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Sauro Lab
University of Washington
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What is SBW 
Research Impact 
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Available Positions 
CSB Links 
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
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New Software Positions Available

29 August, 2010

A number of new positions have opened up in the lab as a result of a new NIH grant to support our software efforts. In particular we will be focusing in model reproducibility (in relation to SED-ML), model publishing in journals, full cross-platform support, version control and model change tracking. I will therefore be offering a number of positions in my lab to support this effort. If anyone is interested in modeling, SBML, visualization, programming and developing a single cross-platform tool with a plugin interface to consolidate SBW into one main tool, please get in touch at hsauro at u.washington.edu and I can send you further details.

New Look for the Site Coming Soon

28 August, 2010

We are in the process of transitioning to a new web site, same url but different look. The reason is to give us an opportunity to reorganize the site and to make it easier to edit the content.

Version 2.8.3 SBW Aug 2011

We are pleased to announce the release 2.8.3 of the Systems Biology Workbench.

SBW logo

DOWNLOAD Windows version of Systems Biology Workbench: 2.8.3

Go to Sourceforge page for other OS specific downloads

NSR Modeling Course Workshop August 2011

Workshop Page

Announcing the Joint SBW & CompuCell3D Workshop August 2011

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. For more information see our Workshop Page

Annoucement: Modeling Webinar Hosted by Rosa

A Webinar will be held on Tuesday 26th of July at 12:00 to 1:00 pm EDT on Standards and Software in Biomedical Systems Modeling. Register here if you wish to attend

The webinar will describe the development of biomedical modeling standards during the last 10 years and how that has stimulated a great many other initiatives. Dr Sauro will also describe software developments he has been involved in and possible future developments in high performance computing and real-time simulation. He will demonstrate software and discuss future plans for the current suite of systems biology modeling tools.

Rosa is a company that specializes in creating robust mathematical models that simulate drug effects and trial outcomes. See their Web site for further details.

Group Blogs and Web Pages

Visit our group blogs at:

TinkerCell Blog by Deepak Chandran

AnalogMachine Blog: Cells, Networks and Computation

UW Synthetic Biology Blog

Multiscale Blog by Ryan Roper

Visit our member web pages at:

Dr Kyung Kim, Stochastic Systems

Dr Sean Sleight, Experimental Synthetic Biology

New Textbook

Enzyme Kinetics for Systems Biology
by Herbert M Sauro
Published at analogmachine.org
318 pages, 94 illustrations and 75 exercises

e-book: $9.95 ; paperback $29.95 Purchase at Amazon Store
Special discounts are availble for class purchases and international sales of the e-book.

This new monograph introduces students to basic reaction kinetics, including enzyme kinetics, cooperativity, allostery and gene regulatory kinetics. The text introduces a number of modern concepts such as generalized rate laws, elasticities and systems biology thermodynamic quantities. The text is suitable for junior undergraduate level in the US and 2nd year undergraduates in the UK. The text can also be used as a reference text for graduates and other researchers.

Goto analogmachine.org for more information or Google books for a preview.

Version 2.8.2 SBW March 2011

We are pleased to announce the release 2.8.2 of the Systems Biology Workbench.

SBW logo

DOWNLOAD Windows version of Systems Biology Workbench: 2.8.2

Go to Sourceforge page for other OS specific downloads (SBW 2.8.1)

Note that for existing users, you can use the update application found under Systems Biology Workbench/Utilities in the start menu.

JDesigner

JDesigner Read more... is our visual network design tool for systems biology. A simplar tool for synthetic biology, called TinkerCell is also available and developed by graduate student Deepak Chandran Funded in part by grants Microsoft, NSF and the NIH.




Old News

Announcing the ICSB 2010 SBW Tutorial

We are pleased to announce the ICSB 2010 SBW Tutorial, to be held on Sunday October 10th. For more information see our Tutorials Page.

Announcing the UW JSim/SBW Course August 2010

Part of this course will focus on the use of SBW in relation to metabolic modeling. A text book, models and notes will be provided. For more information see our Workshop Page

Announcing the Joint SBW & CompuCell3D Workshop 2010

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. For more information see our Workshop Page

SBW Paper Published

If SBW is used to generate research results or a citation is required in a review, please use the following citation:

Frank T. Bergmann, Herbert M. Sauro. SBW - a modular framework for systems biology. Frank T. Bergmann, Herbert M. Sauro December 2006 Proceedings of the 37th conference on Winter simulation WSC '06 Publisher: Winter Simulation Conference Pages: 1637 - 1645 BibTex link

ICSB Tutorial coming up

The SBW Team will be giving a tutorial at the ICSB 2009. More information is available on the tutorial wiki page.

Standards and Specifications in Synthetic Biology

Workshop Logo On April 26-27, 2008 we organized a Workshop on Standards and Specifications in Synthetic Biology at the Talaris Conference Center in Seattle, Washington. The conference was a success and participants from various countries presented and discussed:

  • experimental standards,
  • organization/storage/sharing of biological parts,
  • computer languages for modeling synthetic biology and
  • software tools for synthetic biology.

A proposed data model for Biobricks was created to describe the minimal amount of information needed to specify a Biobrick and how to classify Biobricks into families. A report of the workshop will be published in IET Synthetic Biology.

Read more...

Systems and Synthetic Biology Course 498: Spring 2008

This course will cover the basics of cellular network dynamics, control and function. Genetic, protein signaling and metabolic pathways will be discussed in relation to their properties and enginering. A special section on practical aspects of synthetic biology will be given with possible hands-on experience in the lab in using basic molecular biology techniques (Web page).

Comparing Simulation Results

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.

Read more

ICSB Tutorial coming up

The SBW Team will be giving a tutorial at the ICSB 2007. More information is available on the tutorial wiki page.

Version 2.7.7 of SBW Released April 2008

We are pleased to announce a release of the Systems Biology Workbench 2.7.7 ,available

SBW logo

DOWNLOAD the Systems Biology Workbench

CompuCell3D and SBW

CompuCell3D is a tissue and organ simulator based on the Cellular Potts Model. In collaboration with the CompuCell3D team at Indiana University (Glazier et al.) we have demonstrated a combined tool, linking CompuCell3D with SBW. The demonstration illustrates the use of Python as a flexible scripting glue that combines the Cellular Potts Model with the portable reaction based simulator (roadRunner) that is available with the Systems Biology Workbench. The movie available here demonstrates a 2D tissue made up of 115 cells, in each cell there is a simple reaction network that generates an oscillatory signal. This signal is used to modify the properties of the cell membrane which in turn influences the movement of cells through the tissue. The movie itself was generated from one of ComputeCell3D's tools. All simulations were run on Linux but could easily have been generated on Windows or the Mac OS X.

Online Services started

As of Nov. 17th 2005 several Web Applications are available on sys-bio org. Including:

For BioSPICE users, download the SBW Analyzers here
Version 1.2 is compatible with BioSPICE 6.0

biomodels.net logo

NEW BIOMODELS: We are very pleased to announce that we are a contributor to the first formal database of computational models for Systems Biology. This is a joint venture between EBI, Caltech, Sys Bio Institute, Japan, KGI and Stellenbosch, S. Africa. The database infrastructure was developed by Marco Donizelli and Nicolas Le Novère at EBI. KGI will be providing curation expertise (Harish Dharuri). Download models from BIOMODELS and simulate then under a large number of simulators including the Systems Biology Workbench.

This site is devoted to computational aspects of biochemical networks, their dynamics, function and evolution, be they metabolic, signal or gene networks. Various labels have been used to describe the study of such networks, including 'Systems Biology', 'Computational Biology' or even perhaps Molecular Physiology. We will use the label Computational Systems Biology to cover an area of research concerned with how chemical networks within living systems behave.

Computational Biology

Funding Provided by:

NIH logo NSF logo

Visitor Map

This map displays the last 20 visitors to the site, starting September 22nd, 2007.

Last updated:  Wednesday, July 30, 2014


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