12th December 2011
We are pleased to report that Bennett Ng in out group has been awarded Mary Gates Scholarship, well done Bennett!
11th December 2011
Genetically identical cells can show phenotypic variability. This is often caused by stochastic events that originate from randomness in biochemical processes involving in gene expression and other extrinsic cellular processes. From an engineering perspective, there have been efforts focused on theory and experiments to control noise levels by perturbing and replacing gene network components. However, systematic methods for noise control are lacking mainly due to the intractable mathematical structure of noise propagation through reaction networks. Here, we provide a numerical analysis method by quantifying the parametric sensitivity of noise characteristics at the level of the linear noise approximation.
8th November 2011
Congratulations to the University of Washington team who this week won the grand prize at the international synthetic biology iGEM competition! For details their work on biofuels and a gluten eating enzyme see their web site at:
27th, October 2011
We are pleased to report that Bennett Ng in out group has been awarded the Levinson Emerging Scholars Award in order to continue his research on cost effective microchemostats.
20 October, 2011
A number of new positions have opened up in the lab as a result of a new NIH grant to support our software efforts. If you’re interested in developing the next-generation of modeling and model management software tools for systems biology please contact me at hsauro at u.washington.edu. The position will involve collaboration with industry and local research institutes in Seattle with possible commercialization opportunities.
19 October, 2011
IMAG/MSM Webinar held 19 Oct, topic:
”’Discussion topic: Model reproducibility and component/parts repositories”’
Model Reproducibility and Parts Repositories
5th October, 2011
I am pleased to announce the release of the draft specification of SBOL 1.0. The current draft defines a standard way to describe in a hierarchical manner a DNA strand and associated information. Once the draft is finalized in December 2011 we will begin to start considering extensions to SBOL which is where it gets much more exciting. These extensions will include:
1. Host/Chassis Context
2. Assembly Provenance
3. Performance metrics and Experimental Data
4. Visualization
5. Modeling
This is not an exclusive list but is the first set of extensions that will be developed by the community.
I should also add that along side the draft there is also under development a supporting software library (currently in Java) to assist developers.
Details of the draft and where to download it is given below:
BBF RFC 84: Synthetic Biology Open Language (SBOL) Version 1.0
DOI 1721.1/66172
http://dspace.mit.edu/handle/1721.1/66172
The list of authors who contributed to this draft is given below. I want to congratulate them for their tremendous effort and considerable number of man hours in producing this draft!
Laura Adam (Virginia Bioinformatics Institute),
Aaron Adler (BBN Technologies),
J. Christopher Anderson (University of California Berkeley),
Jacob Beal (BBN Technologies),
Matthieu Bultelle (Bioengineering, Imperial College London),
Kevin Clancy (Life Technologies),
Kendall G. Clark (Clark & Parsia, LL C.),
Douglas Densmore (Elect and Comp Engineering, Boston University),
Omri Drory (Genome Compiler),
Drew Endy (BIOFAB and Bioengineering, Stanford University),
Michal Galdzicki (Biomed and Health Info, UW, Seattle)
John H. Gennari (Biomed and Health Info, University of Washington),
Raik Gruenberg (EMBL-CRG Systems Biology program, CRG),
Jennifer Hallinan (School of CompScience, Newcastle University),
Timothy Ham (Joint BioEnergy Institute),
Allan Kuchinsky (Agilent Technologies),
Matthew W. Lux (Virginia Bioinformatics Institute),
Curtis Madsen (School of Computing, University of Utah),
Akshay Maheshwari (UCSD),
Barry Moore (Human Genetics, University of Utah),
Chris J. Myers (Electrical and Comp Engineering, University of Utah),
Carlos Olguin (Autodesk Research),
Jean Peccoud (Virginia Bioinformatics Institute),
Hector Plahar (Joint BioEnergy Institute),
Matthew Pocock (School of Comp Science, Newcastle University),
Cesar A. Rodriguez (BIOFAB),
Nicholas Roehner (Elect and Comp Engineering, University of Utah),
Vincent Rouilly (Biozentrum, University of Basel),
Herbert M. Sauro (Bioengineering, UW, Seattle)
Trevor F. Smith (Agilent Technologies),
Guy-Bart Stan (Bioeng, Centre for Synth Biol and Innovation, Imperial College London),
Vinod Tel (Bioengineering, Imperial College London),
Alan Villalobos (DNA 2.0, Inc.),
Mandy Wilson (Virginia Bioinformatics Institute),
Chris Winstead (Elect and Comp Engineering Utah State University),
Anil Wipat (School of Computing Science, Newcastle University),
Fusun Yam an Sirin (BBN Technologies).
1 October, 2011
We (Deepak Chandran – deepakc at u.washington.edu) have just released a beta version of a new api for Copasi. This api is much simpler to use that than the native api that is supplied with Copasi. Further details including documentation can be found at Copasi Simple API together with example code, This work was funded by subcontract NIGMS grant: GM076692 from James Glazier, Indiana University.
29 August, 2011
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.
August 20, 2011
Summer Course. Course participants will learn basic physiological systems-level modeling, using the cardiovascular and respiratory systems as their guide. On the Thursday morning participants will learn about metabolic modeling using SBW.
August 1, 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 and blog entry Modeling Course
DOWNLOAD Windows version of Systems Biology Workbench: 2.8.3
Go to Sourceforge page for other OS specific downloads
This link will actually install 2.8.2, however find the update utility in the start mennu under the Systems Biology Workbenach entry and start the update, this will retrieve and install 2.8.3.
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.
June, 2011
Graduate student Deepak Chandran was awarded an AutoDesk summer fellowship that allowed him to spend part of his summer at Autodesk’s IDEA Studio . Deepak explored the possibilities of applying Autodesk technology, Maya, to synthetic biology.
