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cMonkey1/2 cmonkey2_logo

PI: Nitin S. Baliga

URL: https://baliga.systemsbiology.net/projects/cmonkey/
Contact: Serdar Turkarslan | [email protected]
Source Code: https://github.com/baliga-lab/cmonkey2

Reference: Reiss, D.J.; C.L. Plaisier, W.J. Wu, N.S. Baliga (2015) cMonkey2: Automated, systematics, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Research. [doi]:10.1093/nar/gkv300 {PMID}:25873626 PMCID:PMC4513845

Reference: Reiss, D.J.; N.S. Baliga, R. Bonnaeu (2006) Integrated biclustering of heterogeneous genome-wide datasets for the influence of global regulatory networks. BMC Bioinformatics. [doi]:10.1186/1471-2105-7-280 {PMID}:16749936 PMCID:PMC1502140

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. cMonkey2 is the Python implementation of the cMonkey algorithm based on the original R implementation.


EGRIN2 egrin2

PI: Nitin S. Baliga

URL: http://egrin2.systemsbiology.net
Contact: Serdar Turkarslan | [email protected]
Source Code: https://github.com/baliga-lab?&q=egrin.

Reference: Brooks, A.N.; D.J. Reiss, A. Allard, W.J. Wu, D.M. Salvanha, C.L. Plaisier, S. Chandrasekaran, M. Pan, A. Kaur, N.S. Baliga (2014) A system-level model for the microbial regulatory genome. Molecular Systems Biology [doi]:10.15252/msb.20145160 {PMID}:25028489 PMCID:PMC4299497

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


Fitness BrowserFitness Browser

PI: Adam P. Arkin

URL: http://fit.genomics.lbl.gov/
Contact: Morgan Price | [email protected]

Reference: Price, M.N.; K.M. Wetmore, R.J. Waters, M. Callaghan, J. Ray, H. Liu, J.V. Kuehl, R.A. Melnyk, J.S. Lamson, Y. Suh, H.K. Carlson, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, G.M. Zane, B.E. Rubin, J.D. Wall, A. Visel, J. Bristow, M.J. Blow, A.P. Arkin and A.M. Deutschbauer (2018) Mutant Phenotypes for Thousands of Bacterial Genes of Unknown Function. Nature. [doi]:10.1038/s41586-018-0124-0 {PMID}:29769716

Genome-wide mutant fitness data from diverse bacteria.


GLAMM: Genome-Linked Application for Metabolic Maps GLAMM

PI: Adam P. Arkin

URL: http://glamm.lbl.gov/
Contact:

Reference: Bates, J.T.; D. Chivian, A.P. Arkin (2011) GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Research. [doi]:10.1093/nar/gkr433{PMID}:21624891 PMCID:PMC3125797

The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and investigating the construction of the novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline [Dehal et al. (2010) Nucleic Acids Research, 38, D396–D400]. GLAMM is available for free to the scientific community.


Inferelator Inferelator

PI: Nitin S. Baliga

URL: https://baliga.systemsbiology.net/the-inferelator/
Contact: Serdar Turkarslan | [email protected]
Source Code: https://github.com/baliga-lab/cMonkeyNwInf

Reference: Bonneau, R.; D.J. Reiss, P. Shannon, M. Facciotti, L. Hood, N.S. Baliga, V. Thorsson (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology. [doi]:10.1186/gb-2006-7-5-r36 {PMID}:16686963 PMCID:PMC1779511

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


KBase — DOE Systems Biology Knowledgebasekbase

PI: Adam P. Arkin

URL: http://kbase.us/
ENIGMA data stored at KBase →
Contact: John-Marc Chandonia | [email protected]

Reference: Arkin, A.P.; R.W. Cottingham, C.S. Henry, N.L. Harris, R.L. Stevens, S. Maslov, et al. (2018) KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. [doi]:10.1038/nbt.4163 {PMID}:29979655 PMCID:PMC6870991

Open-source software and data platform that enables data sharing, integration, and analysis of microbes, plants, and their communities. KBase maintains an internal reference database that consolidates information from widely used external data repositories; such as Genomes, Protein, Protein Interaction data, and in the near future: Communities data, Expression data, MAK biclusters, Phenotype data, etc.


METLIN: Metabolite and Tandem MS Database  METLIN metabolite logo

PI: Gary Siuzdak

URL: http://metlin.scripps.edu/index.php
Contact: Paul Benton | [email protected]

Reference: Zhu, Z.J; A.W. Schultz, J. Wang, C.H. Johnson, S.M. Yannone, G.J. Patti and G. Siuzdak (2013) Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nature Protocols. [doi]:10.1038/nprot.2013.004. {PMID}:23391889 PMCID:PMC3666335

Repository of over 75,000 endogenous and exogenous metabolites that include metabolites from essentially any living creature, including bacteria.


MicrobesOnline microbesonline

PI: Adam P. Arkin

URL: http://microbesonline.org
Contact: Morgan Price | [email protected]

Reference: Dehal, P.S.; M.P. Joachimiak, M.N. Price, J.T. Bates, J.K. Baumohl, D. Chivian, G.D. Friedland, K.H. Huang, K. Keller, P.S. Novichkov, I.L. Dubchak, E.J. Alm and A.P. Arkin (2010) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research. [doi]:10.1093/nar/gkp919 {PMID}:19906701 PMCID:PMC2808868

Database, browser, and tools for comparative and functional genomics.


MicroDesignhelix

PI: Jizhong Zhou

URL: http://www.ou.edu/ieg/tools/data-analysis-pipeline.html
Contact: Naijia Xiao | [email protected]

Reference: Shi, Z.; Yin, H., Van Nostrand, J.D., Voordeckers, J.W., Tu, Q., Deng, Y., Yuan, M., Zhou, A., Zhang, P., Xiao, N., Ning, D., He, Z., Wu, L., Zhou, J. (2019) Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. mSystems. [doi]:10.1128/mSystems.00296-19 {PMID}:31213523 PMCID:PMC6581690

This pipeline was developed to comprehensively analyze microbial functional genes for the design of Functional Gene Microarrays (FGAs). The program contains multiple modules to download gene sequences, remove low-homology sequences, design oligonucleotide probes, check probe specificity, output selected oligonucleotide probes, and finally store data in local databases. This pipeline is currently in beta testing by internal ENIGMA members, and the designed high throughput microarrays are available to all applicable ENIGMA studies.


Network PortalNetwork Portal

PI: Nitin S. Baliga

URL: http://networks.systemsbiology.net/
Contact: Serdar Turkarslan | [email protected]
Source Code: https://github.com/baliga-lab/network_portal

Reference: Turkarslan, S.; E.J. Wurtmann, W.J. Wu, N. Jiang, J.C. Bare, K. Foley, D.J. Reiss, P. Novichkov, N.S. Baliga (2014) Network Portal: A Database for Storage, Analysis, and Visualization of Biological Networks. Nucleic Acid Research. [doi]:10.1093/nar/gkt1190 {PMID}:24271392 PMCID:PMC3964938

The Network Portal is a database of gene regulatory networks and enables exploration, annotation, and comparative analysis for 13 species.

D. vulgaris Hildenborougxz Regulatory Network Within Network Portal D. vulgaris Regulatory Network

URL: http://networks.systemsbiology.net/dvu

A visual interface for the analysis of D. vulgaris Hildenborough Regulatory Network within the Network Portal. We have initiated a program to perform a high-quality reconstruction of the transcriptional regulatory network (TRN) of DvH and build a predictive model for transcriptional control of its physiology.


OpenMSI: Open Mass Spectrometry Imaging open msi

PI: Trent Northen

URL: https://openmsi.nersc.gov/openmsi/client
Contact: Ben Bowen | [email protected]

Reference: Rübel, O.; A. Greiner, S. Cholia, K. Louie, E.W. Bethel, T.R. Northen, and B.P. Bowen (2013) OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging. Analytical Chemistry. [doi]:10.1021/ac402540a {PMID}:24087878

Advanced science gateway for web-based visualization, analysis, and sharing of extremely large metabolic images.


PaperBLASTPaperBLAST

PI: Adam P. Arkin

URL: http://papers.genomics.lbl.gov/
Contact: Morgan Price | [email protected]

Reference: Price M.N.; and A.P. Arkin (2017) PaperBLAST: Text-mining papers for information about homologs. mSystems. [doi]:10.1128/mSystems.00039-17

Find papers about a protein or its homologs.


RegPrecise RegPrecise

PI: Pavel Novichkov

URL: http://regprecise.sbpdiscovery.org:8080/WebRegPrecise/
Contact: Dimitry Rodionov | [email protected]

Reference: Novichkov, P.S; A.E. Kazakov, D.A. Ravcheev, S.A. Leyn, G.Y. Kovaleva, R.A. Sutormin, M.D. Kazanov, W. Riehl, A.P. Arkin, I. Dubchak and D.A. Rodionov (2013) RegPrecise 3.0 — A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. [doi]:10.1186/1471-2164-14-745 {PMID}:24175918 PMCID:PMC3840689

Database for capturing, visualization, and analysis of transcription factor regulons reconstructed by comparative genomic approaches in a variety of prokaryotic genomes.


Syntrophy Portal syntrophy_portal_logo

PI: Nitin S. Baliga

URL: http://networks.systemsbiology.net/syntrophy/
Contact: Serdar Turkarslan | [email protected]

Reference: Turkarslan, S.; A.V. Raman, A.W. Thompson, C.E. Arens, M.A. Gillespie, F. von Netzer, K.L. Hillesland, S. Stolyar, A. López García de Lomana, D.J. Reiss, D. Gorman-Lewis, G.M. Zane, J.A. Ranish, J.D. Wall, D.A. Stahl, N.S. Baliga (2017) Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment. Molecular Systems Biology. [doi]:10.15252/msb.20167058 {PMID}:28320772 PMCID:PMC5371734

Syntrophy Portal is a web tool to explore gene regulatory network models, genome annotations, and genomic variants for Desulfovibrio vulgaris Hildenborough and Methanococcus maripaludis S2.


XCMS Online: Scripps Center for Metabolomics xcms online

PI: Trent Northen

URL: https://xcmsonline.scripps.edu/
Contact:  Paul Benton | [email protected]

Reference: Huan, T.; E.M. Forsberg, D. Rinehart, C.H. Johnson, J. Ivanisevic, H.P. Benton, M. Fang, A. Aisporna, B. Hilmers, F.L. Poole, M.P. Thorgersen, M.W.W. Adams, G. Krantz, M.W. Fields, P.D. Robbins, L.J. Niedernhofer, T. Ideker, E.L. Majumder, J.D. Wall, N.J.W. Rattray, R. Goodacre, L.L. Lairson, and G. Siuzdak (2017) Systems biology guided by XCMS Online metabolomics. Nature Methods. [doi]:10.1038/nmeth.4260 {PMID}:28448069 PMCID:PMC5933448

Cloud-based metabolomic data processing platform that provides high-quality metabolomic analysis in a user-friendly, web-based format.