Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and to reproduce scientific results. Over the past …
Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell …
Synthetic biology promises to leverage engineering principles to enable model-based design of genetic circuits. To be successful, advancements are needed in both experimental and computational methods to support this new approach. This paper focuses …
COMBINE (Computational Modeling in Biology Network) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE's aim is to act as a coordinator, facilitator, and …
Recent experimental advances facilitate the collection of time series data that indicate which genes in a cell are expressed. This information can be used to understand the genetic regulatory network that generates the data. Typically, Bayesian …
Researchers are now developing synthetic genetic circuits to manipulate the biochemical processes within living cells. In order to model and predict the behavior of these circuits, the designer must account for numerous reactions among many chemical …