Annual Meeting – Workshops

On Sunday, August 11, SIMB will hold 3 pre-meeting workshops at the Sheraton San Diego Harbor Island Hotel from 8 am – 4 pm.

Workshop 1: Fermentation Basics
Workshop 2: Shake Flask Fermentation Engineering
Workshop 3: Introduction to Design of Experiments (DoE) for Bioprocess Analysis and Optimization

Workshop Fees

Advanced Registration Fees (before July 11, 2013):
SIMB Member: $450
Non-member: $600
Students: $225

Registration Fees (after July 11, 2013):
SIMB Member: $525
Non-member: $675
Students: $225
Cost includes Workshop materials, continental breakfast, lunch and breaks.

Register for Workshops

Registration for the workshops online is CLOSED.

If you have any questions please contact

Workshop 1:
Fermentation Basics

Sunday, August 11, 2013
8 am – 4 pm
Sheraton San Diego Harbor Island Hotel, San Diego, CA

Workshop Organizer: Mark Berge, Medimmune
2010-Current: Sr. Scientist at MedImmune, Inc. in the Process Cell Culture & Fermentation group leading a team responsible for fermentation and cell culture process development activities. 2006-2010: Sr. Scientist at Amgen Inc. in Cell Science & Technology group developing processes for therapeutic protein production using fermentation. 1999-2005: Sr. Scientist at Pfizer Inc. in Global Biologics division developing processes for therapeutic protein production using cell culture. 1995-1999: Process Engineer at FermPro Manufacturing in deep tank toll manufacturing for varied customers of food grade materials. Mark holds a B.S. and M.S. in Chemical Engineering from the University of New Hampshire.

About the Fermentation Basics Workshop

This workshop’s focus is to provide individuals with an introduction to fermentation concepts in industrial settings. The workshop will be lecture-based with visual aids to help the attendees understand the fermentation principles discussed. The workshop will be broken into sections based upon the topics that are being presented. After each section has been completed, the attendees will be given real life fermentation case studies that they will work through to reinforce the just discussed topics. The first section of the workshop will include topics on fermenter design including aspect ratios, agitator design, sparger design and sterilization of equipment and media. The second section will deal with actual operational issues of fermentation processes. Included will be discussions about media considerations, foam control strategies, shear, mixing, aeration, feeds and different types of fermentations and the controls involved. The workshop will finish with a section that covers issues involved in scale-up to production size fermentors.

Workshop Schedule

8:00 am
Fermentation introduction
Aerobic; Anaerobic Fermentation Organisms; Bacteria; Yeast
Filamental fungus; Microbial Growth & Production; Growth measurement methods;
Basic kinetics; Production systems

Problem Set #1
Fermentation Media
Carbon sources; Nitrogen sources; Trace elements
Fermentation Methods
Batch; Fed-Batch; Continuous

Problem Set #2
Types of Fermenters
Airlift; Stirred

Fermentation Equipment; Agitation; Spargers; Cooling; pH probes; DO probes

Basics; Methods

Problem Set #3
9:30 am Break

9:45 am
Impellers; Power input; Shear input

Problem Set #4
Aeration; Gassing strategies; Flooding; Entrainment
Effect on agitation; Oxygen transfer; Oxygen uptake measurement; Carbon dioxide evolution

Problem Set #5

Noon – 1 pm Lunch

1:00 PM
Fermenter Mass Balance
Fermenter Energy Balance

Problem Set #6
Fermentation Scaling
Benefits/ challenges

2:30 pm Break

2:45 Case Study

4:00 Workshop Ends

Workshop 2:
Shake Flask Fermentation Engineering

Sunday, August 11, 2013
8 am – 4 pm
Sheraton San Diego Harbor Island, San Diego, CA

Workshop Organizer: Duen Gang Mou, Ph.D., Founder Moubio Fermentor Shop; Ph.D. Biochemical Engineering – Massachusetts Institute of Technology Workshop
Founder of MOUBIO since 2001, develop, patent and manufacture palm size table-top plug-and-play stirred engineering vessel systems for microbiologist and everyday lab use. Forty years of research and industrial fermentation experience include Bristol-Myers Industrial Division Pilot Plant in Syracuse, NY (1979-1980), Eastman Kodak Biosciences Research Laboratories in Rochester, NY (1980-1986), Development Center for Biotechnology in Taiwan (1986-2001), visiting professor of MIT Bioprocess Engineering Program graduate teaching at Malaysia Univ of Sci & Technol, Kuala Lumpur (2002-2005), in addition to broad spectrum bio/pharma R/D and fermentation manufacturing consulting, research management support, government science & technology program advising, market/industrial information services, undergraduate and graduate adjunct teaching, industrial and business workshops, biotechnology business development, industrial liaisons, and government-industry-university networking. Publications include two Chinese biotech business books, 10+ US & international patents; 50+ publications in technical journals, conference posters and presentations. Dr. Mou is a 30-plus-year member of American Chemical Society and Society for Industrial Microbiology & Biotechnology. (Click here for for product & contact info and click here for complete CV)

To bring: calculator, pen, ruler and notepaper

About the Workshop

This one day workshop covers small fund hands-on fermentation laboratory basics from flask shaker’s to jar fermentors assembling, cleaning, maintenance, autoclaving, instrumentation for monitoring and control, to basic process calculations & diagnostics, novel flask-fermentor hybrid vessel and high experiment turnover for fermentation microbiologist of all trades. Lecture and Powerpoint slides will aid discussions on fundamentals of microbial fermentation from flask to jar fermentor and pilot to production plant. This workshop is also about practical lab culture revolution where small and simple are transformed into speed and smart, $100s and $1,000s expenses can respectively par the harvest of $1,000s and $10,000s.


I. Equipment basics: flask shaker vs. jar fermentor

  • Gas-liquid contact and mixing
  • Agitation, aeration and working volumes
  • Experiment set up and autoclaving
  • Sterility control & aseptic technique
  • Monitoring and control options
  • Equipment cleaning and maintenance

II. Jar fermentor cleaning and assembly basics

  • Standard STR fermentor construct & functions
  • Pros and cons of jar fermentor vs. shake flask
  • Flask-fermentor hybrid (US Pat 8162295)– a fermentor-like stirred flask
  • Use of antifoam, sterility control and maintenance
  • K.I.S.S.: Keep it simple and smart – mass produced multi-use consumables

Exercise Session: STR fermentor kit assembly and test run

III. Monitoring and control for high throughput studies

  • YES – rpm / air flow / off-gas
  • YES/NO – temp / pH / ORP
  • NO – DO / OD

Exercise Session: generic multi-channel monitoring and control hardware

IV. Calculation and pre-scale-up of flask culture

  • Shake flask data and their constraints
  • Shake flask data calculation
  • Shake flask data scale-up and improvement opportunities
  • Shake flask scale down and process screening

Workshop 3:
Introduction to Design of Experiments (DoE) for Bioprocess Analysis and Optimization

Sunday, August 11, 2013
8 am – 4 pm
Sheraton San Diego Harbor Island, San Diego, CA

Workshop Organizer: Marcello Fidaleo, Biomanufacturing Training and Education Center (BTEC) (Raleigh, NC, USA), University of Tuscia (Italy)
Dr. Marcello Fidaleo is an assistant professor at the University of Tuscia, where he teaches unit operations and design and analysis of experiments for the food industry. He also holds an appointment as a teaching fellow at BTEC. His research interests include modeling of membrane processes and enzymatic and microbial processes in the area of food biotechnology. He has carried out research as a visiting scholar at the Biotechnology Institute of the University of Minnesota and as a Fulbright scholar at the Department of Chemical and Biomolecular Engineering of North Carolina State University. Dr. Fidaleo holds a master’s degree in chemical engineering from the Sapienza University of Rome and a doctorate in food biotechnology from the University of Tuscia.

About the Workshop
The aim of this workshop is to provide the attendees with an introduction to the Design of Experiments (DoE) methods applied to analysis and optimization of bioprocesses. The workshop focuses on the practical application of DoE methods through the use of lectures, JMP statistical software (SAS Institute) and bioprocess case studies. The case studies, which focus on microbial fermentation and provide real data, look at the effects of factors such as medium components, induction temperature, and time on protein (product) production. Attendees will receive a practical overview of the following topics: basic statistical concepts required for DoE (hypothesis testing, confidence intervals, statistical models and Analysis of Variance – ANOVA); how to use factorial, fractional factorial, and response surface designs for the characterization and optimization of bioprocesses; how to interpret the output of experimental design software (normal probability, interaction, contour and residual analysis plots or ANOVA tables for factorial or surface response models). The workshop is targeted at all those interested in bioprocess development and optimization, particularly those new to DoE techniques.
To bring: attendees are invited to bring their own laptops with JMP pre-installed (a free 30-day trial can be downloaded on-line at prior to the workshop and activated on the day of the workshop), pen and notepaper.

Workshop Material: paper copy of PowerPoint slides, files with data for exercises.

Workshop Outline

  1. Lecture: Introduction to DoE and application to bioprocess analysis and optimization.
  2. Lecture: Basic concepts for DoE: mean and experimental error, statistical models, confidence intervals, hypothesis testing, normal probability plot.
  3. Lecture: Introduction to factorial designs: main effects and interactions and corresponding plots, analysis of variance, contour and surface plots, cube plot, residuals plot.
    Exercise: Using JMP to design and analyze factorial designs.
    Exercise: A replicated factorial design: Green Fluorescence Protein (GFP) expression by E. coli.
  4. Lecture: Unreplicated and Fractional factorial designs.
    Exercise: A fractional factorial design: GFP expression by E. coli.
  5. Lecture: Response surface designs.
    Exercise: Optimization of protein production by a response surface design.