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CATEGORIES:CL-CompBio
SUMMARY:A Standard-Enabled Workflow for Synthetic Biology 
 - Professor Chris J. Myers University of Utah
DTSTART;TZID=Europe/London:20191010T160000
DTEND;TZID=Europe/London:20191010T170000
UID:TALK131065AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/131065
DESCRIPTION:A synthetic biology workflow is composed of data r
 epositories that provide information about genetic
  parts\, sequence-level design tools to compose th
 ese\nparts into circuits\, visualization tools to 
 depict these designs\, genetic design tools to sel
 ect parts to create systems\, and modeling and sim
 ulation tools to evaluate alternative design choic
 es.  Data standards enable the ready exchange of i
 nformation within such a workflow\, allowing repos
 itories and tools to be connected from a diversity
  of sources. This talk describes one such\nworkflo
 w that utilizes the growing ecosystem of software 
 tools that support the Synthetic Biology Open Lang
 uage (SBOL) to describe genetic designs\, and the\
 nmature ecosystem of tools that support the System
 s Biology Markup Language (SBML) to model these de
 signs.   In particular\, this presentation will de
 monstrate a workflow using tools including SynBioH
 ub\, SBOLDesigner\, and iBioSim.  SynBioHub (http:
 //synbiohub.org) is a database designed for storin
 g synthetic biology designs captured using the SBO
 L data model\, and it provides\nboth a RESTful API
  for computational access and a user-friendly Web-
 based frontend.  SBOLDesigner is a sequence editor
  that allows the designer to fetch\nparts from a S
 ynBioHub repository and compose them to construct 
 larger designs.\nFinally\, iBioSim is genetic mode
 ling\, analysis\, and design tool that provides a 
 means to construct SBML models for these designs t
 hat can be simulated and\nanalyzed using a variety
  of techniques. Both SBOLDesigner and iBioSim also
 \nsupport uploading these larger system designs ba
 ck to the SynBioHub repository.\nFinally\, this ta
 lk will demonstrate how this workflow can be utili
 zed to produce a complete record of a genetic desi
 gn facilitating reproducibility and\nreuse.\n\n\n=
 =================================\n\nChris J. Myer
 s received the B.S. degree in Electrical Engineeri
 ng and Chinese\nhistory in 1991 from the Californi
 a Institute of Technology\, Pasadena\, CA\, and\nt
 he M.S.E.E. and Ph.D. degrees from Stanford Univer
 sity\, Stanford\, CA\, in 1993\nand 1995\, respect
 ively. He is a Professor and Associate Chair in th
 e Department\nof Electrical and Computer Engineeri
 ng\, University of Utah\, Salt Lake City\, UT.\nDr
 . Myers is the author of over 170 technical papers
  and the textbooks\nAsynchronous Circuit Design an
 d Engineering Genetic Circuits. He is also a\nco-i
 nventor on 4 patents. His research interests inclu
 de asynchronous circuit\ndesign\, formal verificat
 ion of analog/mixed signal circuits and cyber-phys
 ical\nsystems\, and modeling\, analysis\, and desi
 gn of genetic circuits. Dr. Myers\nreceived an NSF
  Fellowship in 1991\, an NSF CAREER award in 1996\
 , and best paper\nawards at the 1999 and 2007 Symp
 osiums on Asynchronous Circuits and Systems.\nDr. 
 Myers is a Fellow of the IEEE\, and he is a Member
  of the Editorial Board\nfor ACS Synthetic Biology
 \, Engineering Biology\, and Synthetic Biology\, a
 nd has\nserved on the Editorial Boards for the IEE
 E Transactions on VLSI Systems\, IEEE\nDesign & Te
 st Magazine\, IEEE Life Sciences Letters\, and For
 mal Methods in\nSystem Design. Dr. Myers has also 
 served as an editor for the Systems Biology\nMarku
 p Language (SBML) standard and is the Chair of the
  Synthetic Biology Open\nLanguage (SBOL) standard 
 steering committee\, as well as the COMBINE standa
 rd\ncoordination board.\n\n
LOCATION:Department of Computer Science and technology\, Le
 cture Theatre 2
CONTACT:Pietro Lio
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