Workshops

NOTE: Jobs workshop is now filled. Will be repeated Thursday afternoon, August 5, 2-4:30 pm. No signup required.

Workshops 1 and 2 include continental breakfast, lunch and two breaks plus workshop materials.

WORKSHOP 1
Use of small-scale screening systems to predict results from high-throughput formats

NOTE: Workshop is now full.

Sunday, August 1, 2010
TIME: 8 am - 4 pm
LOCATION: University of California, San Francisco (UCSF)

Organizers
David Laidlaw, Applikon Biotechnology
John Poppleton, Applikon Biotechnology

Design of experiment (DOE) approaches to media development, host strain selection, and process development demand high-throughput tools capable of accommodating a large number of experiments in a manageable format. A wide range of vessel and technology alternatives are available; when the advantages and limitations of the platforms are understood, they offer enormous benefits for upstream fermentation and process development work.

In this workshop, we will use an E. coli fermentation process as a model to discuss strategies for implementing high throughput screening processes for predicting results in bioreactors. The importance of kLa values, media composition, and growth parameters at well-plate stages of development will be discussed in detail. The use of online well-plate data and control cultures for prediction of stirred vessels will be investigated.

The hands-on component of this workshop will include laboratory experiments with advanced well-plate systems, sensored well-plate systems, high-throughput microbioreactors, and traditional autoclavable bioreactors.

This workshop is targeted to individuals responsible for upstream process development and increasing overall fermentation throughput.

Workshop price:
SIM Members: $375
Nonmembers: $525
Students: $187.50

Note: Late fees apply after July 1. There must be a minimum of 5 individuals registered to hold workshops with fees.

WORKSHOP 2
Pathway Tools and BioCyc: Software and databases for pathway and genome data in support of metabolic engineering

NOTE: Spaces available. Register onsite in Seacliff Foyer starting 7:30 am, Sunday, August 1.

Sunday, August 1, 2010
TIME: 8 am - 4 pm
LOCATION: San Francisco Hyatt Regency Embarcadero

Presenters
Tomer Altman, SRI International
Peter D. Karp, SRI International (Organizer)
Suzanne Paley, SRI International

The tutorial will introduce new or occasional users of BioCyc and Pathway Tools to the rich bioinformatics functionality and comprehensive data content that this site provides.

BioCyc couples genome data with metabolic pathways and operons for 500 sequenced organisms. Its EcoCyc and MetaCyc databases are very highly curated; the information in EcoCyc and in MetaCyc were each derived from more than 18,000 publications. EcoCyc provides the most detailed description of the regulatory network of any organism. BioCyc provides tools for analyzing gene expression and other omics data, and for comparative genomics and comparative pathway analysis.

Additionally, in its role as a repository of metabolic information, BioCyc provides an ideal platform with which to develop genome-scale metabolic models.

Format
The tutorial will combine lectures and hands-on classroom exercises, with approximately equal time devoted to each during the course of the six hour tutorial. We hope to have computers available for tutorial participants. In addition, some participants may choose to install Pathway Tools on their laptops prior to the tutorial.

Topics to be covered include:

  1. Survey of microbial pathway databases
  2. Data content of BioCyc
    1. Data content of the EcoCyc Escherichia coli database
    2. Data content of the MetaCyc datatabase of experimentally elucidated metabolic pathways and enzymes
    3. Data content of other BioCyc databases
  3. Survey of BioCyc data pages
    1. Pathway page
    2. Reaction page
    3. Compound page
    4. Protein page
    5. Gene page
    6. Transcription unit page
  4. Methods of searching BioCyc
  5. Pathway Tools genome browser
  6. Pathway Tools omics viewers and object groups
Faculty contact information
Peter D. Karp, PhD
Director, Bioinformatics Research Group
SRI International, AE206
333 Ravenswood Ave
Menlo Park, CA 94025
Voice : 650-859-4358
Fax : 650-859-3735
E-mail: pkarp@ai.sri.com

Bios
Peter D. Karp is director of the Bioinformatics Research Group within the Artificial Intelligence Center at SRI International. Dr. Karp has authored more than 90 publications in bioinformatics and computer science. Dr. Karp is the bioinformatics architect of the EcoCyc and MetaCyc databases. He has developed algorithms for visualization of metabolic pathways, and for prediction of metabolic pathways from genome data. His research interests include metabolic pathway bioinformatics, genome annotation, scientific visualization, biological ontologies, and database interoperation. He received the PhD degree in Computer Science from Stanford University in 1989.

Suzanne Paley and Tomer Altman are scientific programmers in the SRI Bioinformatics Research Group.

Workshop price:
SIM Members: $375
Nonmembers: $525
Students: $187.50

Note: Late fees apply after July 1. There must be a minimum of 5 individuals registered to hold workshops with fees.

WORKSHOP 3
I AM A MICROBIOLOGIST - NOW WHAT?

NOTE: The Sunday workshop is filled. It will be repeated on Thursday afternoon, August 5 from 2-4:30 pm. No signup required. Attendees may bring a copy of their resume for critique (optional).

Sunday, August 1, 2010
TIME: 1 p.m.
LOCATION: San Francisco Hyatt Regency Embarcadero
No meals Included.

FREE Job Workshop for New Graduates and Postdocs
Presented by Bob Berger, BB and Associates, Sarasota, Florida; SIM Placement Chair

Topic areas:

  • Job Search
  • Resume Writing
  • Networking Tips

WORKSHOP 4
Synthetic Biology: From theory to application

NOTE: Spaces available. Register onsite at the main SIM registration desk, Grand Foyer by noon, Sunday, August 1.
Sunday, August 1, 2010
TIME: 1:00 - 5:00 pm
LOCATION: San Francisco Hyatt Regency Embarcadero

Presenters
J. Christopher Anderson, University of California, Berkeley
Leonard Katz, Synthetic Biology Research Center, University of California, Berkeley (Organizer)
Christopher Voigt, University of California, San Francisco

Synthetic biology employs the fundamentals of molecular and systems biology, chemistry, physics, engineering, and computer science for the design and construction of new biological parts, devices, and systems as well as for the redesign of existing systems. Synthetic biology provides useful products and applications in a host of fields including medicine, agriculture, chemicals, biofuels, and food. The challenge is developing scalable, reliable, and cost effective strategies for building ever more complex designs. The need for streamlined workflows is a goal with many technical barriers, some of which are conceptual in nature. Some require the development of new software; others require new wetware tools. The purpose of this workshop is to introduce the emerging field of synthetic biology and to present examples of work currently being undertaken to achieve these goals.

In this workshop, we will:
  • highlight the tools and practices for building complex engineered organisms through examples of construction of genetic and biochemical devices, and the description of methodologies used for host engineering.
  • describe some of the basic principles for the design, construction, and tuning of different types of genetic circuits. A focus will be on genetic logic, where biochemical interactions, either at the protein or nucleic acid level, are combined to integrate multiple input signals and control a single output signal.
Mathematical modeling has been an effective tool in tuning and optimizing the circuits; examples of modeling and simulation will be described. We will:
  • outline the design principles employed for the construction of several systems and describe how these approaches can be combined to create programs that control cellular processes relevant to current and future applications in many areas that employ biotechnology.
  • Briefly describe SynBERC, a multi-university initiative in synthetic biology.
Instructors' Contact Information
J. Christopher Anderson, PhD
Assistant Professor
Department of Bioengineering
University of California, Berkeley
Tel: (510) 666-3611
jcanderson@berkeley.edu

Leonard Katz, PhD
Research Director
Synthetic Biology Research Center
University of California-Berkeley
Tel: (510) 486-5085
katzl@berkeley.edu

Christopher Voigt, PhD
Associate Professor
Department of Pharmaceutical Chemistry
University of California-San Francisco
Tel: (415) 514-9727
cavoigt@picasso.ucsf.edu

Workshop price
SIM Members: $187.50
Nonmembers: $262.50
Students: $93.75

Note: Late fees apply after July 1. There must be a minimum of 5 individuals registered to hold workshops with fees.