27016 Design Build 1

January 3-week, 09:00-17:00

Devices for measuring

cell growth
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Bioengineering
Bioengineering 1
 Design Build courses are multidisciplinary

Design Build 1 Biology Computing

Hardware/
Electronics

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 Design Build 1 Course is different from
• Not a typical lecture course • No text book
• No reading assignments
• Not a typical lab course • Activities more like ‘play’ than ‘work’

• You will learn by doing

• Learning depends on the effort you
• You will need to work independently and put into it!
apply yourselves – You will learn a lot if you simply apply
– Not all tasks specified in complete yourselves
detail (as this tends to prevent – Casual observers will not learn much
independent thinking, problem solving) (and as a result you may not pass the
course)
• You will make decisions sometimes with
minimal input or feedback

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 Course Teachers (“Senior Consultants”)

Bioengineering Bioengineering Health Tech Compute

Arto Heiskanen Chris Workman Johan Ulrik Lind Edward Todirica

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 Teaching Assistants (“Technical Consultants”)

GE Autonomous
GE
Systems Eng.

Jianan Xu Mattias Erik Tammi Ivan Doudka

Section A Section B Section C

Contact for Contact for Contact for
Groups 1-15 Groups 16-30 Groups 31-45

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 Additional support (“Technical Consultants”)

3D Design Circuit design and programming

Health Tech Health Tech Compute

Irene Papiano Sarkhan Butdayev Charalampos

Orfanidis

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 Additional support (“Technical Consultants”)

Lab work

Bioengineering Biosustain Biosustain

Louise La Barbera Mohammad Radi Matin Nuhamunada

Kastberg

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 Structure of the course
• Short lectures or announcements in the morning

• Group projects/assignments

• Individual assignments

• Group work supported by TAs (time varies daily)

• Independent group work (time varies daily)

• Laboratory work (from day 7 in B207)

 Requirement: Passed Safety Quiz

• Evaluation Pass/Non-Pass assessed on

 Exercises (group and individual)
 Short MC Exam (Wed 18/1) (individual)
 Video presentation (group)

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 What you will do…
• You will design, build and test a device to measure cell growth

• Learn to make 3D designs to solve a technical challenge

• Design and build a circuit

• Program a microcontroller

• Analyze the performance of your devise

• Analyze and extract features from biological data

• Make a short video of you project

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 How will you do it…
• Project work in groups of 3
– The main venue for project work is B303A-A042

• You will make a project plan and follow your plan (group assignment)

• All groups are divided into 3 Sections:

– Section A: Groups 1-15 (Jianan Xu)
– Section B: Groups 16-30 (Mattias Erik Tammi)
– Section C: Groups 31-45 (Ivan Doudka)

• Lab work: 1 section (15 groups) per lab session (3 h)

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 How will you do it…
• Follow course on DTU Learn

• Overview page has many important links

• Questions start with your Section TA

• TA guidance is also available on Piazza (linked to

DTU Learn)

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 Course plan overview (Subject to change)

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 Locations: B303A/A042, B207/037 (+ group room 048)

LAB – B207

”HQ” – B303A

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 Additional locations: B306/A032, B116/081)

• B306 – Jan 2 and Jan 6

B116 • B116 – Jan 5

B306

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 Types of activities, things you will learn
• Device design:
– 3D design software
– 3D printing
– Simple circuit design

• Device build:
– Programming a microcontroller
– Simple circuit build, breadboard prototyping

• Laboratory:
– Basic lab safety
– Use of micropipette
– Use of a spectrophotometer
– Cultivation of microorganisms
– Microscopy
– Analysis of Colony forming units (CFU)

• Data analysis:
– Calculate optical density (OD)
– Standard curves (linear regression)
– Calibration
– Fitting an exponential function

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 Learning objectives for the course
• Describe the innovation and engineering process
• Devise a project plan based on the decomposition of a larger problem into
component tasks
• Apply design principles to design a measurement device for studying a
living system
• Design and construct a measurement device using tools for automated
fabrication, e.g. 3D printing, and prefabricated sensors and light sources
• Analyze data from a living system
• Evaluate the performance and limitations of the developed device
• Describe the value of working in a project team
• Communicate the project work and results in a video

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 Motivation
Why is it important to measure living systems?

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 Important production animals and plants with
easily measurable traits

Example traits?
How to influence them?

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 Important production organisms are less
easy to measure or count
Microorganisms are very small.

1 micron
1 um

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 How small is a micrometer (or micron) μm?

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 Exploiting the biochemistry of living cells

INPUTS Carbon Nitrogen

O2
source source
Bacteria

metabolism Yeast
CELL
(fermentation)

Other fungi

Ethanol
Penicillin
OUTPUTS CO2 Byproducts
Insulin
Enzymes

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 Which products do not involve fermentation?
butter yogurt
wine chocolate
beer

cheese spegepølse
chorizo

soy kimchi
vinegar
potato chips sauerkraut Insulin

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 Problem Definition (Hypothetical)
• A company developing a new bio-based process have hired you to find a
new strain of yeast that can decrease the time of the production process.

• Candidate strains should have growth characteristics suitable for large

scale production

• Initial screening should characterize the growth rate of 100s of strains in

a cost effective manner

• For this problem, you are to design and build a low cost cell growth
analyzer

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 Growth curve: cell density profile

Alsuhaim H et al. IFMBE Proceedings 39, 2012

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 Growth profiler: essential components
Photodiodes (Light to
LED Cuvette voltage converter)

TSL257-LF

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 Overview of growth profiler system

Device Controller Computer

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 Items each team will have in kit box (Wednesday)
1 HUZZAH32 - ESP32
1 Photodiode USB-A 2 – MICRO-B 5V adapter
Microcontroller

10-15 Resistors

3 LED’s

1 RGB LED

2 Tactile
switches 1 Cuvette
Cuvettes
magnet

2 Potentiometers

1 Breadboard

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 Items you will need
• Pencil or pen, and paper

• Computer or laptop that can be connected to USB-A

– If you only have USB-C connections, you will need an adapter

• A small box or coffee cup to cover the entire device while measuring from detector
(photodiode). This is to minimize light contamination of your readings

• Possibly a few new accounts (Fusion360, etc.)

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 Laboratory equipment

Magnetic stirrers

Pipettes
Light microscopes
Spectrophotometers 600nm

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 Overview of the 3-weeks

• Week 1: Design your device, Build a prototype, Test settings

• Week 2: Calibrate your device, Run growth experiments

• Week 3: Analyze experimental data, Make project video

• After week 1, your tasks and time management are primarily defined by
executing your plan.

• You will manage your own projects and consultants will give technical
guidance and advice
– Consultants (teachers,TAs) are not project managers who to tell you
what to do next

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 Group profiles

• ProjComm: Project Management &

Communication
• Lab: Laboratory Work
• TechApp: Technology Application
• ModProg: Data Analysis, Modeling &
Programming
• HwElec: Hardware and Electronics

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 Examples of group profiles

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 Group contract

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 Questions?

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