Scope

Scope of the Special Session

Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Integrative Bioinformatics is a new area of research using the tools of computer science and electronic infrastructure applied to Biotechnology.

We solicit submissions that describe the use of Immersive Analytics for data analysis in biology and Bioinformatics – potential topics include (but are not limited to):

  • Virtual and Augmented Reality approaches for data analysis
  • Semi- and fully immersive data exploration
  • Metabolic and Regulatory Network Modelling and Simulation
  • Data Integration and Text Mining Approaches
  • Signal Pathways and Cell Control
  • Network Analysis
  • Medical Informatics, Biomedicine and Biotechnology
  • Integrative whole cell and molecular modelling
  • Visual Analytics, Visualization, and Animation

The special session proceedings  can be found here!

Program

 This double session is jointly sponsored by:
Stereoscopic Displays and Applications XXIX, and
the Engineering Reality of Virtual Reality 2018.

Stereoscopic Applications:
VR to Immersive Analytics in Bioinformatics 1

Tuesday January 30, 2018, 8:50 – 10:10 AM 

Mesoscopic rigid body modeling of the ExtraCellular Matrix’s self assembly, Hua Wong, Nicolas Belloy, and Manuel Dauchez; University of Reims Champagne-Ardenne (France)

Semantics for an integrative and immersive pipeline combining visualisation and analysis of molecular data, Mikael Trellet2, Nicolas Ferey2, Patrick Bourdot2, and Marc Baaden1; 1IBPC and 2LIMSI (France)

3D-stereoscopic modeling and visualization of a Chlamydomonas reinhardtii cell, Niklas Biere4, Mehmood Ghaffar4, Daniel Jäger4, Anja Doebbe4, Nils Rothe4, Karsten Klein2,3, Ralf Hofestädt4, Falk Schreiber1,3, Olaf Kruse4, and Björn Sommer1,3; 1University of Konstanz, 2University of Konstanz, Germany, 3Monash University (Australia), and 4Bielefeld University (Germany)

Immersive analysis and visualization of redox signaling pathways integrating experiments and computational modelling, Alexandre Maes2, Karen Druart1, Sean Guégan1, Xavier Martinez1,3, Christophe Marchand2, Stéphane Lemaire2, and Marc Baaden1; 1Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, 2Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Université Paris 06, and 3CNRS-LIMSI, VENISE team, Univ Paris-Sud (France)

Session Chair: Björn Sommer, University of Konstanz (Germany)

Stereoscopic Applications:
VR to Immersive Analytics in Bioinformatics 2

Tuesday January 30, 2018, 4:30 – 5:30 PM

Christoph Müller, Michael Krone, Markus Huber, Verena Biener, Guido Reina, Daniel Weiskopf, and Thomas Ertl; University of Stuttgart (Germany)

Molecular Dynamics Visualization (MDV): Stereoscopic 3D display of biomolecular structure and interactions using the Unity game engine, Michael Wiebrands, Chris Malajczuk, Andrew Woods, Andrew Rohl, and Ricardo Mancera; Curtin University (Australia)

Session Chair: Marc Baaden, IBPC (France)

SD&A/ERVR

Stereoscopic Displays and Applications XXIX

29 Jan – 31 Jan 2018, Burlingame, California

Since 1990, SD&A focuses on developments covering the entire stereoscopic 3D imaging pipeline from capture, processing, and display, to perception. SD&A XXIX will be held as part of the 2018 IS&T International Symposium on Electronic Imaging: Science and Technology at the Hyatt Regency San Francisco Airport, Burlingame, California, USA. The conference brings together practitioners and researchers from industry and academia to facilitate an exchange of current information on stereoscopic imaging topics.

http://stereoscopic.org

The Engineering Reality of Virtual Reality 2018

30 Jan – 1 Feb 2018, Burlingame, California

Virtual and augmented reality systems are evolving. In addition to research, the trend toward content building continues and practitioners find that technologies and disciplines must be tailored and integrated for specific visualization and interactive applications. This conference serves as a forum where advances and practical advice toward both creative activity and scientific investigation are presented and discussed. Research results can be presented and applications can be demonstrated.

http://www.imaging.org/site/IST/IST/Conferences/EI/EI_2018/Conference/C_ERVR.aspx

CfP

Call for Papers

February 2018, Burlingame, California, USA

Call For Papers
Special Session at the Stereoscopic Displays and Applications XXIX, Burlingame, California
Special Issue of the Journal of Integrative Bioinformatics, vol 15, de Gruyter Berlin

Bioinformatics usually deals with the smallest entities of life, therefore, visualization plays an important role in this field. Stereoscopic rendering has already been used for a long time for visualizing biological structures, dating back to the first hype of virtual reality technologies 25 years ago when the CAVE was invented and Head-Mounted Displays (HMD) became affordable. Triggered by the success of new, modern HMDs such as Oculus Rift and HTC Vive, Virtual Reality has recently gained a lot of attention again. On the other hand, a new generation of large-scale “computational microscopes” is being established, such as the CAVE2, representing large, nearly 360 degree-spanning visualization facilities.

At the same time, advanced “Visual Analytics” solutions have become an important tool in all areas of scientific data analysis, combining visualization, data mining and analysis methods, and user interaction. Uniting both VR and VA, “Immersive Analytics” now starts to make use of new technologies, immersing the scientist into the data, and, in the best case, enabling advanced insights.

This special issue will focus on:

  • What is the legacy of the past?
  • Which approaches (partly) failed, and which success stories were triggered by Virtual/Augmented Reality in the context of Bioinformatics?
  • Which new ideas exist to approach now immersive analysis of biological data?
  • Which methods, technologies and/or applications are expected to change the way we see and perceive biology?

Key Dates

  • August 15, 2017: Abstract to SD&A 2018
  • Deadline Extension: September 10, 2017: Abstract to SD&A 2018
  • September 18, 2017: Abstract Acceptance Notification
  • November 17, 2017: Registration Opens
  • January 5, 2018: Hotel Reservation Deadline
  • January 8, 2018: Early Registration Deadline
  • January 10, 2018: Full manuscript submission due to JIB
  • January 28, 2018: Conference starts
  • January 30, 2018: Conference Presentation
  • April 2018: Review and revision process finished
  • May to June 2018: Publication of accepted papers

The special session proceedings  can be found here!

Organizers

  • Bjorn Sommer, University of Konstanz, Germany/
    Monash University, Melbourne (main contact)
  • Marc Baaden, Institut de Biologie Physico-Chimique, Paris
  • Michael Krone, University of Stuttgart, Stuttgart
  • Andrew Woods, Curtin University, Perth

For more information, please contact us via email:

VR2IAinBioInf@immersive-analytics.org

 

JIB

Journal of Integrative Bionformatics

The Journal of Integrative Bioinformatics (JIB) is an international open access journal publishing original peer-reviewed research articles covering all aspects of integrative bioinformatics. It was established in 2004 and joined the Open Access family of de Gruyter – one of the oldest German publishers – in 2017. JIB (ISSN 1613-4516) is indexed by PubMed, DBLP Computer Science Bibliography, SCOPUS and Google Scholar.

https://www.degruyter.com/view/j/jib

For 2017 and 2018 there is no publication fee for articles accepted and published by JIB!

Submission

Submit here you 500-word abstract (use option 2 – presentation only), as the full paper will be submitted to our journal in the next step (Deadline: September 10, 2017).

http://stereoscopic.org/2018/index.html#submit

Please follow the SD&A guidelines for writing the abstract. During the abstract submission process, please add the keyword “Bioinformatics” to indicate the special session.

http://stereoscopic.org/2018/index.html#sag

Please submit here your full paper (Deadline: January 10, 2018).

https://mc.manuscriptcentral.com/dgjib

More info and templates you will find here:

https://www.degruyter.com/view/j/jib

Journal Templates:

JIB_word_template_2017_2

JIB_LaTeX_Template_v7_2017

Review Process

Each abstract and the corresponding paper submitted to this special session/special issue will be rigorously evaluated in a peer review process. Accepted papers will appear in a special issue of the Journal of Integrative Bioinformatics (JIB). By submitting an abstract, the author(s) agree that, if their abstract is accepted, they will:

  • Submit a full manuscript version to de Gruyter on or before the paper deadline.
  • Register at least one author to attend the conference on or before the registration deadline.
  • Attend the conference (at least one author).
  • Present the accepted paper at the conference.