BioNet protocols

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BioNet specifications

Information


Unique identifier OMICS_06989
Name BioNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for BioNet

BioNet in pipeline

2010
PMCID: 3017767
PMID: 20565887
DOI: 10.1186/1471-2164-11-386

[…] available s/mar analysis tools - marfinder (downloaded from http://genomecluster.secs.oakland.edu/marwiz/) smartest (http://www.genomatix.de/smartest.html), marscan (emboss) and chrclass (http://ftp.bionet.nsc.ru/pub/biology/chrclass/chrclas2.zip). the tools and the description of the datasets as well as the parameter information were done according to evans et al [], with modifications wherever […]


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BioNet in publications

 (228)
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] a global relationship between mirna expression and the microbiome in crc., overview of analysis. paired tumor and normal tissues were collected from 44 crc patients by the university of minnesota’s bionet as a part of a previous study. the 16s rrna gene sequencing was performed earlier, as a part of the previous study. the small rnas were sequenced on an illumina hiseq 2000 platform. a detailed […]

PMCID: 5945850
PMID: 29748583
DOI: 10.1038/s41598-018-25582-7

[…] rates., target data of the anti-inflammatory markers were excavated and the target information of candidate components were derived from stitch (http://stitch.em-bl.de/), batman-tcm (http://bionet.ncpsb.org/batman-tcm), tcmid (https://omictools.com/traditio), tcmsp (http://ibts.hkbu.edu.hk/lsp/tc) and chembl (https://www.ebi.ac.uk/chembl/). stitch database could generate a score […]

PMCID: 5943519
PMID: 29743638
DOI: 10.1038/s41598-018-24481-1

[…] noncoding rna potential from the three candidate regions, respectively, and calculated the nucleosome formation potential for candidate intergenic regions using the recon web service (http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/) with default settings. 1 kb regions with the lowest nucleosome formation potential were preferred and indicated by black circles (fig. ).figure 1, for the three […]

PMCID: 5961220
DOI: 10.1167/iovs.17-23536

[…] this program applies a restriction on pedigree size, 8 of the 15 pedigrees were split into nonoverlapping fragments of ≤18 bits using the pedstr program (provided in the public domain, http://mga.bionet.nsc.ru/soft/pedstr/pedstr.tar.gz), which breaks inbreeding loops and identifies subpedigrees having the maximal total relationship between individuals of interest, resulting in a total of 26 […]

PMCID: 5932995
PMID: 29744384
DOI: 10.17245/jdapm.2018.18.2.97

[…] end-tidal co2 partial pressure and respiratory rate were measured via a capnography monitoring device (loflotm co2 sensor, respironics co. inc, mn, usa) and recorded with a patient monitor (bm7, bionet, seoul, korea) (). an rra sensor (masimo corp., irvine, ca, usa) was attached to each subject's right cervical area near the trachea for the monitoring of respiratory rate ()., the clinical […]


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BioNet institution(s)
Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany

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