ATLAS in silico: Overview  
Overview
System
Data & Mappings
Texts
ATLAS in silico (ATLAS) is an interactive generative virtual environment created utilizing the complete first release of the Global Ocean Sampling Expedition (GOS) oceanic microorganism metagenomics dataset (Parthasarathy, Hill and MacCallum, 2007). The data was collected by the J. Craig Venter Institute(JCVI, no date) to study the genetics of communities of marine microorganisms throughout the world's oceans.
  
 
Subsections:
  1. Description
  2. Exhibitions
  3. Press & Written by Others
  4. Funding
  5. Collaboration
  
     
     
     
Go to top of page Description  
 
ATLAS in silico provides an aesthetic encounter wtih metagenomics data and contextual metadata, and a visceral and poetic experience of data abstraction. Participants are immersed in a dream-like, highly abstract, data-driven virtual world. The aesthetics of fine-lined copper engraving and grid-like layouts of the composite images presenting comparative morphology in 19th Century naturalistic illustration atlases are combined with contemporary digital and algorithmic aesthetics such as wireframes, particle systems, and virtual spatiality.
The virtual environment appears as a vast and multicolored flow of colored particles enveloping the participant. The scale and scope of the environment far exceeds the scale of the human body. It is an unbounded space. The body is immersed inside an ocean of data that is instantiated as shimmering  particles forming currents witin a fluid dynamics simulation. Each particle is one database record from the Global Ocean Sampling Expedition (GOS). Particles move in the virtual environment within a fluid dynamics simultation according to the values within each database record and its metadata, and in relation to the metadata attributes that structure any given region of the virtual space. Each region has characteristic sonic attributes based on the range of metadata from which it is constructed.  Embodied interaction within the virtual environment immerses the body within a new kind of data-driven abstract and poetic spatiality termed a Scalable Metadata Environment (West et al. 2014) that reveals its characteristics through exploration of its dynamic and responsive patterns. Data is procedurally rendered and sonified within this virtual environment at multiple levels of scale and resolution in response to participant interaction. Initially developed for the Varrier™ 100-million pixel auto-stereographic display (Sandin et al., 2005), with 10.1 spatialized audio, and tetherless head and hand tracking running on a 16 node compute cluster, it tours to exhibition venues on a rear-projected stereoscopic VR display with 8.2 spatialized audio, a three workstation compute network and tetherless head and hand tracking.
Embodied interaction within the virtual environment is designed to recapitulate the scientific processes of sampling, data collection, analysis and interpretation. Making aesthetic use of the scale and physical structure and display surface of the Varrier semi-circular display system, the interaction includes reaching and streching motions to reach into the virtual world and beyond the display to "capture" / "collect" samples of data particles from the virtual fluid/ocean of data. 
 
     
     
     
 
Video: (2:02 duration) of ATLAS in silico on the Varrier 100-million pixel autostereographic display system.
 
     
     
     
 
Video:  (2:55 duraction) of ATLAS in silico on stereoscopic 3D rear projection based display system
  
     
     
     
Go to top of page Exhibitions  
 
Museum of Old and New Art (MONA), MONAFOMA Festival, Hobart, Tasmania, Australia, 2017
50th Anniversary Exhibition of Nine Evenings, 9e2 Seattle, King Station, Seattle Washington, USA, 2016
National Academy of Sciences / Keck Futures Initiative Exhibition, Beckman Center, Irvine, California, USA, 2015
Algorithmic Shape Grammar Objects from ATLAS in silico exhibited in "Out of the Box" Mobile AR Exhibition, San Francisco, California, USA 2012
ACM SIGGRAPH 2009 Art Gallery: Information Aesthetics Showcase: meta-shape grammar objects exhibited along with stereogram, USA 2009
File09 CAVE, Centro Cultural Fiesp Ruth Cardoso, Sao Paolo, Brazil
Algorithmic Shape Grammar Objects from ATLAS in silico exhibited in, Scalable Relations Exhibition, (Curator: Christiane Paul) UC Santa Barbara, California, USA 2009
Los Angeles Municipal Art Gallery, Los Angeles, California, USA, 2009
Ingenuity Festival, Cleveland, Ohio, USA, 2008
  
     
Go to top of page Press & Written by Others  
 
Digitized Ocean the New Wave
David Beniuk
The Mercury, Australia
January 22, 2017
Read: PDF
MOFO Brings Art and Science Together for 3D Experience David Beniuk
The Mercury, Australia
January 22, 2017
Read: PDF
ATLAS in silico featured listing for 9e2 Seattle New Music World
October 21, 2016
http://www.green-wave-email.com/mailsrvc/html/201610210001901.html
9e2 Brings Tech and Art Together Again T.S. Flock
Seattle Weakly, August 31, 2016
http://www.seattleweekly.com/arts/9e2-brings-tech-and-art-together-again/
Can Art Communicate Big Data at a Glance?
The Chronicle of Higher Education
December 13, 2013, Pg. A10-11
Featured in Journal article written by others:
M. Jue, Proteus and the Digital: Scalar Transformations of Seawater's Materiality in Ocean Animations, Animation: An Interdisciplinary Journal, 2014, Vol. 9(2) 245-260, SAGE Publications, DOI: 10.1177/1746847714526671
Featured in book written by others:
M. Jue, Wild Blue Media: Thinking through Seawater. Durham: Duke University Press Books, 2020. ISBN: 978-1-4780-0697-8
Featured in book written by others:
S. Wildevuur, "Invisible Vision: Could Science learn from the Arts?" in Invisible Vision: Could Science learn from the Arts?, 2009.
 
     
     
Go to top of page Funding  
 
Funding for development and exhibition of the artwork includes:
US National Science Foundation (NSF) IIS 084103 Grant: $101,457 USD
CAMERA funding: $25,000 USD
Calit2 funding: $25,000 USD
Meyer Sound Laboratories, in-kind $15,000 USD
CPNAS / NAKFI, sponsorship for exhibition, cash/in-kind $15,000 USD
NVIDIA University Professor Partnership: in-kind $10,000 USD
Da-Lite Screen Company: in-kind $10,000 USD
Ingenuity Festival Cleveland, funding: $5,000 USD
Mechdyne/VRco, in-kind: $2,500
ActivMotif/TimeLogic funding: $500 USD
In-kind computational resources: SDSC, EVL, NCMIR, CENS.
Funding provided support for collaborator and student participation, materials, fabrication, and exhibition costs. The US National Science Foundation (NSF) is one of several major federal agencies created by the US congress to support research and the creation of knowledge. NSF funding is peer reviewed and highly competitive, with funding rates in the IIS (Information and Intelligent Systems) program, which awarded the NSF grant for this research, ranging as low as 7% in 2016, the year with most recent publicly available data. In 2008, the year of this NSF grant award, the fund rate was 14% (Kaplan, 2016). Additional sponsorship for the project, such as exhibition support, industry in-kind (E.g. NVIDIA, Da-Lite, Meyer Sound) and support from CAMERA and Calit2 are also highly competitive.
  
     
     
Go to top of page Collaboration  
 
ATLAS in silico was conceptualized and created at University of California, San Diego, whilst I was acting as diector of visual analytics and interactive technologies at the National Center for Microscopy and Imaging Research (NCMIR)and concurrently affiliated with the UCSD Center for Research in Computing and the Arts (CRCA). Following its initiation at UCSD, I have continued to develop this research whilst acting as founder/director of xREZ Art + Science Lab at University of North Texas. It was developed in collaboraiton with scientists, composers, technologists and students as part of an art + science collaboration. Members of the art + science collaboration have changed as the project has undergone multiple phases of development and exhibition.
In addition to West the collaboration has included (alphabetical order): Kayo Arima, Tommy Chheng (*), Tom Casey(*), Sam Fernald(*), Paul Gilna, Javier Girardo, Joachim Gossmann(*), Ben Hackbarth(*), Tom Henthorn, Alex Horn, Violet Johnson(*), Mason Katz, JP Lewis, Jeff Lien(*), Weizhong Li, Andrew Prudhomme, Todd Margolis, Iman Mostafavi(*), Jurgen Schulze, Rajvikram Singh, Daniel Tenedorio(*), Toshiro Yamanda(*), I Chen Yeh(*). Scientific Consultants: Kayo Arima, Paul Gilna, Weizhong Li. Note: (*) denotes students at the time of their participation. Not all collaborators participated in all phases of the project.
As project director, I led the project, its conceptualization and creative direction, research, project development, management, fundraising and production (including visuals, interface/interaction design, metadata environment design, data analysis, multiscale visual and auditory data mapping design for scalable representations). My collaborators included: Margoliz, Schulze and Lewis whose roles included idea and project development and programming. Gossmann and Hackbarth's role included composition and sound design, spatialization and programming. Girardo, Henthorn, Horn, Margolis, Mostafavi, Prudhomme, Singh and Schulzes roles included display, compute clulster, and development and programming. Yeh and Johnsons role includes programming and exhibition support. Chheng, Casey, Lien, Fernald and Yamada participated as part of projects for courses or through summer internships assisting with general production tasks and exhibition support.
Data was supplied by Global Ocean Sampling Expedition/CAMERA (Scientific) collaborators: PaulGilna was executive director of the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis project (CAMERA) which computed the assembly of, and hosted the online repositories for, the Global Ocean Sampling expedition (GOS) metagenomics dataset. Gilna along with CAMERA/GOS researchers Kayo Arima, Mason Katz and Weizhong Li, provided the GOS dataset and bioinformatics/scientific collaboration and consultation.
  
     
Go to top of page References  
 
  • Global Ocean Sampling Expedition (GOS). (no date). J. Craig Venter Institute. Available from https://www.jcvi.org/research/gos/ [Accessed 10 May 2021].
  • Parthasarathy, H., Hill, E. and MacCallum, C. (2007). Global Ocean Sampling Collection. PLOS Biology, 5 (3), e83. Available from https://doi.org/10.1371/journal.pbio.0050083.
  • NSF.gov. (no date). NSF - National Science Foundation. Available from https://www.nsf.gov/ [Accessed 15 July 2020].
  • Kaplan, N. (2016). NSF, National Science Foundation, Funding Rate History. Available from https://catalog.data.gov/dataset/nsf-funding-rate-history-web-api [Accessed 15 July 2020].
  • National Center for Microscopy and Imaging Research | NCMIR. (no date). Available from https://a.ncmir.ucsd.edu/ [Accessed 30 May 2021].
  
     
     
     
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