Program

The workshop will be one and a half days. The first day is primarily aimed at the communication between the biomedical and the informatics communities. The second (half) day is intended for more informatics-focused discussions, thus mostly, but by no means exclusively, targeting computer scientists from the SICSA and INCF UK groups. 


Presentations are primarily by invitation, but we have kept some slots open for participants who would like to propose their own talk. If you are interested in presenting at the workshop, please get in touch with the organisors (see contact details) with a title and a short abstract. 


Day 1: Cross-Community Interaction

The morning of the first day will provide a general introduction to Atlas Informatics and describe a range of existing atlas systems. Presentations will focus on currently available and potential future atlas application features, rather than detailed discussions of the underlying informatics techniques. The aim here is to give the end user community an up-to-date review of the current state of the art of the field.

The following talks will focus on the requirements and challenges in Atlas Informatics, discussed by experts from the biomedical user community. The use cases will be drawn from biomedical research as represented by scientists at the MRC Human Genetics Unit, clinical applications and the field of neuroscience. Group discussions are planned to foster focused discussions in selected areas. 


Agenda (Day 1):

  • 9.00 - 9.30:  Coffee and Registration
  • 9.30 - 9.40:  Welcome and Introduction to Biomedical Atlases,
    Prof Richard Baldock (MRC Human Genetics Unit, IGMM, UK);
  • 9.40 - 11.00:  Atlas Systems:
    • 9.40 - 10.00: The Virtual Fly Brain; Prof Douglas Armstrong (Edinburgh University, UK);  [details]
    • 10.00 - 10.20: New Dimensions to eMouseAtlas; Dr Chris Armit (MRC Human Genetics Unit, IGMM, UK); [details]
    • 10.20 - 10.40: The Scalable Brain Atlas and the 3d Brain Atlas Reconstructor; Dr Piotr Majka (Nencki Institute of Experimental Biology, Poland); [details]
    • 10.40 - 11.00: The INCF Digital Atlas Infrastructure; Dr Ilya Zaslavsky (University of California, San Diego, USA); [details]
  • 11.00 - 11.30: Coffee
  • 11.30 - 12.30:  Atlas Systems / Use Cases:
    • 11.30 - 11.50: Application of Atlases in the Segmentation of Medical Datasets; Dr Ian Poole (Toshiba Medical Visualisation Systems, UK); [details]
    • 11.50 - 12.10:  The use of anatomical atlases on neuroimaging and their importance in clinical research; Dr. Maria del Carmen Valdés Hernández (Brain Research Imaging Centre, University of Edinburgh, UK); [details]
    • 12.10 - 12.30: Using Atlas Informatics to Improve Cancer Treatment; Dr Bill Nailon (NHS Lothian: Department of Oncology Physics, and University of Edinburgh: Edinburgh Cancer Research Centre & School of Engineering, UK); [details]
  • 12.30 - 13.00:  Discussion 
  • 13.00 - 14.00:  Lunch
  • 14.00 - 15.00:  Use Cases:
    • 14.00 - 14.20: A Use Case of Transcriptome Analysis Frameworks in the Web-Accessible Anatomical Space of the Mouse Brain; Yuko Okamura-Oho (RIKEN Advanced Science Institute, Japan); [details]
    • 14.20 - 14.40:  Wnt pathway gene expression: toward comprehensive coverage using a test-case set of functionally related gene expression patterns; Dr Paula Murphy (Trinity College, University of Dublin, Ireland); [details]
    • 14.40 - 15.00:  Large-scale data production requiring new solutions for data integration; Prof Jan G. Bjaalie  (University of Oslo, Norway);  [details]
  • 15.00 - 15.15:  Discussion and Organisation into Groups
  • 15.15 - 15.30:  Coffee
  • 15.30 - 16.15:  Breakout Sessions (in groups);
  • 16.15 - 16.45:  Reporting back from groups;
  • 16.45 - 17.00:  Discussion / Final Comments;
  • 18.30:  Dinner



Day 2: Computational Challenges

Building on the outcomes of the first day, the second (half) day is dedicated to explore the research challenges to the computer science and informatics communities, e.g. SICSA. Questions about how best to abstract and represent biomedical space, how to manage large amounts of image data (Big Data challenge), and how to leverage cloud computing and semantic web technologies in atlas informatics, will be discussed. A number of technical presentations in the above areas will be combined with further group discussions to identify what research challenges need to be tackled to support the next generation of biomedical atlas systems. The discussions are intended to be technical and thus primarily aimed at informatics researchers, although of course all others are equally welcome to attend. 


Agenda (Day 2):

  • 9.00 - 9.15:  Coffee and Registration
  • 9.15 - 9.30:  Recap of Day 1; [details]
  • 9.30 - 11.00: Technical Presentations:
    • 9.30 - 9.50:  Brain Atlas Systems and Ontologies; Dr David Osumi-Sutherland (Cambridge University, UK); [details]
    • 9.50 - 10.10:  Spatio-temporal Biological Process Modelling; Dr Vashti Galpin (Edinburgh University, UK); [details]
    • 10.10 - 10.30:  Large Deformation Atlas Registration; Dr Bill Hill (MRC Human Genetics Unit, UK); [details]
    • 10.30 - 10.50:  Atlas Interoperability Challenges; Dr Ilya Zaslavsky (University of California, San Diego, USA); [details]
    • 10.50 - 11.10:  Scalable Workflow; Dr Adam Barker (University of St Andrews, UK); [details]
  • 11.10 - 11.30:  Coffee
  • 11.30 - 12.15:  Group Discussions
  • 12.15 - 12.45:  Feedback from Groups
  • 12.45 - 13.00:  Final Comments / Future Plans
  • 13.00:  Lunch