Workshop Objectives
Biocomplexity X
The first section will bring together experimentalists and modelers studying aspects of developmental biology related to tissue and organ development, homeostasis, regeneration and diseases related to developmental mechanisms. The goals will be: 1) for modelers to identify key missing experimental information needed for the construction of predictive models (virtual tissues) useful to experimentalists and clinicians. 2) for experimentalists to inform model developers of new experimental data and opportunities and their desired data in new model development. 3) to jump start new experimental/computational collaborations. We plan to produce a brief (few page) white paper summarizing these discussion points.
CBO Follow-Up
The second section (to which we hope almost all participants will contribute and to which we especially invite experimentalists) will continue the discussions begun this April at NIH to discuss the development of an ontology to describe cell behaviors at a phenomenological level (a Cell Behavior Ontology, CBO). The reason for this apparently arcane topic is that the lack of such an agreed-upon language has greatly impeded the development of cell level models of the development-related biological phenomena addressed in the first section of the workshop. Existing schema like the Cell Processes subtree of the Gene Ontology (GO), while very important, were not developed for this purpose, making them cumbersome to apply. The CBO will be a crucial step towards the development of a model-description language that focuses on the biology of the developmental problem addressed allowing models to be developed independently of specific implementation details and migrated between modeling platforms. Such a language will also be essential for consistent annotation of new high-resolution time series datasets on development. The goal of this section is a draft top-level CBO that can be published as a draft standard for future refinement and modification.Talk Suggestions
We strongly encourage all speakers to focus their talks specifically on these aims.
For experimentalists: we ask that you specify clearly the biological model organism/organ and the relationship to other biological models, the key questions your research addresses, the type of data your experiments generate, the key cell and tissue-level types and dynamic mechanisms involved, the key areas here you feel simulations could be of assistance and the possible extension of your experimental methods to generating additional types of quantitative data for simulations. Please think about how you might be able to describe your biological problem in a precise way using a CBO-like syntax. Are there specific places where you could apply a CBO in your work or contribute to the development of a CBO (e.g. annotation of microscopy images, exploration of hypotheses, automatic generations of experimental parameters...)? What level of detail do you believe is necessary to build a working model of your problems?
For modelers: we ask that you explain very briefly your methodology (agents, dynamics,continuum, etc.) and its domain of suitability, the biological problems to which it has been applied and the mechanisms which it includes. What additional biological problems could your methodology appropriately treat? What experimental data would be most useful for the validation/creation/extension of your models? What features would an eventual model specification language require to be able to build automatically models of your type from such a model specification? What issues must be addressed to convert your simulations into simulation environments? To attach your simulations to other methodologies at coarser or finer length scales? have you developed any methodologies for cross-scale integration which might be generally useful? What are key missing biological components/mechanisms that you would like to add to your core methods? How could your methods and models be shared?