Resources

All our software and resources are open source, and licensed under the GNU Lesser General Public License (LGPL).

 a machine-learning based method for clustering

cMonkey

cMonkey detects putative co-regulated gene groupings by integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence motifs.

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 a machine-learning based method for clustering

cMonkey2

This is the Python implementation of the cMonkey algorithm based on the original R implementation by David J. Reiss, Institute for Systems Biology.

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Reference

Inferelator

The Inferelator is an algorithm for inferring predictive regulatory networks from gene expression data.

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Reference

EGRIN2.0

EGRIN 2.0 is a systems-level model that delineates the complex relationship between environment, gene regulation, and phenotype in prokaryotes

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SYGNAL

We developed the SYstems Genetic Network AnaLysis (SYGNAL) pipeline to integrate correlative, causal and mechanistic inference approaches into a unified framework that systematically infers the causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients.

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Github
Reference

gbmSYGNAL

This website was developed to provides easy access to the gbmSYGNAL network by allowing searching of somatically mutated genes, regulators, or genes in biclusters.

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Reference

MTB Portal

MTB Portal serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions.

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Reference

Diatom Portal

The Diatom Portal is a new resource for the diatom community to provide a repository for experimental and computational results, as well as an interface to existing resources.

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Reference

Chlamy Portal

The Chlamy Portal is a community-wide web-resource to explore the Transcriptional Regulatory Network model for Chlamydomonas reinhardtii. 

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Reference

Syntrophy Portal

The Syntrophy Portal is a community-wide web-resource to explore the Transcriptional Regulatory Network model for syntrophic model organisms Desulfovibrio vulgaris Hildenborough and Methanococcus maripaludis S2. 

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Reference

miRvestigator

The miRvestigator framework is designed to take as input a list of co-expressed genes and will return the most likely miRNA regulating these genes.

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Reference

Cancer miRNA Regulatory Network

The cancer miRNA regulatory network was constructed by inferring miRNA mediated regulation for 2,240 gene co-expression signatures from 46 cancer transcriptome profiling studies.

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Reference

PF1010 Data Management

Project Feed 1010 aims to educate citizens in sustainable food production and research these systems for optimization.

Halobacterium species NRC-1 Genome

You can search Halobacterium sp. NRC-1 annotations from SBEAMS database.

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Reference