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.
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.
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
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
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
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.
Funding Provided by:
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