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Protocols

SBEAMS specifications

Information


Unique identifier OMICS_01011
Name SBEAMS
Alternative name Systems Biology Experiment Analysis Management System
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Eric W. Deutsch

Publication for Systems Biology Experiment Analysis Management System

SBEAMS citations

 (22)
library_books

Improvement of peptide identification with considering the abundance of mRNA and peptide

2017
BMC Bioinformatics
PMCID: 5311845
PMID: 28201984
DOI: 10.1186/s12859-017-1491-5

[…] e can be downloaded at NCBI’s Gene Expression Omnibus (GEO) repository and PeptideAtlas [RNA-Seq data: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1104129; MS/MS data: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?identifier=PASS00215]. The RNA-Seq and proteomics data sets of mouse liver can be downloaded at Short Read Archive and iProx [RNA-Seq data: www.ncbi.nlm.nih.gov/sra/S […]

library_books

The lysine methyltransferase Ehmt2/G9a is dispensable for skeletal muscle development and regeneration

2016
PMCID: 4882833
PMID: 27239264
DOI: 10.1186/s13395-016-0093-7

[…] digestion alone or by any commonly used digestion method. The reported MYOD peptide is also not found in the tandem mass spectrometry proteomics repository PeptideAtlas (https://db.systemsbiology.net/sbeams/cgi/shortURL?key=1mk36ybs). More intriguingly, the proposed mechanism [] was based on liquid chromatography–mass spectrometry (LC-MS) results, showing that the different methylation states of t […]

call_split

Prediction of colorectal cancer diagnosis based on circulating plasma proteins

2015
PMCID: 4568950
PMID: 26253081
DOI: 10.15252/emmm.201404873
call_split See protocol

[…] PeptideProphet (Keller et al, ) and ProteinProphet (Nesvizhskii et al, ), respectively. Data and search results were uploaded to the PeptideAtlas and can be accessed at https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=374. […]

library_books

Identification and Validation of Potential New Biomarkers for Prostate Cancer Diagnosis and Prognosis Using 2D DIGE and MS

2015
Biomed Res Int
PMCID: 4312578
PMID: 25667921
DOI: 10.1155/2015/454256

[…] If all of the above criteria were met, peptides were ranked based on their previous detection using both The GPM (http://gpmdb.thegpm.org/index.html) and Peptide Atlas (https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search) databases. All of the SIS-peptides used in this study are listed in Supplementary Table 8. […]

call_split

The Worker Honeybee Fat Body Proteome Is Extensively Remodeled Preceding a Major Life History Transition

2011
PLoS One
PMCID: 3182174
PMID: 21969861
DOI: 10.1371/journal.pone.0024794
call_split See protocol

[…] sed on one peptide it was 0.6%). Peptide ratios were averaged in order to obtain a protein ratio. The data is accessible at the Honey Bee PeptideAtlas, March 2010 Build (https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=282). […]

library_books

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

2011
BMC Bioinformatics
PMCID: 3062597
PMID: 21385461
DOI: 10.1186/1471-2105-12-71

[…] ronic lab notebooks, alteration or addition of data types typically requires database alterations[]. Tools designed for integrating raw research data often work only with specific data formats (e.g., SBEAMS[], caIntegrator[] and GenePattern[]) or support the introduction or extension of data types only when the system is not running (e.g., Intermine[]). Even when tools provide flexibility in defin […]

Citations

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SBEAMS institution(s)
Institute for Systems Biology, Seattle, WA, USA

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