http://www.sys-bio.org/sbwWiki/ 2010-07-29T06:39:46-07:00 http://www.sys-bio.org/sbwWiki/ http://www.sys-bio.org/sbwWiki/lib/images/favicon.ico text/html 2010-07-02T13:24:02-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/tutorials/bloomington2010 We are pleased to announce Joint User-Training Workshop “Developing Multi-Scale,Multi-Cell Developmental and Biomedical Simulations with CompuCell3D and SBW ”. It will focus on teaching the basics of multi-cell, multi-scale modeling using the open-source packages CompuCell3D and SBW. The workshop will be taught by many of the CompuCell3D and SBW developers. In addition to participating in lectures and hands-on exercises, each participant should prepare a 30 min presentation covering her/his area… text/html 2010-06-25T10:20:13-07:00 Ryan Roper http://www.sys-bio.org/sbwWiki/journalclub Welcome to the Synthetic Biology Journal Club page. Meetings for the 2010 Summer Quarter will be held every Friday from 1:30-2:30pm in Foege N303. Below are the synthetic biology papers we will discuss each week and the person who chose the paper. Please email Ryan if you have questions. text/html 2010-01-19T13:32:17-07:00 http://www.sys-bio.org/sbwWiki/sysbio/labmenbers/meetings Group Meetings Schedule At the group meetings each week there will be a dedicated discussion from one of the focus groups. Each group should self-organize and arrange a meeting when it is their turn. Discussion topics should include work accomplished or currently underway. The focus group may also mention any interesting or relevant papers related to the focus group and bring up topics of general interest to the focus group. text/html 2010-06-10T09:54:35-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/aboutus The chart below shows the research themes and topics my group is involved in. The overarching aim is to further the art of cellular engineering (also known as synthetic biology), that is to develop the technological expertise and theoretical underpinning that will enable us to use biological systems as a new technological substrate. Unlike existing technologies such as microelectronics, biological systems offer some unique engineering challenges. For example biological systems evolve and adapt … text/html 2010-02-03T20:54:26-07:00 http://www.sys-bio.org/sbwWiki/sysbio/labmembers Group Meetings The Sauro Lab meets regularly for group meetings. Since we have grown in size, they are split up into three focus groups. Have a look at the detailed schedule. We also meet regularly for the synthetic biology journal club. Current Members Herbert M. Sauro website | email: hsauro@u.washington.edu Group Leader Post-docs: Kyung Hyuk Kim website | <kkim@u.washington.edu> Post-doc: Stochastic control analysis for biological networks: an extension of metabolic control analysi… text/html 2010-06-07T15:05:23-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/studentprojects 2007-2008 Alex Bratt Engineering Robust Gene Regulatory Networks for Synthetic Biology 2008-2009 Alec Nielsen Ribosomal Binding Site Measurements and Translation Rate Standardization Charles Watts Ordering Rules in Stoichiometric Matrices to find Meaningful Conservation Laws text/html 2010-05-12T15:18:17-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sbw/stats Every once in a while it is interesting to see what our current download statistics are. With the project split into several sourceforge projects, it might be interesting to collect this information here: Jdesigner SF project SBW SF project text/html 2010-02-01T15:00:03-07:00 http://www.sys-bio.org/sbwWiki/welcome Welcome to the SBW Wiki. This wiki is intended to help users to get a first impression on how to use all the available SBW modules or how to create new SBW modules. Getting Started We constantly strive to improve the SBW modules we distribute with the framework. The ChangeLog details bug fixes and improvements we make to the modules, the framework and online services. If you have any problems or questions please file a Bug Report or post a question to the Forum. There also is a sparsely popu… text/html 2007-01-10T23:26:14-07:00 http://www.sys-bio.org/sbwWiki/sbw/simdriver The Simulation Tool is one of the main entry points into SBW. The tool has the following features: * Time course simulation with load, simulate and reset. Set time start, end and number of points. Select X and Y axis variables, including concentrations, fluxes, rates of changes, volumes, parameters and time. * Continuous time course with panning graph. * Steady State, compute and reset with optional pre-simulation. Compute eigenvalues as well as steady state values for concentration, flu… text/html 2010-05-10T13:06:07-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio-news/may10sbwrelease We are pleased to announce a release of the Systems Biology Workbench 2.8.0, available from: <http://sys-bio.org> This release is about improving performance and making it easier to simulate models. We have improved Roadrunners' performance and stability again (Including support for simultaneous discrete events!). It now correctly handles all SBML features except for delay differential equations and algebraic rules. Perhaps more significantly, we have updated the 'Simulation Tool' as the primar… text/html 2010-04-20T19:51:23-07:00 Deepak Chandran http://www.sys-bio.org/sbwWiki/sysbio/downloads Systems Biology Workbench SBW Simulators Jarnac (and Model Editor) roadRunner SBW Simulation GUI Interfaces Generic Simulation Interface(SimDriver) SBW Model Editors JDesigner Jarnac Lite Auto Layout Generation SBW Analysis Tools Frequency Analysis Tool Other SBW Supporting Tools SBML Layout Support Module Inspector Other SBW Non-GUI Modules Matrix Support via CLAPACK SBML Support SBML Translators Download SBW Simulate 3D Simulate 3D Download Simulate 3D Bifurca… text/html 2010-04-19T14:35:52-07:00 Sean Sleight http://www.sys-bio.org/sbwWiki/sysbio/papers 2010 Kim HK and Sauro HM. Sensitivity Summation Theorems for Stochastic Biochemical Reaction Systems 2010, Mathematical Biosciences, in press Sleight SC, Bartley BA, Lieviant JA, and Sauro HM. In-Fusion BioBrick Assembly and Re-engineering. Nucleic Acids Research, 2010, gkq179. <http://nar.oxfordjournals.org/cgi/content/full/gkq179> text/html 2010-02-22T15:28:13-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio/parametersets This document describes the elements of a SBML annotation, for storing multiple parameter sets in an SBML model. A user might wish to store different parameter sets that exhibit interesting behavior of computational models. One common example would be to store parameter values for steady states, or even oscillating regimes. text/html 2009-12-28T10:54:28-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/424_advanced_systems_and_synthetic_biology_winter_2010 424 Advanced Systems and Synthetic Biology text/html 2009-12-21T13:30:32-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio-news/tinkercell TinkerCell: a modular CAD tool for synthetic biology. Journal of Biological Engineering 2009, 3:19doi:10.1186/1754-1611-3-19. TinkerCell is a an example of a computer aided design application specifically geared towards synthetic biology. See www.tinkercell.com for more details and downloads. text/html 2009-11-25T07:54:19-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/498a_systems_and_synthetic_biology_winter_2010 Start Date for Spring Term: January 4th End Date for Spring Term: March 12th. This page describes the systems and synthetic biology elective course, 424. UW General Catalog Course Description: This course offers an advanced course on system and synthetic biology. The course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. Topics include kinetics, modeling, stoichiometry, control theory, metabolic systems, signaling, motifs … text/html 2009-11-13T14:12:59-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/498_systems_and_synthetic_biology_winter_2009 Start Date for Spring Term: January 5th End Date for Spring Term: March 13th. This page describes the systems and synthetic biology elective course, 498. <http://pbd.lbl.gov/sbconf/about.php> Course Description and Objectives [Syllabus] text/html 2009-11-13T14:09:34-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/courses 498 Systems and Synthetic Biology Winter 2009 To those coming from the 424 link on Advanced Systems and Synthetic Biology Course, click here to get to the course apge (MyUW won't let me enter a long URL to point you directly at the page so I have to go via this page): text/html 2009-10-16T12:07:39-07:00 Lucian Smith http://www.sys-bio.org/sbwWiki/sysbio-news/antimony1.3 Version 1.3 of antimony has been released at antimony.sourceforge.net <http://antimony.sourceforge.net/> The latest version includes small changes to the Antimony language (most notably, the ability to set the display name of elements), and larger enhancements to the QTAntimony editor. Various stability issues have been finally tracked down and fixed, and new features have been added such as a more robust error message handling, the ability to convert SBML to different levels and versions, an… text/html 2009-09-29T09:48:01-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/304_engineering_physiology_2009 Course Schedule for BIOEN 304 (2009) - updated Sept. 09 This course is a mixture of basic physiology and engineering aspects related to physiology. Schedule Topics Assignments Schedule Grading Grading will be based on Mastery-Based Grading which is based solely on a students' master of the material. In terms for breakdown, the final grade is based on the following partitioning: text/html 2009-09-15T11:41:33-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio/fluxbalanceproposal Flux Balance Analysis is a computational technique for analyzing metabolic network in the absence of kinetic information. Within the SBML community there have been some attempts specify a way to include flux balance constraints and objective functions in SBML. This has been done either in custom annotations that cannot be shared between tools, or by using SBML features which will lead most SBML capable tools to misinterpret the model. text/html 2009-08-26T22:39:35-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/august_2009_physiology_course Notes for the August 2009 Physiology Course Download and software notes * [Stoichiometry] * [Modeling with Jarnac] * [Introduction to Quantitative Control and Regulation] * [Connectivity and Control Equations ] * [Introduction to Negative Feedback Control] * [Response to External Effectors] text/html 2009-08-23T18:40:08-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/evolcomputing Evolving Systems with Multiple Functions A system with multiple functions might reveal features of a complex system. Evolutionary methods were used to construct reaction networks with multiple functions. The networks were analyzed for modularity -- regions in the network that are utilized by different functions. Individual molecular species were removed as well as perturbed to see how each species affects the rest of the network. text/html 2009-08-20T10:22:17-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio-news/enumeration Our network enumeration page was hard to find. It now has a dedicated link in the Research Page. The enumeration page gives download links to roughly 300 million mass-action reaction networks stored in a compact format. The page also gives details and downloads for command line utilities and online tools for working with the networks. Funded by NSF FIBR. text/html 2009-08-20T10:15:15-07:00 Herbert Sauro 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 2009-08-19T12:21:49-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio-news/aug19sbw2710released We are pleased to announce the a release of the Systems Biology Workbench 2.7.10, available from: <http://sys-bio.org> The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms - to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, open-source software infrastructure which is eas… text/html 2009-08-12T20:46:18-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/libstructural Purpose The structural analysis library is a C/C++ portable software library for analyzing the structural properties of stoichiometric networks. The library supports the analysis of both flux balance and moiety conservation. The library will accept models in the form of either standard SBML or raw stoichiometry matrices. The software is distributed under the BSD license and was developed through funding from NIH grant 1R01GM081070-01. text/html 2009-08-12T12:46:01-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio-news/jsimsbwgraduateposition A new 3 to 4 year graduate position is now available in our group to work on SBW and matters related to JSim. SBW is a popular simulation software platform for systems biology and JSim a software platform for physiologists. One of the aims of the project is to bring the two applications together. Contact hsauro@u.washington.edu for details. text/html 2009-07-12T20:54:27-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/tutorials/icsb2009 The SBW team is holding a tutorial on the use of SBW at the ICSB 2009. Time and Location will be anounced soon. Link to Registration Page. Download Systems Biology Workbench 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 bifurcatio… text/html 2009-07-12T20:50:22-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio-news/jul12icsbtutorial2009 The SBW team is holding a tutorial on the use of SBW at the ICSB 2009. For more information and registration see our tutorials page. text/html 2009-06-18T14:50:28-07:00 Lucian Smith http://www.sys-bio.org/sbwWiki/sysbio/labmembers/sauro Herbert M. Sauro Associate Professor Department of Bioengineering University of Washington NEW 498_systems_and_synthetic_biology_winter_2009 August 2009 Physiology Course 304 Engineering Physiology 2009 OLD 498 Systems and Synthetic Biology Spring 2008 text/html 2009-06-08T18:05:17-07:00 Lucian Smith http://www.sys-bio.org/sbwWiki/antimony Antimony is a SBML compatible, human-readable, human-writable, model definition language. For more information about the inspiration for Antimony, see <http://sys-bio.org/sbwWiki/#human_readable_model_definition_language> For detailed documentation, source code and binaries please see the sourceforge site at: text/html 2007-02-01T03:16:17-07:00 http://www.sys-bio.org/sbwWiki/sbw/welcome Availability We are committed to bringing the same applications to all supported operating systems, be it Windows, OS X or Linux. We are making great progress on this, here some screenshots. SBW Modules There is a great variety of SBW modules available: text/html 2009-06-08T15:35:03-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sbw/platforms For the longest time SBW focussed mainly on the Windows operating systems. However we do realize that many scientists and researchers in the field of computational and systems biology are working with OS X and Linux operating systems. For this reason we are renewing our efforts in porting some of our most popular applications to those operating systems with a complete suite of tools ready by the end of the year. text/html 2009-01-21T22:36:42-07:00 http://www.sys-bio.org/sbwWiki/sysbio/enumeration_page For a detailed discussion of the networks and how they enumerated, please read our paper on arXiv.org: Enumeration and Online Library of Mass-Action Reaction Networks All data files available here are ZIP archives of text files containing encoded Network strings. We describe the format in detail here: text/html 2009-05-19T22:24:48-07:00 Sean Sleight http://www.sys-bio.org/sbwWiki/sysbio/labmembers/498_systems_and_synthetic_biology_winter_2009/fluorescence_microscopy Photo 1 Photo 2 Photo 3 Photo 4 Photo 5 Photo 6 Photo 7 Photo 8 Photo 9 text/html 2009-02-14T05:13:26-07:00 http://www.sys-bio.org/sbwWiki/playground/playground test ok ... this seems to work text/html 2009-03-01T18:48:03-07:00 http://www.sys-bio.org/sbwWiki/sysbio/softwarelibraries Here we list software libraries written by our lab. Antimony Antimony is a SBML compatible, human-readable, human-writable, model definition language. For detailed documentation, source code and binaries please see the sourceforge site at: <http://antimony.sourceforge.net/> text/html 2009-02-11T17:11:56-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/jobs None at this time. text/html 2009-01-22T15:12:55-07:00 Kyung Hyuk Kim http://www.sys-bio.org/sbwWiki/sysbio/jarnac Download SBW Jarnac is only recommended for very experienced users. If you want a nice easy tool to do simulations then use JDesigner which comes with SBW Jarnac is a language for describing and manipulating cellular system models and can be used to describe metabolic, signal transduction and gene networks, or in fact any physical system which can be described in terms of a network and associated flows. Jarnac is basically version 2 of SCAMP. text/html 2009-01-15T10:54:49-07:00 Lucian Smith http://www.sys-bio.org/sbwWiki/sysbio/labmembers/networkenumeration In the following table, rows represent species, and columns reactions. (x) = currently running (@) = Too big to run Estimated times are from Frank's Vista Machine: About those estimations, they are obviously rather rough, one 1-2 hour estimate is running since 6 hours, with 3 more to go. The estimate will get more accurate, the further along the computation goes. text/html 2009-01-08T14:30:19-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/algorithmdevelopment In silico Evolution Network Enumeration Conservation Analysis Conservation Analysis Additional Conservation Analysis Information Small Models Large Models Optimization Methods Model Fitting Tools for BioSPICE and the Systems Biology Workbench text/html 2008-12-03T15:45:07-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio-news/christmasparty2008 There will be a Christmas party at the PI's house on the 12th of December, 7 pm. Address: 10425 Roosevelt Way NE, Seattle, 98125. Drinks and food will be provided. text/html 2008-11-24T09:15:27-07:00 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/304_engineering_physiology Course Schedule for BIOEN 304 (2008) - updated Sept. 08 This course is a mixture of basic physiology and engineering aspects related to physiology. Schedule Grading Grading will be based on Mastery-Based Grading which is based solely on a students' master of the material. In terms for breakdown, the final grade is based on the following partitioning: text/html 2008-08-25T22:53:38-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sysbio-news/aug26positionavailable We have a NSF funded research position available immediately to study functional modularity in cellular networks with particular reference to how dynamic properties relate to modularity. See also jobs text/html 2008-08-18T15:20:28-07:00 Herbert Sauro 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 2008-08-04T01:28:06-07:00 Frank Bergmann 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 Herbert Sauro 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] text/html 2008-06-19T16:40:37-07:00 Sean Sleight http://www.sys-bio.org/sbwWiki/modularity text/html 2008-06-19T16:37:24-07:00 Sean Sleight http://www.sys-bio.org/sbwWiki/meetingnotes June 18 Modularity text/html 2008-06-12T17:50:30-07:00 Frank Bergmann 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 Frank Bergmann 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 Frank Bergmann 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 Herbert Sauro http://www.sys-bio.org/sbwWiki/sysbio/labmembers/jarnac_notes Q1 How do I set the random number generator seed? Use the command: rndseed (timer); Q2 How do I output data to a file? The following code will generate a matlab formated matrix to a file. f = createfile ("c:\\data.txt"); f.write ("m = ["); for i = 1 to rows (m) do begin for j = 1 to columns (m) do f.write (m[i,j]); f.write (";\n"); end; f.write ("]\n"); f.close; text/html 2008-04-29T12:45:45-07:00 Frank Bergmann http://www.sys-bio.org/sbwWiki/sbw/sbml C# Bindings now in official libsbml release The libsbml C# bindings are now included with the official libsbml release. So the code below should be seen only as example. Please download the official version from the SBML Homepage libsbml C# bindings 30th Apr. Update: updated prototype, added memory handling, OStreams, inlining of enums, replaced uints in signatures with int's text/html 2008-04-23T10:04:01-07:00 Sean Sleight 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 Sean Sleight 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 Sean Sleight 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 Sean Sleight http://www.sys-bio.org/sbwWiki/igem/insulin INSULIN!!! text/html 2008-03-05T21:02:13-07:00 Sean Sleight http://www.sys-bio.org/sbwWiki/igem/projects Possible iGEM Projects InsulinPROJECT #1... #2,.,,. text/html 2008-03-05T14:06:48-07:00 Sean Sleight 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 UW iGEM OWW site text/html 2008-02-20T10:36:33-07:00 Sean Sleight 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 Frank Bergmann 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 Sean Sleight 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 Frank Bergmann 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 Frank Bergmann 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 Sean Sleight 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 Frank Bergmann 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 Herbert Sauro 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