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Aquaria specifications


Unique identifier OMICS_12255
Name Aquaria
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Aquaria

Publication for Aquaria

Aquaria citations


Challenges for visualizing three‐dimensional data in genomic browsers

PMCID: 5638070
PMID: 28771695
DOI: 10.1002/1873-3468.12778

[…] be classified by its density, activity, or accessibility . Indeed, the application of validation in browsers for 1D and 2D data already assists, but is far behind for, the classification of 3D data. Aquaria is a successful example of the use of precalculated classifications in the study and analysis of protein structures. Aquaria not only integrates 3D models with sequence data but also assists a […]


Lessons from the first dorsal fin in atheriniforms—A new mode of dorsal fin development and its phylogenetic implications

PMCID: 5434871
PMID: 28370120
DOI: 10.1002/jmor.20679
call_split See protocol

[…] si (Ahl, 1936), Melanotaenia lacustris (Munro, 1964) and Popondichthys furcatus (Nichols, 1955) and one cyprinodontiform species (Pachypanchax omalonotus [Duméril, 1861]) were attained by breeding in aquaria (zoological garden permit HAST/ZOO/05/430/2005 issued by Staatliches Amt für Umwelt und Natur Stralsund). Before storage in 70% ethanol, larvae were euthanized using an overdose of benzocain a […]


Comparative visualization of protein secondary structures

BMC Bioinformatics
PMCID: 5333176
PMID: 28251875
DOI: 10.1186/s12859-016-1449-z

[…] r globally.As the domain experts need to fully understand molecular mechanisms to find related structures with respect to sequence-based features, Stolte et al. integrated a visual analysis [] in the Aquaria system []. The representation aims to encode the structural matches and differences of similar molecules only in the juxtaposed protein chains which can be hard to interpret. On the other hand […]


PyMine: a PyMOL plugin to integrate and visualize data for drug discovery

BMC Res Notes
PMCID: 4590260
PMID: 26429562
DOI: 10.1186/s13104-015-1483-3

[…] for visualization and analysis of molecular structures and related data []. Both Cytoscape and Chimera are stand-alone software packages and were not developed exclusively for drug discovery purpose. Aquaria [] and PDBpaint [] were developed to retrieve features from various databases and map them onto the protein structures. Both programs focus primarily on structural features such secondary stru […]


Integrated visual analysis of protein structures, sequences, and feature data

BMC Bioinformatics
PMCID: 4547178
PMID: 26329268
DOI: 10.1186/1471-2105-16-S11-S7
call_split See protocol

[…] The development of the Aquaria user interface was an iterative, user-centred design process, based upon understanding of users, tasks, and context. Visual mock-ups were created in Adobe Illustrator and Adobe Photoshop for e […]


Individually Unique Body Color Patterns in Octopus (Wunderpus photogenicus) Allow for Photoidentification

PLoS One
PMCID: 2579581
PMID: 19009019
DOI: 10.1371/journal.pone.0003732
call_split See protocol

[…] We solicited photographs from fifteen underwater photographers known to document W. photogenicus in the wild, as well as people known to have kept them in aquaria. We had specifically requested images taken of the dorsal mantle from above because this view allows easy comparison of spot patterns, and it can be photographed easily.Images depicting the do […]


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Aquaria institution(s)
Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia; School of Molecular Bioscience, The University of Sydney, Sydney, Australia; School of Information Technologies, The University of Sydney, Sydney, Australia; Department for Bioinformatics and Computational Biology, Technische Universität München, Munich, Germany; Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Instituto de Sistemas e Robótica, Lisboa, Lisbon, Portugal; St. Vincent's Clinical School, The University of New South Wales (UNSW), Sydney, Australia
Aquaria funding source(s)
This work was supported by CSIRO’s OCE Science Leader program and its Computational and Simulation Sciences platform, as well as the Alexander von Humboldt Foundation.

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