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IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS # BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. # # # Plugin description # # # 2009/4/2 - RoySoc have moved to HighWire. Keep this so that # old linkouts work, but change to regexp so that it never matches. # Mind you, none of the test cases below seem to work - they all redirect to # a home page. It seems they haven't bothered to set up redirects. # # regexp {http://[^/]*journals.royalsoc.ac.uk[^/]*/content|http://journals.royalsociety.org/content} plugin { version {1} name {Royal Society} url {http://www.royalsociety.org/} blurb {} author {Fergus Gallagher} email {fergus.gallagher@citelike.org} language {perl} regexp {XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX} } # Linkout formatting # Raw ingredients required to build the full text URL dynamically using the following variables # collected by the plugin: type ikey_1 ckey_1 ikey_2 ckey_2 format_linkout ROYSOC { return [list RoyalSociety "http://journals.royalsociety.org/content/${ckey_1}"] } #Tests test {http://www.journals.royalsoc.ac.uk/content/lppjn7wqvrr7tx11/} { formatted_url {DOI http://dx.doi.org/10.1098/rsif.2005.0045} formatted_url {RoyalSociety http://journals.royalsociety.org/content/lppjn7wqvrr7tx11} linkout {DOI {} 10.1098/rsif.2005.0045 {} {}} linkout {ROYSOC {} lppjn7wqvrr7tx11 {} {}} type JOUR title "Modelling biological complexity: a physical scientist's perspective" journal "Journal of The Royal Society Interface" volume "2" issue "4" start_page 267 end_page 280 year 2005 day 22 date_other "" url {http://dx.doi.org/10.1098/rsif.2005.0045} abstract {We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter.The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.} author {Coveney Peter PV {Coveney, Peter V.}} author {Fowler Philip PW {Fowler, Philip W.}} doi 10.1098/rsif.2005.0045 status ok } test {http://www.journals.royalsoc.ac.uk/content/v125l44343734657/?p=b49316d24aea4710964e2f4bedd54871&pi=0} { formatted_url {DOI http://dx.doi.org/10.1098/rspa.2007.1839} formatted_url {RoyalSociety http://journals.royalsociety.org/content/v125l44343734657} linkout {DOI {} 10.1098/rspa.2007.1839 {} {}} linkout {ROYSOC {} v125l44343734657 {} {}} type JOUR title "Germ of a synthesis: space–time is spinorial, extra dimensions are time-like" journal "Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences" volume "463" issue "2083" start_page 1665 end_page 1679 year 2007 month 7 date_other "" url {http://dx.doi.org/10.1098/rspa.2007.1839} abstract {A pressing issue for modern physics is the possibility of extra dimensions of space–time. Here, a novel approach to this question is put forward, with three facets:First, an integral transform is introduced into Einstein's general relativity that is non-local and spinorial. For Minkowskian space–time, the transform intertwines three spaces of six dimensions, which a priori are on an equal footing, linked by the octavic triality of Cartan. Two of these spaces are interpreted as null twistor spaces; the third may be regarded as giving space–time two extra time-like dimensions, for which the ordinary space–time is an axis of symmetry.Second, it is suggested that the extra dimensions perdure for a general space–time: the overall structure is controlled by a generalized Fefferman tensor. Accordingly, it is posited that the additional time-like dimensions arise naturally and constitute an aspect of space–time reality that ultimately will be amenable to experimental investigation. Conceivably, devices such as the Large Hadron Collider will uncover this reality.Third, it is argued that the structure hints at a synthesis of ideas deriving from general relativity, string theory, condensed matter physics, category theory and non-commutative geometry.} author {Sparling George GA {Sparling, George A.J.}} doi 10.1098/rspa.2007.1839 status ok } # same as above, but with .org url test {http://journals.royalsociety.org/content/v125l44343734657/?p=b49316d24aea4710964e2f4bedd54871&pi=0} { formatted_url {DOI http://dx.doi.org/10.1098/rspa.2007.1839} formatted_url {RoyalSociety http://journals.royalsociety.org/content/v125l44343734657} linkout {DOI {} 10.1098/rspa.2007.1839 {} {}} linkout {ROYSOC {} v125l44343734657 {} {}} type JOUR title "Germ of a synthesis: space–time is spinorial, extra dimensions are time-like" journal "Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences" volume "463" issue "2083" start_page 1665 end_page 1679 year 2007 month 7 date_other "" url {http://dx.doi.org/10.1098/rspa.2007.1839} abstract {A pressing issue for modern physics is the possibility of extra dimensions of space–time. Here, a novel approach to this question is put forward, with three facets:First, an integral transform is introduced into Einstein's general relativity that is non-local and spinorial. For Minkowskian space–time, the transform intertwines three spaces of six dimensions, which a priori are on an equal footing, linked by the octavic triality of Cartan. Two of these spaces are interpreted as null twistor spaces; the third may be regarded as giving space–time two extra time-like dimensions, for which the ordinary space–time is an axis of symmetry.Second, it is suggested that the extra dimensions perdure for a general space–time: the overall structure is controlled by a generalized Fefferman tensor. Accordingly, it is posited that the additional time-like dimensions arise naturally and constitute an aspect of space–time reality that ultimately will be amenable to experimental investigation. Conceivably, devices such as the Large Hadron Collider will uncover this reality.Third, it is argued that the structure hints at a synthesis of ideas deriving from general relativity, string theory, condensed matter physics, category theory and non-commutative geometry.} author {Sparling George GA {Sparling, George A.J.}} doi 10.1098/rspa.2007.1839 status ok }