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GRENDEL specifications

Information


Unique identifier OMICS_13531
Name GRENDEL
Alternative name Gene REgulatory Network Decoding Evaluations tooL
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data Degree distributions, parameter distributions, experiment design, noise level
Output data Multiple sbml files, one for each rendition of the network, i.e. one for each sample, and a reference file which represents the wildtype; Multiple .prm files, one for each rendition of the network, this format corresponds to an internal representation; A net_topo.csv that is a binary valued adjacency matrix
Output format XML, CSV
Operating system Unix/Linux
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michael Brent

Publication for Gene REgulatory Network Decoding Evaluations tooL

GRENDEL citations

 (3)
library_books

How drugs get into cells: tested and testable predictions to help discriminate between transporter mediated uptake and lipoidal bilayer diffusion

2014
Front Pharmacol
PMCID: 4215795
PMID: 25400580
DOI: 10.3389/fphar.2014.00231

[…] ” Counter: although not especially relevant, the notion of passive lipoidal permeation is in fact traced back to long before the invention of model membrane systems, or even our knowledge (Gorter and Grendel, ) of the bilayer thickness of biological membranes; Smith and colleagues do in fact cite the work of Overton in 1899 that initiated it (Overton, ). We have dealt with correlations enough. […]

library_books

Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe Active Microorganisms

2012
Front Microbiol
PMCID: 3312321
PMID: 22470372
DOI: 10.3389/fmicb.2012.00109

[…] eratures, and Sulfolobales strain MK5-like populations were slightly more abundant in OSPD.Two additional Fe-oxide mat samples evaluated using pyrotag sequencing included locations within Beowulf and Grendel Springs (Figure ). Although similar to end-member amorphous Fe-oxide mats of NGB including the OSP series discussed above, BEE and GRND_L reveal slightly different community types compared to […]

library_books

Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira hyodysenteriae Reveals Adaptations to Its Lifestyle in the Porcine Large Intestine

2009
PLoS One
PMCID: 2650404
PMID: 19262690
DOI: 10.1371/journal.pone.0004641

[…] GenBank and other bacterial genomes.The second stage of annotation used the BLAST program suite to compare the predicted nucleotide and protein ORF sequences on the CCG (http://ccg.murdoch.edu.au/) Grendel HPC system against the following databases 1) NCBI non-redundant protein and patent databases (http://www.ncbi.nlm.nih.gov/) 2) String version 7 database built on Unicellular (COGs) and Euka […]

Citations

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GRENDEL institution(s)
Center for Genome Sciences and Department of Computer Science, Washington University, St Louis, MO, USA
GRENDEL funding source(s)
National Human Genome Research Institute (grant T32 HG000045) and Washington University

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