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Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking.Availability: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3.Contact: Natalio.Krasnogor@nottingham.ac.uk

De novo DNA synthesis is in need of new ideas for increasing production rate and reducing cost. DNA reuse in combinatorial library construction is one such idea. Here, we describe an algorithm for planning multistage assembly of DNA libraries with shared intermediates that greedily attempts to maximize DNA reuse, and show both theoretically and empirically that it runs in linear time. We compare solution quality and algorithmic performance to the best results reported for computing DNA assembly graphs, finding that our algorithm achieves solutions of equivalent quality but with dramatically shorter running times and substantially improved scalability. We also show that the related computational problem bounded-depth min-cost string production (BDMSP), which captures DNA library assembly operations with a simplified cost model, is NP-hard and APX-hard by reduction from vertex cover. The algorithm presented here provides solutions of near-minimal stages and thanks to almost instantaneous planning of DNA libraries it can be used as a metric of "manufacturability" to guide DNA library design. Rapid planning remains applicable even for DNA library sizes vastly exceeding today's biochemical assembly methods, future-proofing our method.

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Compartmentalisation is thought to have been a crucial step in the origin of life. To help us bridge the gap between selfassembly processes behind the formation of bio-compartments and metabolic and information bearing processes we refer to DPD and P Systems Simulations. In this paper we outline a new software platform linking a high level abstract computational formalism (P Systems) with a molecular scale model (Dissipative Particle Dynamics) by linking the membranes which delimit the cellular regions within P Systems to self-assembled phospholipid based vesicles in DPD. We test the platform by modelling a passive transport process involving vesicles containing membrane inclusions similar to pore complexes such as α-hemolysin. In doing so, we illustrate the usefulness of the modelling approach and derive a more realistic parameter set for the P system through the dissipative particle dynamics simulation.