http://www.sys-bio.org/sbwWiki/ 2008-08-19T17:42:23-07:00 http://www.sys-bio.org/sbwWiki/ http://www.sys-bio.org/sbwWiki/lib/images/favicon.ico text/html 2008-08-19T17:30:00-07:00 ssleight http://www.sys-bio.org/sbwWiki/journalclub Welcome to the Synthetic Biology Journal Club page. Meetings for the 2008 summer quarter will be held every Thursday from 3:30-5pm in Foege N303. Below are the synthetic biology papers we will discuss each week and the person who chose the paper. Please email if you have questions. text/html 2008-08-18T15:20:28-07:00 hsauro http://www.sys-bio.org/sbwWiki/tutorials/icsb2008 The SBW team is holding a tutorial on the use of SBW at the ICSB 2008 Friday August 22nd, 10-13. Registration This tutorial aims to familiarize participants with the tools provided in the Systems Biology Workbench for building and analyzing deterministic and stochastic models. Using SBW and integrated 3rd party software, we will introduce modeling, time course and steady state concepts, parameter sensitivity (MCA) and bifurcation analysis. text/html 2008-08-15T17:15:42-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/papers Kim, K. H., Qian, H., and Sauro, H. M. (2008) Sensitivity Regulation Based on Noise Propagation in Stochastic Reaction Networks. eprint arXiv:0805.4455v1 [q-bio.MN]. Sauro, H. M. (2008) Modularity Defined. Molecular Systems Biology vol 4 (166) Feb 2008. text/html 2008-08-08T10:07:33-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/research Summary: The Sauro lab is concerned with understanding the control systems that govern cellular networks. Areas of study include developing computational standards and algorithms for systems and synthetic biology, theoretical studies on stochastic and deterministic biochemical networks and their control and the evolution of control systems using both experimental and computational approaches. Current projects include, understanding the propagation of noise through cellular networks, understandi… text/html 2008-08-04T01:28:06-07:00 fbergman http://www.sys-bio.org/sbwWiki/sbw/copasi Copasi is a software application for simulation and analysis of biochemical networks. It has significant capabilities for parameter estimation. With the release of the open source version of Copasi, it is possible to make Copasi SBW enabled. This means it is possible for example to move directly from tools such as celldesigner, JDesigner or JarnacLite to Copasi. Moreover it is also possible to move models from Copasi to any other SBW enabled tool, for example Oscill8. text/html 2008-07-22T19:25:34-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/498_systems_and_synthetic_biology_spring_2008 Start Date for Spring Term: March 31st End Date for Spring Term: June 6th. This page describes the systems and synthetic biology elective course, 499. <http://pbd.lbl.gov/sbconf/about.php> Course Description and Objectives [Syllabus] This course offers an introduction to system and synthetic biology. This course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. Students will be introduced to the field of synthetic biology … text/html 2008-06-19T21:59:12-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/jobs We do not currently have any positions available. text/html 2008-06-19T16:40:37-07:00 ssleight http://www.sys-bio.org/sbwWiki/modularity text/html 2008-06-19T16:37:24-07:00 ssleight http://www.sys-bio.org/sbwWiki/meetingnotes June 18 Modularity text/html 2008-06-12T17:50:30-07:00 fbergman http://www.sys-bio.org/sbwWiki/sysbio-news/jun12icsbtutorial2008 The SBW team is holding a tutorial on the use of SBW at the ICSB 2008 Friday August 22nd, 10-13. For more information and registration see our tutorials page. text/html 2008-06-02T18:41:59-07:00 fbergman http://www.sys-bio.org/sbwWiki/compare Comparing Simulation Results among SBML capable simulators has always been of interest to us. Not knowing the correct result of an SBML simulation, we figured that it would be best to compare what sort of results common simulators would give on a set of curated SBML files. text/html 2008-05-17T10:43:34-07:00 fbergman http://www.sys-bio.org/sbwWiki/sbw/matlab The SBW-Matlab Interface is exactly what it says it is, it permits Matlab to call out to SBW modules and allows users to write Matlab functions so that other SBW modules can call Matlab. The use of Matlab functions once packaged as SBW modules does not require Matlab to be installed on the client machine. Thus developers can write Matlab based modules and easily distribute them to other users even though the user may not have Matlab installed. This took kit was developed by Cameron Wellock as pa… text/html 2008-05-01T21:50:00-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/jarnac_notes Q1 How do I set the random number generator seed? Use the command: Q2 How do I output data to a file? The following code will generate a matalb formated matrix to a file. text/html 2008-04-29T12:45:45-07:00 fbergman http://www.sys-bio.org/sbwWiki/sbw/sbml 30th Apr. Update: updated prototype, added memory handling, OStreams, inlining of enums, replaced uints in signatures with int's I'm currently working on libsbml C# bindings, to provide an alternative way of SBML support (that is other than via SBW) for the .NET languages. I currently have a working prototype (relying on SWIG generated code) that is available here: text/html 2008-04-23T10:04:01-07:00 ssleight http://www.sys-bio.org/sbwWiki/workshops/standardsandspecifications08/travel If you have received an invitation, here is some information on traveling to and from the workshop, lodging, and local restaurants/cafes/shops. Flights Try kayak.com for booking flights. You should fly into the Sea-Tac Airport (airport code: SEA). Please email us your receipt as soon as you book your flight and you will be reimbursed. text/html 2008-04-23T09:48:55-07:00 ssleight http://www.sys-bio.org/sbwWiki/workshops/standardsandspecifications08/schedule Friday, April 25 * 5:30 - 6:00pm : Open bar (Talaris Dining Room) * 6:00 - 8:00pm : Welcome dinner (Talaris Dining Room) Saturday, April 26 * 8:00 - 9:00am : Breakfast (Cedar Foyer) Opening: Overview (Cedar Room) * 9:00 – 9:15am : Herbert Sauro, Welcome and Introduction * 9:15 – 9:45am : Raik Grüenberg, Summary of BioBrick technical standards and definitions * 9:45 – 10:30am : Discussion * 10:30 – 10:45am : Break text/html 2008-04-22T19:50:40-07:00 ssleight http://www.sys-bio.org/sbwWiki/workshops/standardsandspecifications08 When: April 26-27, 2008 Location: Talaris Conference Center, Seattle, Washington [Workshop logo] Registration Travel info Schedule Google Groups [Workshop Book] The objective of the workshop is to bring together thirty or so of the most prominent researchers in this field and to focus on issues pertaining to how parts might be specified, organized and constructed. text/html 2008-03-05T21:02:31-07:00 ssleight http://www.sys-bio.org/sbwWiki/igem/insulin INSULIN!!! text/html 2008-03-05T21:02:13-07:00 ssleight http://www.sys-bio.org/sbwWiki/igem/projects Possible iGEM Projects InsulinPROJECT #1... #2,.,,. text/html 2008-03-05T14:06:48-07:00 ssleight http://www.sys-bio.org/sbwWiki/igem Welcome to the UW iGEM 2008 page. See below for info related to UW iGEM and other links you may find useful. UW iGEM iGEM 2008 iGEM Help iGEM Journal Club iGEM Blog Links Registry of Standard Biological Parts Registry Help OpenWetWare text/html 2008-03-04T10:45:45-07:00 kkim http://www.sys-bio.org/sbwWiki/sysbio/labmembers Current Members Herbert M. Sauro website | email: hsauro@u.washington.edu Group Leader Frank T. Bergmann website | email Development of a 3D reaction-diffusion simulator and Systems Biology Workbench Developer. Primary developer of SBW.Kyung Hyuk Kim website | <kkim@u.washington.edu> Post-doc: Stochastic control analysis for biological networks: an extension of metabolic control analysis, Modularity of stochastic gene regulartory networksSean Sleight website | email: sleight@u.… text/html 2008-02-20T10:36:33-07:00 ssleight http://www.sys-bio.org/sbwWiki/igem/journalclub Welcome to the UW iGEM 2008 Journal Club page. Here we will have the iGEM projects or papers to read each week. For those of you with little or no background in molecular biology and genetics, or want a quick refresher in these subjects, check out excerpts from The Cartoon Guide to Genetics below. text/html 2008-02-20T09:52:29-07:00 fbergman http://www.sys-bio.org/sbwWiki/igem/welcome This is the start page for the igem team ... Please use entries below in the iGem namespace, that is all entries should be in the form of First Topic Second Topic The reason for this being, that the igem accounts will have only rights to modify the igem pages ... this also allows setting the permissions on those page, such as making them available only to igem team members. For now only people with an account to this wiki will be able to see them. text/html 2008-02-19T23:29:23-07:00 ssleight http://www.sys-bio.org/sbwWiki/igem-journalclub Welcome to the UW iGEM 2008 Journal Club page. Here we will have the iGEM projects or papers to read each week. For those of you with little or no background in molecular biology and genetics, or want a quick refresher in these subjects, check out excerpts from The Cartoon Guide to Genetics below. text/html 2008-02-05T00:04:05-07:00 fbergman http://www.sys-bio.org/sbwWiki/sysbio-news/feb04update We updated the simulation results page to accomodate new results submitted by BioUML,SBToolBox2 and VCell. We also updated the results generated by COPASI and roadRunner. Read more text/html 2008-02-04T15:47:21-07:00 fbergman http://www.sys-bio.org/sbwWiki/compare/themysterysolved Comparing simulation results between simulators will ultimately demonstrate differences in the interpretation of the SBML between the simulators. But what to do in cases where all simulators seem to yield different results? This case occurred for the longest time with Biomodel #104: text/html 2008-01-12T16:38:34-07:00 ssleight http://www.sys-bio.org/sbwWiki/sysbio/synthetic_biology Synthetic biology has been described as the design and construction of new biological entities such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It is a useful tool to investigate the dynamics of small biological networks and to assess our capacity to predict their behavior from computational models. We are currently engaged in several synthetic biology efforts. text/html 2007-12-19T18:08:15-07:00 fbergman http://www.sys-bio.org/sbwWiki/sysbio-news/dec19nihaward NIH Award (2007): We are pleased to announce a three year NIH award to continue development of our systems biology software. Highlights include collaborating with the SBGN community to implement the SBGN standard and investigating the modular frameworks that have been proposed by the SBML community (cf. Stefan Hoops). text/html 2007-12-19T15:43:45-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/news As of now news will be captured on the sysbio-news page. Old Entries News: Dec 18, SBW has now been downloaded over 25,000 times. News: Oct 24th, SBW 2.7.6 Released for Win32, Linux and OS X News: June 1st, SBW 2.7.1 Released for Win32 News: November 20th, SBW 2.6.0 Released for Win32 text/html 2007-12-10T09:21:26-07:00 hsauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/304_engineering_physiology Course Schedule for BIOEN 304 (2007) - updated Nov. 01. * Ch 2 – Molecular Interactions * Ch 3 – Cells and Tissues * Ch 4 – Energy and Cellular Metabolism * Ch 5 – Membranes * Ch 10 - Sensory Physiology * Ch 19 – The Kidneys * Ch 20 – Integrative Physiology * Ch 21 – The Digestive System * Ch 22 – Metabolism and Energy Balance * Ch 23 –Endocrine Control * Ch 24 –Immunology * Ch 25 – Integrative Physiology