Comparison: [http://allegroviva.com/allegromcode/gpu-acceleration/] * Test Video on an MacBook Pro 2010-Mid: [http://youtu.be/kBhnM0BFaNc Turning your laptop into Supercomputer] * **Less Working Memory** * It uses much less working memory than the MCODE plugin by using its own graph data structure optimized for low memory usage. * It use the graphics memory as the working memory in case of GPU processing. * Test Video: http://youtu.be/IWJSkM5OgxM * **Interactive Cluster Explorer** * Helps you to navigate and fine-tune clusters interactively. * Selecting nodes and edges of a cluster. * Zooming in/out a cluster * Individual Cluster Fine-tunig by size threshold and post processing options. For more information, please visit us at http://allegroviva.com/allegromcode/cluster-explorer/ ### Installation * Please download the plugin jar file to the "plugins" folder in the Cytoscape or use the “install plugin from file” menu under Cytoscape “plugins” menu. * To use the GPU acceleration on Mac OS, you need to install Nvidia CUDA Driver for Mac: http://www.nvidia.com/object/cuda-mac-driver.html. For more details, please read the *How to install CUDA Driver on Mac* at http://allegroviva.com/faqs/. * For Windows and Linux, you don't need to install CUDA driver to use the GPU acceleration, which is already included by NVIDIA graphics driver. ### System Requirements * O/S: Windows, Mac, or Linux * Supported GPU: Any CUDA-capable Nvidia GPU (all Nvidia graphics cards except very old models). You can check the CUDA Capability Table at https://developer.nvidia.com/cuda-gpus ### Support Forums * We provide various support forums where you can get help from our team and other users. http://allegroviva.com/support/ *** **Please note that this free community edition supports CPU clustering and includes the 15-day free evaluation of the professional edition, which supports GPU clustering.** *** Please check out our another GPU-accelerated Layout App of [http://apps.cytoscape.org/apps/allegrolayout AllegroLayout] for Cytoscape 3. *** If you need more time to evaluate the professional edition, please contact us at info@allegroviva.com. A professional license key can be purchased in our [http://sites.fastspring.com/allegroviva/product/store online store].
CYTOSCAPE 2

Version 2.1

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Released 20 May 2013

Works with Cytoscape 2.6, 2.7, 2.8

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