Model Sharing Strategies - One Day Mini-Workshop


Verifiability and reproducibility of scientific results and the ability to share models are key to collaborative scientific work. However, the typical model description published in peer-reviewed literature is not sufficient for model duplication. When it is, reproducing models is extremely labor intensive. Existing model frameworks are generally not designed to support interoperability or model sharing. While most scientists would agree that everyone should be able to reproduce published simulations and incorporate them into their own work, they tend to take the status quo for granted and may not be aware of exiting successful approaches to model sharing or how these might apply to their own work. To help the IMAG Multiscale Modeling (MSM) grantees learn about model-sharing approaches relevant to their work the MSM consortium will host a tutorial mini-workshop on model-sharing strategies. The topics to be discussed include, but are not limited to:

• The basics of markup languages (MLs) – a basic tool for model sharing.

• A brief introduction to most popular MLs used in bioscience, their application and a history of their development (not a history lecture, but a brief discussion of the context in which the MLs were developed).

• How to incorporate MLs in scientific research.

• Introduction to web services and their application to model sharing.

• Key needs with regard to model sharing.

• Model composition

• Possible road maps to a model sharing platform.

The workshop will include hands-on tutorials. Each speaker will have at least two hours and we will encourage participants to ask all sorts of questions related to any aspect of model sharing. The focus of the workshop will be tutorial; exposing participants to the basic concepts and advantages of model sharing is more important than presenting overwhelming amounts of technical detail.

The workshop will start at 8.00 AM and run until approximately until 6.00 PM


Geoffrey Fox, Pervasive Technology Lab, Indiana University

Peter Hunter, Department of Bioengineering, University of Auckland

Wilfred Li, SDSC

Andrew Miller, Department of Bioengineering, University of Auckland

Christopher Mueller,Open Systems Lab, Indiana University

Herbert Sauro, Department of Bioengineering, University of Washington

Benjamin Zaitlen, Biocomplexity Institute, Indiana University


Organizing Committee:

Maciej Swat ( , Biocomplexity Institute, Indiana University

James Glazier (, Biocomplexity Institute, Indiana University

Grace Peng, (, NIH

Katie Serrano, (, NIH

Financial Support provided by NIBIB and NIH-BISTIC

Tutorial Session:

In order to fully participate in the tutorial session, participants are asked to bring their own laptops. The specific instructions regarding the software required for the tutorial session will be given at the workshop. For the sake of time, we would ask participants to install the software during the breaks, ideally before tutorials begin.

Expected Outcomes:

Based on the feedback from the workshop participants, organizers and workshop speakers will prepare a proposal for a series of workshops that would address needs of modeling community in terms of introducing new standards and tools for efficient model sharing and collaborative work. A more direct goal of the workshop would be to identify key areas where participants feel model sharing could benefit their work and the key features they would require from the model sharing framework in order to begin using it in their work.


Workshop Agenda

April 10, 2007 Lister Hill, NIH Campus

Breakfast on your own


8:00 – 12:00 Lister Hill Visitor’s Center 


8.00-8.40 Geoffrey Fox

• “Lessons on Process and Standards in other science communities”

8.40-9.20 Christopher Mueller

• "Software Architectures and Tools for Model Sharing"

9.20-10.05 Peter Hunter

• “Model sharing with CellML”

10.05-10.20 Break

10.20-11.05 Herbert Sauro

• “Standards Development in Biology, SBML and SBW case studies”

11.05-11.50 Wilfred Li

• “Introduction to the Opal Web Service Toolkit for Scientific Applications”

• Sriram Krishnan Opal Tookit

12:00 – 1:00 Lunch on your own


1:00 – 5:00 Lister Hill Auditorium

Hands-On Tutorials

1.00-2.00 Peter Hunter, Andrew Miller

• “Use of the CellML simulation/editing tool PCEnv and the CellML model repository”

2.00-3.00 Herbert Sauro

• "The Systems Biology Workbench”

2.00-2.20 Break

3.20-4.20 Wilfred Li

• “Introduction to the Opal Web Service Toolkit for Scientific Applications”

4.20-4.50 Benjamin Zaitlen

• “Introduction to CompuCell3D - cell-level modeling environment”

4.50-5.00 Break

5:00 – 6:00 Discussion of MSM Model Sharing Strategy


Workshop Feedback

Please direct all comments and suggestions from the workshop to Maciej Swat (

Workshop Summary

The following document contains brief summary of Model Sharing Mini-Workshop:

Event Start Date
Event End Date