Atomizer

What is Atomizer?

What is in a model? is a question that any person has to ask himself when dealing with a novel system. With what is in a model, we mean understanding how the different elements in a system (species, reactions) are related to each other. What are the set of biological processes that each reaction encodes? How are downstream complexes in a signaling cascade related to those at the beginning?

Atomizer is a framework for the extraction of these implicit modeling assumptions from reaction-networks. In particular, we receive reaction-network models encoded in the Systems Biology Modeling Language (SBML) and encode the model together with the information we recover as a BioNetGen model.

Where can I learn more information about Atomizer?

We have a user manual you can access in this page. We have also made available the slides from our presentation at COMBINE here. We have a publication for Atomizer that you can refer to:

Tapia, Jose-Juan, and James R. Faeder. "The atomizer: Extracting implicit molecular structure from reaction network models." Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. ACM, 2013.

We are also working on a journal publication to be published shortly.