BLACKSBURG, Va., Sept. 21, 2011 – The Center for Modeling Immunity to Enteric Pathogens (MIEP) at VBI has contributed code developed to enhance the utility of CellPublisher to the open source community.
CellPublisher is a free and open source program used to make highly interactive representations of biochemical processes. It converts a file in the Systems Biology Markup Language (SBML) created with the popular modeling tool CellDesigner into an interactive Web application, which allows the user to explore the model and access detailed explanations of the model component, including references to the scientific publications. MIEP makes use of CellPublisher to disseminate the models developed in the program to the scientific community in a user-friendly way.
Dr. Stefan Hoops, a Computational Systems Biologist at VBI and the Bioinformatics Lead for MIEP, noted “The CellPublisher code we started with was exceptionally well-documented, so we acclimated to it very quickly. We would like to thank the original authors for the great tool they provided us.”
The Bioinformatics Team at the Nutritional Immunology and Molecular Medicine Laboratory and MIEP, including Dr. Hoops and Dr. Yongguo Mei, a Research Software Engineer at VBI’s Nutritional Immunology and Molecular Medicine Laboratory, incorporated three major enhancements to CellPublisher:
• One improvement allows annotating reactions in addition to species, thereby allowing scientists to convey more information about the interactions in their models.
• Google map markers are only shown for objects which have been annotated in the MIEP models. It is immediately visible to the user where information is available. This behavior is similar to the road maps one sees in Google.
• Finally, the capability to display 3D protein structures through JMol has been enhanced by making it compatible with all major Web browsers on common operating systems.
For the purposes of clarity the MIEP/NIMML Bioinformatics team also made a minor change and reduced the size of annotation markers so that they do not interfere with the network information conveyed through the graphic representation of the model.
”Working with the open source community is a fun and enjoyable journey. As a member of the MIEP Bioinformatics team, I am very pleased to make contributions back to the software development community. Because the MIEP team is developing analyses, visualization and modeling tools, the benefits of these collaborative efforts are not just for programmers, but for the broader research community as well,” Dr. Mei said.
Possibly the biggest advantage of open source software is that everybody has the right to modify the source code. This means that the code can be implemented in other pieces of software and adapted to changing environments. The MIEP bioinformatics team has utilized these advantages to the benefit of the immunology and infectious disease research community, contributing our modifications back to the original source code so that other scientists have the same opportunity.
“The MIEP Bioinformatics Team has made substantial progress in the implementation of a fully integrated experimental environment for studying the mechanisms of immunoregulation underlying immune responses to enteric pathogens. The development of user-friendly and interactive network models of CD4+ T cell differentiation and mucosal immunity to Helicobacter pylori will facilitate dissemination of MIEP’s modeling efforts. In addition, MIEP’s open framework approaches to software development, including CellPublisher, facilitate efficient and well-modulated collaborations,” said Dr. Bassaganya-Riera, an Associate Professor at VBI, Principal Investigator of MIEP, and Director of the Nutritional Immunology and Molecular Medicine Laboratory.
For more information, please visit the MIEP Web Portal at www.modelingimmunity.org . MIEP is funded by the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, under Contract No. HHSN272201000056C to VBI.
About the Nutritional Immunology and Molecular Medicine Laboratory
The Nutritional Immunology and Molecular Medicine Laboratory conducts translational research aimed at developing novel therapeutic and prophylactic approaches for modulating immune and inflammatory responses. The Laboratory combines computational modeling, bioinformatics approaches, immunology experimentation, and pre-clinical and clinical studies to better understand the mechanisms of immune regulation at mucosal surfaces and ultimately accelerate the development of novel treatments for inflammatory, infectious and immune-mediated diseases.
About the Virginia Bioinformatics Institute
The Virginia Bioinformatics Institute at Virginia Tech is a premier bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches to science, combining information technology, biology, and medicine. These approaches are used to interpret and apply vast amounts of biological data generated from basic research to some of today’s key challenges in the biomedical, environmental, and agricultural sciences. With more than 240 highly trained multidisciplinary, international personnel, research at the institute involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology, and medicine. The large amounts of data generated by this approach are analyzed and interpreted to create new knowledge that is disseminated to the world’s scientific, governmental, and wider communities.
September 21, 2011