<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>23</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Florian Erhard</style></author><author><style face="normal" font="default" size="100%">Caroline C. Friedel</style></author><author><style face="normal" font="default" size="100%">Ralf Zimmer</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Sangdun Choi</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">FERN - Stochastic Simulation and Evaluation of Reaction Networks</style></title><secondary-title><style face="normal" font="default" size="100%">Systems Biology for Signaling Networks</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><publisher><style face="normal" font="default" size="100%">Springer</style></publisher><language><style face="normal" font="default" size="100%">eng</style></language><custom2><style face="normal" font="default" size="100%">Global publication list</style></custom2></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lars Dölken</style></author><author><style face="normal" font="default" size="100%">Georg Malterer</style></author><author><style face="normal" font="default" size="100%">Florian Erhard</style></author><author><style face="normal" font="default" size="100%">Sheila Kothe</style></author><author><style face="normal" font="default" size="100%">Caroline C. Friedel</style></author><author><style face="normal" font="default" size="100%">Guillaume Suffert</style></author><author><style face="normal" font="default" size="100%">Lisa Marcinowski</style></author><author><style face="normal" font="default" size="100%">Natalie Motsch</style></author><author><style face="normal" font="default" size="100%">Stephanie Barth</style></author><author><style face="normal" font="default" size="100%">Michaela Beizinger</style></author><author><style face="normal" font="default" size="100%">Diana Lieber</style></author><author><style face="normal" font="default" size="100%">Susanne M. Bailer</style></author><author><style face="normal" font="default" size="100%">Reinhard Hoffmann</style></author><author><style face="normal" font="default" size="100%">Zsolt Ruzsics</style></author><author><style face="normal" font="default" size="100%">Elisabeth Kremmer</style></author><author><style face="normal" font="default" size="100%">Sebastien Pfeffer</style></author><author><style face="normal" font="default" size="100%">Ralf Zimmer</style></author><author><style face="normal" font="default" size="100%">Ulrich H Koszinowski</style></author><author><style face="normal" font="default" size="100%">Friedrich Grässer</style></author><author><style face="normal" font="default" size="100%">Gunter Meister</style></author><author><style face="normal" font="default" size="100%">Jürgen Haas</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays</style></title><secondary-title><style face="normal" font="default" size="100%">Cell Host &amp; Microbe, accepted</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><language><style face="normal" font="default" size="100%">eng</style></language><custom2><style face="normal" font="default" size="100%">Global publication list</style></custom2></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Florian Erhard</style></author><author><style face="normal" font="default" size="100%">Caroline C. Friedel</style></author><author><style face="normal" font="default" size="100%">Ralf Zimmer</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">FERN - a Java framework for stochastic simulation and evaluation of reaction networks</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">networks</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.biomedcentral.com/1471-2105/9/356</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">356</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND:Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary.RESULTS:In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment.CONCLUSION:FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modelled easily with FERN.</style></abstract><custom2><style face="normal" font="default" size="100%">Global publication list</style></custom2><custom5><style face="normal" font="default" size="100%">&lt;a href=&quot;/software/fern&quot; class=&quot;intern&quot;&gt;Project website&lt;/a&gt;</style></custom5></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>32</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Florian Erhard</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Petri Net Based System for Spatio-Temporal Simulation of Gene Regulation</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">gene regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">petri net</style></keyword><keyword><style  face="normal" font="default" size="100%">pnma</style></keyword><keyword><style  face="normal" font="default" size="100%">simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">spatio temporal</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">July</style></date></pub-dates></dates><publisher><style face="normal" font="default" size="100%">LFE Bioinformatik/LMU München</style></publisher><language><style face="normal" font="default" size="100%">eng</style></language><work-type><style face="normal" font="default" size="100%">Diploma Thesis</style></work-type><custom2><style face="normal" font="default" size="100%">Global publication list</style></custom2></record></records></xml>