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Protocols

BaMBa specifications

Dataset

Information

Unique identifier	OMICS_12502
Name	BaMBa
Alternative name	Brazilian Marine Biodiversity
Restrictions to use	None
Community driven	No
Data access	File download, Browse
User data submission	Allowed
Maintained	Yes

Maintainer

BaMBa Team

Publication for Brazilian Marine Biodiversity

BaMBa: towards the integrated management of Brazilian marine environmental data

2015

PMCID: 4600340

PMID: 26454874

DOI: 10.1093/database/bav088

BaMBa citations

(6)

Application of a newly developed software program for image quality assessment in cone beam computed tomography

2017

PMCID: 5489672

PMID: 28680843

DOI: 10.5624/isd.2017.47.2.75

[…] pen-source software and allows one to add, adjust, or implement other functions within the plugin. Since ImageJ is free software, this is an inexpensive method, as it does not require a user license. Bamba et al. considered this approach very useful and encouraged the development of plugins in ImageJ to evaluate image quality in CBCT with phantoms. Donini et al. showed the feasibility of software […]

Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil)

2016

PLoS One

PMCID: 4993507

PMID: 27548380

DOI: 10.1371/journal.pone.0161168

[…] 4644.3, 4564648.3, 4564643.3, 4564645.3; and fasta files are available at https://marinebiodiversity.lncc.br/files/index.php/s/3HqRMATuGDQWDU6 (fthompson.6.1) (Brazilian Marine Biodiversity Database, BaMBa). […]

The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan

2016

Front Microbiol

PMCID: 4976104

PMID: 27551278

DOI: 10.3389/fmicb.2016.01185

See protocol

[…] aensis, V. communis, V. campbellii, and P. damselae subsp. piscicida, a >99.7% cutoff was adopted to affiliate species. All pyrH and 16S rRNA genes sequences used in this study have been deposited in BaMBa under data package identification number pmeirelles.20.1. To further affiliate unassigned pyrH clusters to new species candidates, 16S rRNA gene sequences of 38 representative strains from pyrH […]

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps

2016

Sci Rep

PMCID: 4764845

PMID: 26905381

DOI: 10.1038/srep21631

See protocol

[…] est sea cucumbers, we used the MG-RAST workbench tool implementing KEGG Orthology and GenBank databases to annotate with the functional features.All sequences generated in this study are deposited in BaMBa under data package identification number pmeirelles.19.1, and DDBJ/GenBank/EMBL database under BioProject number PRJDB4366. […]

Insights into the Microbial and Viral Dynamics of a Coastal Downwelling Upwelling Transition

2015

PLoS One

PMCID: 4556663

PMID: 26327119

DOI: 10.1371/journal.pone.0137090

[…] y available in the MG-Rast website, where it is deposited as part of the “Upwelling Arraial do Cabo” project (http://metagenomics.anl.gov/linkin.cgi?project=2518), or alternatively it is available in BAMBA (Meirelles et al. in press), under project identifier (https://marinebiodiversity.lncc.br/metacatui/#view/pmeirelles.17.1).” […]

MSClust: a tool for unsupervised mass spectra extraction of chromatography mass spectrometry ion wise aligned data

2011

Metabolomics

PMCID: 3397229

PMID: 22833709

DOI: 10.1007/s11306-011-0368-2

[…] on followed by their chromatographic alignment, i.e. ion-wise alignment, has become a popular approach for comparative metabolomics. Software tools that can implement this approach, such as MetAlign (Bamba and Fukusaki ; Boccard et al. ; De Vos et al. ; Ducruix et al. ; Keurentjes et al. ; Lommen ; Lommen et al. ; Mal et al. ; Peters et al. ; Rijk et al. ; Tikunov et al. ; Tikunov et al. ; Vorst e […]

Citations

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BaMBa institution(s)

Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Federal University of Rio de Janeiro (UFRJ) / COPPE, Rio de Janeiro, RJ, Brazil; National Laboratory for Scientific Computing (LNCC), Petropolis, RJ, Brazil; Department of Environment and Engineering, Federal University of Paraíba, Rio Tinto, PB, Brazil; Rio de Janeiro Botanical Garden Research Institute (IP-JBRJ), Rio de Janeiro, RJ, Brazil; Department of Oceanography and Ecology, Federal University of Espírito Santo (UFES), Vitória, ES, Brazil; Environmental Sciences Laboratory (LCA), Northern Rio de Janeiro State University Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil; Oceanographic Institute, University of São Paulo (IO-USP), Sao Paulo, SP, Brazil; Institute of Coastal Studies, Federal University of Para (UFPA), Braganca, PA, Brasil; Department of Oceanography, Federal University of Pernambuco (UFPE), Recife, PE, Brazil; Division of Marine Biotechnology, Marine Studies Institute Admiral Paulo Moreira, Arraial do Cabo, RJ, Brazil; PESC/COPPE - Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Departament of Marine Biology, Federal Fluminense University (UFF), Niteroi, RJ, Brazil; Laboratory of Enzymology, Department of cellular Biology, Institute of Biology, University of Brasília (UnB), Brasília, DF, Brazil

BaMBa funding source(s)

Carlos Chagas Filho Research Foundation of the Rio de Janeiro State (FAPERJ); National Counsel of Technological and Scientific Development (CNPq); Coordination for the Improvement of Higher Education Personnel (CAPES)

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