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Protocols

SimBac specifications

Information


Unique identifier OMICS_20604
Name SimBac
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data Some files of simulated sequences, the clonal genealogy, the local tree contained in the simulated data and a full description of the graph representing the ancestry of the sample.
Output format FASTA, XMFA, Newick
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
GNU Scientific Library
Maintained Yes

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Documentation


Maintainer


  • person_outline Nicolan de Maio

Publication for SimBac

SimBac citations

 (5)
library_books

Computer simulations for assessing cognitively intensive instrumental activities of daily living in older adults

2018
PMCID: 5857723
PMID: 29560411
DOI: 10.1016/j.dadm.2018.01.008

[…] details the results for the receiver operating characteristics analyses using the SIMBAC TA score to predict group membership. AUC was greatest when distinguishing NI participants from DM participants (AUC: 0.97), with almost perfect classification (97%). The AUCs for other group c […]

call_split

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome Based and Gene Based Phylogenetic Trees

2018
Evol Bioinform Online
PMCID: 5826093
PMID: 29511354
DOI: 10.1177/1176934318759299
call_split See protocol

[…] etic study of 12 isolates of Prochlorococcus marinus performed by Prabha et al was used. Simulated data sets with different numbers of isolates (10, 20, 30, 40, and 50) were created using the program SimBac with default parameters as stated in the Web site https://github.com/tbrown91/SimBac. For each data set, 10 simulations were produced. […]

call_split

Development of a video simulation instrument for assessing cognition in older adults

2017
BMC Med Inform Decis Mak
PMCID: 5719572
PMID: 29212493
DOI: 10.1186/s12911-017-0557-7
call_split See protocol

[…] which the instrument as well as its administration could be improved. Phase 3 included a full-scale validation study with a larger sample of participants and led to the creation of a final version of SIMBAC intended for release.Fig. 1 […]

library_books

Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus

2017
PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] n recombination has been shown to have no effect on SFS-based methods of demographic inference in bacteria (). However, external sources of recombination were not modeled in previous studies. We used SimBac () to simulate bacterial populations with a range of internal and external recombination rates. Similarly to previous studies, we found that within-population recombination had no effect on the […]

library_books

Inter and intra specific pan genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation

2013
BMC Genomics
PMCID: 3833655
PMID: 24112474
DOI: 10.1186/1471-2164-14-693

[…] We used SimBac (http://sourceforge.net/projects/bacsim/), a software package for simulating bacterial genome evolution, to predict the total number of genomic lineages in local B. burgdorferi s.s. populations […]

Citations

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SimBac institution(s)
Doctoral Training Centre, University of Oxford, Oxford, UK; Department of Infectious Disease Epidemiology, Imperial College, London, UK; Institute for Emerging Infections, Oxford Martin School, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
SimBac funding source(s)
Supported by the Engineering and Physical Sciences Research Council (EP/F500394/1); the Biotechnology and Biological Sciences Research Council (BB/L023458/1); the National Institute for Health Research (HPRU-2012-10080); the Wellcome Trust. and the Royal Society (101237/Z/13/Z); and the Oxford Martin School.

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