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	<title>Models and Languages for Computational Systems Biology</title>
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		<title>MLCSB 2011 starts next semester</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/10/mlcsb-2011-starts-next-semester/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/10/mlcsb-2011-starts-next-semester/#comments</comments>
		<pubDate>Tue, 12 Oct 2010 10:58:59 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=280</guid>
		<description><![CDATA[The new edition of this course for the 2010&#8211;2011 session will run in Semester&#160;2, starting in January&#160;2011. The course will be lectured by Professor Jane Hillston. Link: Models and Languages for Computational Systems Biology 2010&#8211;2011]]></description>
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		<title>Lecture 17: Compartments in BioPEPA</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-17-compartments-in-biopepa/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-17-compartments-in-biopepa/#comments</comments>
		<pubDate>Thu, 18 Mar 2010 17:23:43 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Lecture Log]]></category>
		<category><![CDATA[BioPEPA]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=271</guid>
		<description><![CDATA[Working through the following paper: Federica Ciocchetta and Maria Luisa Guerriero. Modelling Biological Compartments in Bio-PEPA, in MeCBIC 2008: Proceedings of the Second International Meeting on Membrane Computing and Biologically Inspired Process Calculi. Electronic Notes in Theoretical Computer Science 227:77&#8211;95, January 2009. Adding compartments to BioPEPA: syntax; compositional operational semantics; structured locations including compartments, membranes, [...]]]></description>
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		<slash:comments>0</slash:comments>
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		<title>Lecture 16: Modelling tools for Bio-PEPA</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-16-modelling-tools-for-bio-pepa/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-16-modelling-tools-for-bio-pepa/#comments</comments>
		<pubDate>Tue, 16 Mar 2010 16:21:59 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Lecture Log]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=268</guid>
		<description><![CDATA[Guest lecture by Stephen Gilmore explaining and demonstrating the BioPEPA tools, principally the Eclipse plugin.]]></description>
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		<slash:comments>0</slash:comments>
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		<item>
		<title>2010 Turing Lecture</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/2010-turing-lecture/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/2010-turing-lecture/#comments</comments>
		<pubDate>Mon, 15 Mar 2010 15:23:34 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Advertisements]]></category>
		<category><![CDATA[learning]]></category>
		<category><![CDATA[probabilistic]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=259</guid>
		<description><![CDATA[Embracing Uncertainty: The New Machine Intelligence Christopher Bishop Microsoft Research Cambridge 5.00pm / 5.30pm Thursday 18 March 2010 Appleton Tower Computers are traditionally viewed as logical machines which follow precise, deterministic instructions. The real world in which they operate, however, is full of complexity, ambiguity, and uncertainty. In this year’s Turing Lecture, Professor Chris Bishop [...]]]></description>
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		<slash:comments>0</slash:comments>
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		<title>PEPA Club</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/pepa-club-guerriero/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/pepa-club-guerriero/#comments</comments>
		<pubDate>Thu, 11 Mar 2010 21:26:07 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Advertisements]]></category>
		<category><![CDATA[Announcements]]></category>
		<category><![CDATA[BioPEPA]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=245</guid>
		<description><![CDATA[Complementary Approaches to Understanding the Plant Circadian Clock Maria Luisa Guerriero Centre for Systems Biology at Edinburgh 11am Friday, 12 March, 2010 Room 3.02, Informatics Forum Links: Seminar abstract; About PEPA Club. This talk describes a BioPEPA model for the circadian clock in the green alga Ostreococcus tauri, demonstrating in particular the use of BioPEPA [...]]]></description>
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		<slash:comments>0</slash:comments>
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		<title>Lecture 15: Process Algebras for Systems Biology</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-15-process-algebras-for-systems-biology/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-15-process-algebras-for-systems-biology/#comments</comments>
		<pubDate>Thu, 11 Mar 2010 19:32:36 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Lecture Log]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=239</guid>
		<description><![CDATA[Background on process algebras / process calculi: what they can be useful for, and various domains where they have been applied. Specific applications to systems biology; and the wide range of process calculi proposed for different aspects of biological systems. Brief introduction to PEPA and BioPEPA, with reference to Ciocchetta and Hillston (2009). Link: Slides.]]></description>
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		<slash:comments>0</slash:comments>
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		<title>Lecture 14: Continuous Petri Nets and Differential Equations</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-14-continuous-petri-to-ode/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-14-continuous-petri-to-ode/#comments</comments>
		<pubDate>Mon, 08 Mar 2010 21:00:22 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Lecture Log]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=218</guid>
		<description><![CDATA[Moving from discrete events to continuous flow: semantics of continuous Petri nets; correspondence with chemical reaction equations; deriving ordinary differential equations (ODEs); conservation laws, equilibria, numerical solutions and trajectories through phase space. Relating transition rates for discrete events to reaction rates for continuous flow; dependence on reaction stoichiometry. Some examples, including derivation of Michaelis-Menten semantics. [...]]]></description>
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		<title>Assignment 2: Modelling in BioPEPA</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/assignment-2-modelling-in-biopepa/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/assignment-2-modelling-in-biopepa/#comments</comments>
		<pubDate>Fri, 05 Mar 2010 19:15:30 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Coursework]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=209</guid>
		<description><![CDATA[The second coursework assignment is now out, and due on Thursday 25&#160;March, three weeks from now. The assignment involves modelling a small signalling pathway using the BioPEPA language. Lecture&#160;14, on Thursday 11&#160;March, will include an introduction to BioPEPA; and Stephen Gilmore will give a guest lecture presenting the Eclipse plugin for BioPEPA on Monday 15&#160;March. [...]]]></description>
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		<slash:comments>2</slash:comments>
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		<title>Lecture 13: More Stochastic Kinetics</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-13-more-stochastic/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-13-more-stochastic/#comments</comments>
		<pubDate>Fri, 05 Mar 2010 17:45:12 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Lecture Log]]></category>
		<category><![CDATA[Gillespie]]></category>
		<category><![CDATA[stochastic]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=203</guid>
		<description><![CDATA[More on Gillespie&#8217;s algorithm for stochastic simulation, including the remainder of the slides from Gillespie&#8217;s invited CMSB talk. Various tau-leaping methods to more efficiently simulate larger systems; concerns about bounding the errors in these approximate techniques. Further approximation with continuous models, still stochastic, and then by deterministic systems of differential equations for even large scales. [...]]]></description>
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		<slash:comments>2</slash:comments>
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		<title>Lecture 12: Large Systems and Stochastic Kinetics</title>
		<link>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-12-larger-and-stochastic/</link>
		<comments>http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-12-larger-and-stochastic/#comments</comments>
		<pubDate>Tue, 02 Mar 2010 12:29:40 +0000</pubDate>
		<dc:creator>Ian Stark</dc:creator>
				<category><![CDATA[Lecture Log]]></category>

		<guid isPermaLink="false">http://blog.inf.ed.ac.uk/mlcsb/?p=188</guid>
		<description><![CDATA[Revisiting Kwiatkowska et&#160;al. on probabilistic model-checking for systems biology. Moving from models of a single protein to slightly larger populations, still with symbolic model-checking. The problem of state-space explosion, and the use of simulation. Gillespie&#8217;s algorithm for stochastic simulation. I&#8217;m using the slides from Gillespie&#8217;s invited talk at CMSB&#160;2007 in Edinburgh. So far we have [...]]]></description>
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