Welcome to OpenDiseaseModels.org
Please read this page and the Overview section before doing anything else.
OpenDiseaseModels.org is an open-source disease/systems model development project. Analogous to open-source software development projects, the goal of this effort is to develop better, more useful models in a transparent and public collaborative forum.
Motivation
The motivation for OpenDiseaseModels.org is driven by the following principles:
- Development of disease/systems models is an extremely resource-intensive effort.
- Pre-competitive insight and resources shared across companies/institutions will lead to better systems models than could be developed by a single institution.
- Open models, which are transparently developed and publicly vetted, will be more widely accepted and will be better positioned to impact the entire scientific/biomedical/health community.
Operation Model
OpenDiseaseModels.org will serve as a home for multiple disease/systems modeling projects. Each individual project will be comprised of three participant groups:
- The Core Model Development Team will be comprised of expert modeling and simulation scientists, with prior experience in disease progression or systems biology modeling for the particular biomedical domain of interest. This group will serve as the primary developers and maintainers of the model source code and will also review input from the Advisory Panel and the General Public regarding model revisions and improvements.
- The Advisory Panel will be comprised of scientists, clinicians, policy makers, and patient advocates with demonstrated expertise or interest in the disease(s), which is (are) described by the model. Their role is to provide guidance to the Core Model Development Team regarding clinical and therapeutic utility, biologic plausibility, and potentially, external research and funding opportunities.
- It is anticipated that contributors from the General Public will be other domain-relevant scientists, clinicians, policy makers, patient advocates, and anyone else with an interest in the modeling project. The expected role of this group is to impact the model development process by exploring, challenging, and motivating through contributed examples and open discussion.
All participants will be able to download and review model documentation, data and source code, participate in open discussion groups, and contribute new models or data via discussion group uploads.
Business Model
Initial development of the OpenDiseaseModels.org site has been supported by Metrum Institute. Individual modeling projects have been supported by Metrum Institute and, in some cases, collaborating pharma/biotech industry partners. Additional external support mechanisms, including government and private sector grants are currently being investigated.
Modeling Project Content
Similar to open-source software development, the development of open systems/disease models is envisioned as an iterative development cycle with delivery of key intermediate model milestones, or versions, throughout the course of development. Some important characteristics of OpenDiseaseModel.org development projects are listed here:
- Models will be developed with readily accessible (preferably open-source) modeling tools with model code openly available. Ultimately these models may be translated to a common model language (e.g. an SBML-like language).
- Models will be developed using publicly available data and those data sets will also be openly shared as part of the project.
- Documentation of modeling efforts, features, improvements, and bug fixes will be transparently available within each project.
- All model code, data sets, and documentation will be version-controlled using a modern software development versioning system.
- Publication of modeling results in peer-reviewed literature must be allowed, and will be encouraged, for all development projects.
- Public review, discussion and extension of models will be facilitated via a web-based discussion board.
- All model code is distributed under the GNU General Public License.
