Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

This article presents a critique of conventional collaboration transparency systems, also called "application-sharing" systems, which provide the real-time shared use of legacy single-user applications. We find that conventional collaboration transparency systems are inefficient in their use of network resources and lack support for key groupware principles: concurrent work, relaxed WYSIWIS, and group awareness. Next, we present an alternative approach to implementing collaboration transparency that provides many features previously seen only in collaboration-aware applications. Our approach is based on a replicated architecture where selected single-user interface components are dynamically replaced by multiuser versions. The replacement occurs at run-time and is transparent to the single-user application and its developers. As an instance of this approach, we describe its incorporation into a Java-based collaboration transparency system for serializable, Swing-based Java applications, called Flexible JAMM (Java Applets Made Multiuser). To validate that the flexible collaboration transparency system is truly an improvement over conventional systems, we conducted an empirical study of collaborators performing both tightly and loosely coupled tasks using Flexible JAMM versus a representative conventional collaboration transparency system, Microsoft NetMeeting. Completion times were significantly faster in the loosely coupled task using Flexible JAMM and were not adversely affected in the tightly coupled task. Accuracy was equivalent for both systems. Participants greatly preferred Flexible JAMM.

The eukaryotic cell cycle is regulated by a complicated chemical reaction network. Although many deterministic models have been proposed, stochastic models are desired to capture noise in the cell resulting from low numbers of critical species. However, converting a deterministic model into one that accurately captures stochastic effects can result in a complex model that is hard to build and expensive to simulate. In this paper, we first apply a hybrid (mixed deterministic and stochastic) simulation method to such a stochastic model. With proper partitioning of reactions between deterministic and stochastic simulation methods, the hybrid method generates the same primary characteristics and the same level of noise as Gillespie's stochastic simulation algorithm, but with better efficiency. By studying the results generated by various partitionings of reactions, we developed a new strategy for hybrid stochastic modeling of the cell cycle. The new approach is not limited to using mass-action rate laws. Numerical experiments demonstrate that our approach is consistent with characteristics of noisy cell cycle progression, and yields cell cycle statistics in accord with experimental observations.

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In this paper, a global optimization technique is applied to solve the optimal transmitter placement problem for indoor wireless systems. An efficient pattern search algorithm-DIRECT (DIviding RECTangles) of Jones, Perttunen, and Stuckman (1993)-has been connected to a parallel 3D radio propagation ray tracing modeler running on a 200node Beowulf cluster of Linux workstations. Surrogate functions for a parallel WCDMA (wideband code division multiple access) simulator were used to estimate the system performance for the global optimization algorithm. Power coverage and BER (bit error rate) are considered as two different criteria for optimizing locations of a specified number of transmitters across the feasible region of the design space. This paper briefly describes the underlying radio propagation and WCDMA simulations and focuses on the design issues of the optimization loop.