Pathway Modeling Workshop at UW (Sept 11 -12, 2014)
Our lab investigates how cells operate using experimental, theoretical and computational approaches.See the research page for details.
You may be wondering where the class and teaching pages have gone. Although the domain sys-bio.org is managed by the university it is not an official university URL, therefore we are not permitted to include any teaching material on the web site.
Any views, opinions, data, documentation and other information presented on this web site are solely those of the author and do not represent those of the University of Washington.
News and Views Article Published
17th May 2013
Fellowship to Wilbert Copeland
12th April 2013
I am please to announce that graduate student Wilbert Copeland was awarded one of the much coveted Merck fellowships for this work on Aptamer detection technology he is developing in our lab.
2nd Edition Published
27th December 2012
The second edition of Enzyme Kinetics for Systems Biology has just been released. Copies can be purchased at CreateSpace now (27th Dec, 2012) or from Amazon on the 2nd Jan 2013 for $49.95. Contact hsauro at u.washington.edu if you purchased the 1st edition and would like to purchase the 2nd edition at a 50% discount. If you wish to buy copies for a class, contact hsauro for a class discount.
8, November, 2012
In search of noise-induced bimodality, Kyung Hyuk Kim, and Herbert M Sauro
Kim and Sauro BMC Biology 2012, 10:89, http://www.biomedcentral.com/1741-7007/10/89
SBOL Workshop Today:
7, November, 2012
The 8th SBOL workshop starts today in Boston.
1 November, 2012
Yang S, Sleight SC and Sauro HM Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits, Nucl. Acids Res. (2012), doi:10.1093/nar/gks972
3rd, August 2012
We recently had a successful workshop: “Developing Multi–Scale, Multi–Cell Biological Simulations with CompuCell3D and SBW” held at the Hamner Institute in North Carolina. As the title suggests this was a joint workshop between ourselves and the popular multicellular simulation engine compucell3d. This is the 6th workshop we have help. Given the demand for these workshops we are hoping to expand these to an annual summer school event next year. Those who are interest might like to learn we are also holding a similar European workshop this October (2012), 8th to 13th. Register now if you wish to attend.
10th, July, 2012
Sleight CS and Sauro HM Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems July 2012, doihttp://dx.doi.org/10.7551/978-0-262-31050-5-ch063
Art in Systems Biology
9th, June, 2012
We maintain a piece of software called roadRunner which is a backend simulator used in a variety of software tools. It was originally written in C# by Bergmann and Sauro but this year we decided to rewrite it in C/C++ to broaden its appeal. Totte Karlsson is doing the rewrite which is now close to completion. In the process he used gource to record all the changes that happened in the form of a video as the software was redeveloped. Here is the video he made.
Art in Synthetic Biology
4th, May 2012
Sean Sleight in his work on ways to detect failing synthetic circuits, happened to produce this colorful plate showing randomized assembly of genetic circuits using four promoters (pLacI, pLuxR, pBAD, pTetR), four coding sequences (GFP, eYFP, eCFP, and maxRFP), and four transcriptional terminators (J61048, B0015, B0014, B0011), and one vector (pGA3K3-araC-luxR) in NEB Turbo cells under UV light.
Crowd-Funding Microryza Project:
12, April 2012
There is a new crowd funding site has just started that specializes in funding research. Called Microryza, the organization aims to focus on funding risky research projects or educational outreach efforts. Our group has submitted one of the first projects (no affiliation to the company) to build an interactive and modular electronic system to explore gene regulatory networks.
28, March 2012
Copeland WB, BA Bartley, D Chandran, M Galdzicki, KH Kim, S Sleight, CD Maranas, HM Sauro. 2012. Computational tools for metabolic engineering. Metabolic Engineering. Volume 14, Issue 3, May 2012, Pages 270–280 – Currently the most downloaded paper in the last 90 days at Metabolic Engineering.
New version of libSBOLj available
7th March 2012
A new version of the java library for SBOL that works with the new serialization syntax is now available from Evren Sirin. The library can be found with source code at the following location:
The library comes with an updated version of the XML schema and can read and write SBOL documents and also validate against the schema.
Tenure Track Position in Synthetic Biology at UW
21th February 2012
The University of Washington
Department of Bioengineering
Invites Applications for Tenure Track Position in Synthetic Biology
The Department of Bioengineering at the University of Washington (UW) invites applications for a tenure track position in the area of Synthetic Biology. Successful candidates will have a plan to apply synthetic biology to problems with direct relevance to human health.
Applications are sought at all levels: Assistant, Associate and Full Professor, but those at the Assistant Professor level are particularly encouraged. Ph.D. or M.D. degrees are required. The successful candidate will be expected to develop an internationally recognized research program and to participate in the teaching and service missions of the department. Scientists and engineers who apply should show evidence of excellence, originality and productivity in research and potential for excellent teaching. In order to maximize the impact of this hire, successful candidates will be selected, in part, on the basis of their complementarity to existing UW faculty with expertise in synthetic biology, and to other synthetic biology faculty being hired in other departments at this time (see http://synbio.washington.edu). These candidates will be expected to attract strong support from one or more additional departments within the UW and will be expected to follow UW’s strong tradition of collaboration across disciplinary boundaries. Candidates with interests in translational medicine are also encouraged to take advantage of our active Coulter Translational Research Partnership.
Applications must be submitted electronically at https://www.engr.washington.edu/facsearch/apply.phtml?pos_id=111. Applicant review will begin immediately and continue until the position is filled. All positions are contingent on the availability of funding.
The University of Washington is a recipient of a National Science Foundation ADVANCE Institutional Transformation Award to increase the participation of women in academic science and engineering careers. UW faculty engage in teaching, research, and service. The University of Washington is building a culturally diverse faculty and strongly encourages applications from women and minority candidates. The University of Washington is an Affirmative Action, Equal Opportunity employer.
Mary Gates Scholarship Award
12th December 2011
We are pleased to report that Bennett Ng in out group has been awarded Mary Gates Scholarship, well done Bennett!
New Paper: Adjusting phenotypes by noise control
PLoS Comp Bio, supported by NSF, Theory in Biology
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.
UW wins Grand Prize at the 2011 iGEM Competition
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:
Levinson Emerging Scholars Award
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.
New Software Positions Available
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”’
5th October, 2011
The Synthetic Biology Open Language – SBOL
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
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
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).
New Simple Copasi API
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.
New Software Positions Available
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.
Summer Course in Modeling Transport and Metabolism in Cardiovascular and Respiratory Systems August 2011
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.
Announcing the Joint SBW & CompuCell3D Workshop August 2011
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
Version 2.8.3 SBW Released July 2011
We are pleased to announce the release 2.8.3 of the Systems Biology Workbench.
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.
Announcement: 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.
Deepak Chandran awarded Autodesk Fellowship
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.