About the Network Portal
The Network Portal is a database of gene transcription regulatory networks and enables exploration, annotation and comparative analysis. Deciphering the complexity of biological systems requires a systems-level view of regulatory players and their interactions. However, inference of these complex interactions is challenging, and further, visualizing and analyzing these interactions often requires advanced computational expertise, tools and resources. Network Portal provides analysis and visualization tools for selected gene regulatory networks to aid researchers in biological discovery and hypothesis development.
Network Portal integrates identification of conditionally co-regulated group of genes (performed using cMonkey) and inference of regulatory influences (performed using Inferelator). In addition, it is integrated with MicrobesOnline for genomic information, RegPrecise for collection of manually curated regulatory inferences, and RegPredict for Regulon Inference by Known Position Weight Matrix (PWM).The Network Portal aims to be flexible, modular and comprehensive. Therefore we designed our framework in two interconnected layers.
1. Automated Network Inference Pipeline: The first phase of this module leverages various data (microarray, RNAseq etc.) from validated resources (GEO, MicrobesOnline, ArrayExpress etc), checks for quality control and performs necessary optimizations to ensure compliance with ENIGMA Standards and Best Practises. The second phase of the module integrates algorithms to infer regulatory networks. Currently two algorithms (cMonkey and Inferelator) are integrated with the portal. Upcoming releases will allow developers and researchers to plugin their favorite inference algorithm seamlessly without worrying about data formats or downstream applications. In the final phase of the automated inference pipeline, processed output is transmitted to a database that can be accessed programmatically within and outside of the portal.
2. Visualization and Analysis: This layer provides online tools for visualizing network information in the context of other available data (such as genomics, proteomics, orthology etc.) in order to help with hypothesis validation and creation. Similar to the automated Inference Pipeline, this layer is also designed to be modular and flexible. We already provide tools that highlight important connections between various types of data and network information. Developers are also encouraged to design visualization and data harvesting tools that can be plugged into our visualization framework. For example, in addition to showing regulatory influences for a particular gene, a RegPrecise plugin can leverage verified regulatory informations and integrate with network portal data. Moreover, in order to give researchers more freedom, Network Portal is integrated with Gaggle Framework which enables broadcast of data among various desktop and online tools.
The Network Portal was developed as part of the DOE Knowledgebase effort. While the Network Portal integrates data, algorithms, software, and technologies that have been developed by the community, development of the portal itself is being driven by efforts focusing on the biology of specific organisms including:
- Desulfovibrio vulgaris (funded by ENIGMA)
- Methanococcus maripaludis (funded by ENIGMA and DOE)
- Halobacterium salinarum (funded by NSF, NIH and DOE)
Python, Django, NetworkX, Solr, PostgeSQL, Cytoscape Web, jQuery, the R project
Data sources include: Microbes Online, KEGG, NCBI, GO, TIGR
Sourcecode and Database Downloads
The source code for the Network Portal is available on GitHub.
The latest database download nwportal_dump-20131030.sql.gz Date: 10/30/2013 (111 Mb).
This software is released under the terms of the LGPL. Copyright (C) 2011 Institute for Systems Biology