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Session 1

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Today’s Session

13:00 Welcome & Lesson 1: Introduction

An introduction to us, the grove board, microcontrollers and the XOD IDE

14:00 Break

14:20 Lessons 2 & 3: Getting Started & Explore XOD

Get started with using your board. We’ll start with some simple tasks like

flashing an LED, pressing a button and sounding a buzzer

Get to grips with some of the most useful nodes in XOD

15:50 Round-Up

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Start by introducing yourself and any other trainers, organisers or assistants. Then you can use this slide to explain to participants what Biomaker is.

You can replace this slide with information about your own organization or why you are running these workshops, but please credit the Biomaker project somewhere in your presentation.

Some information on Biomaker:

Biomaker was started in 2014 as an interdisciplinary scheme for project-based learning and innovation, coordinated by the Synthetic Biology Interdisciplinary Research Centre and the University of Cambridge and OpenPlant, one of the UK’s six National Synthetic Biology Research Centres. It has been funded mainly by contributions from the BBSRC and EPSRC research councils in the UK, and an NERC/NSF UK-US collaborative grant programme.

Biomaker provides funding for interdisciplinary team-based projects at the intersection of electronics, computer science, 3D printing, sensor technology, low-cost DIY instrumentation and biology. It aims to build open technologies and promote development of research skills and collaborations. They have funded over 100 interdisciplinary projects so far, both in the UK and with international partners around the world.

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Use this slide to explain what the No-Code Programming for Biology imitative is.

You can replace this slide with information about your organization and/or why you are interested in teaching No-Code Programming for Biology, but please credit Biomaker and the No-Code Programming for Biology team somewhere in your presentation.

Some information on the No-Code Programming for Biology scheme:

Biomaker aims to lower the barriers that impede interdisciplinary work via training programmes such as No-Code programming for Biology. This programme hopes to help biologists get started with making their own instruments for lab and field work. Designed for those with little to no experience working with coding or hardware, the programme makes use of the free open-source software XOD and low-cost, easy set-up hardware from Seeed Studio.

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Before we Start

1 Downloaded the XOD Software

www.xod.io

2 Downloaded the No-Code Programming Beginner’s Guide

www.biomaker.org/nocode-programming-for-biology-handbook

3 Installed USB Drivers (if required)

www.silabs.com/developers/usb-to-uart-bridge-vcp-drivers

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The Starter Kit

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1 LED

2 Buzzer

3 OLED Screen

4 Button

7 Sound Sensor

8 Temperature

and Humidity

Sensor

10 3-Axis

Acceleration

Sensor

6 Light Sensor

9 Air Pressure Sensor

5 Rotary Potentiometer

11 Grove Seeeduino

Microcontroller

Use this slide to introduce the different parts of the Grove board. Clicking through the presentation will bring up each label in turn.

Key points:

The left side of the board contains some simple input and output devices

LED – small low-power red light
Buzzer – buzzer which can emit at different frequencies

The LED and buzzer are useful output devices used for warnings and alarms. You will use them in today’s session.

OLED screen – organic LED screen. Useful screen 128x64 pixels, used to display text or graphics. You will use this in the next session.
Button – simple press button. Can be used to turn something on or off
Potentiometer – a dial you can twist. You will use this in this session to control the buzzer frequency

The right side of the board has an array of sensors useful for environmental monitoring

Light sensor
Sound sensor
Temperature and humidity sensor, also know as a hygrometer
Air pressure sensor, also known as a barometer – measures temperature and air pressure, can be used to measure altitude
3-axis acceleration sensor – like the tilt sensor in phones – can tell when the board is moved or tilted

The central section is the ’brains’ of the board where the Arduino microcontroller is. It also has white plug sockets and yellow header sockets for plugging in extra components

This is the microcontroller chip

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The Microcontroller

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A0-A6 Analog

D0-D13 Digital

I2C I2C (require address)

Use this slide to explain the concept of a microcontroller.

Key points:

This tiny chip is the microcontroller used on the board.
It acts like a small computer – it has a processor and memory
Unlike a normal computer it can only load one programme at a time i.e. it can only do one thing a once
Once you’re programmed it, it will perform the same task each time you turn it on
You can reprogramme it to perform a different task by uploading a new programme
It communicates with the other devices on the board using the metal pins around the edge
Each device is connected to a different pin, and the pins are given names e.g. A1, D6
There are different types of pins – we will be using three types – analog, digital and I2C
Analog pins are used for analog devices that can have any continuous value, like many of the sensors
Digital pins are used for digital devices that can only take on and off signals, like the LED
I2C is a special type of digital communication. You can use it to connect more than one device to the same pin
I2C devices need a name to tell them apart called an address e.g. 19h, 3Ch
In XOD these pins are refered to as ‘ports’

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The XOD IDE

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1 Your Patch

2 Project

Browser:

Buttons

New

Patch

Add

Library

3 Project

Browser:

Project

Patches

4 Project

Browser:

Libraries

5 Inspector

Upload

And

Debug

7 Upload Buttons

6 Quick Help

Use this slide to introduce the XOD software.

Key points:

The central area of the screen is called the patch. It is like a blank canvas or file that you use to build your programme.

You build programmes by adding boxes called nodes to the patch

Next to ‘Project Browser’ are the new page and add library buttons
Below that is your project (like a folder) with patches (like files) in it.

If you can’t see your patches click the down arrow next to your project name

Below that are your libraries – where the parts to build your programme are stored

XOD has some libraries pre-installed, but you can add new ones

Inspector – this is where you change information about the nodes in the programme.
Quick help pane – find information about nodes and pins

If you can’t see the help pane, click on the question mark button

Upload buttons – lightning button uploads your programme, ladybird button uploads and also starts XOD’s ‘debugger’ - a simulation mode

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Nodes

Pins

Links

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Byte

String

Pins

Pulse

Boolean

Number

Port

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Break

20min

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Testing Your Board

Title slide

At this point you should demonstrate Task 1 from the Beginner’s Guide. This will demonstrate much of what they have just learned. Try to show both how you build the programme on your computer screen (using a projector or share screen) and what happens to your board when you upload (via physical demonstration or a video).

During this demonstration it is useful to show participants the different ways of adding nodes to patch, including dragging them from the library and double clicking the patch to search.

You can either demonstrate both Tasks 1 and 2, then get participants to try the tasks (suggested for online workshops), or you can demonstrate task one, get participants to try, then demonstrate task 2 and get participants to try (suggested for in person workshops).

We suggest participants work in groups of 3-5. For online sessions breakout rooms are good for this.

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Try it Yourself – 20min

1 Work in small groups (introduce yourselves if necessary)

2 Complete Task 1

3 Step-by-step instructions are in the Guide (p20-25)

4 Ask if you need help

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Inputs and Outputs

Title slide

At this point you should demonstrate Task 2 from the Beginner’s Guide. This will demonstrate much of what they have just learned. Try to show both how you build the programme on your computer screen (using a projector or share screen) and what happens to your board when you upload (via physical demonstration or a video).

During this demonstration it is useful to show participants the different ways of adding nodes to patch, including dragging them from the library and double clicking the patch to search.

You can either demonstrate both Tasks 1 and 2, then get participants to try the tasks (suggested for online workshops), or you can demonstrate task one, get participants to try, then demonstrate task 2 and get participants to try (suggested for in person workshops).

We suggest participants work in groups of 3-5. For online sessions breakout rooms are good for this.

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Try it Yourself – 20min

1 Work through Task 2 in groups

2 Step-by-step instructions are in the Guide (p26-29)

3 Ask if you need help

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Congratulations!

You can now programme

an Arduino Board!

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Tweak and

Watch Nodes

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Play the video on this slide to demonstrate Task 3: Tweak and Watch Nodes. You can either narrate the video as it plays, or explain what will happen, then play the video. If you can not play the video from the slides you may want to demonstrate yourself, or play a recording from the Biomaker YouTube channel: https://www.youtube.com/watch?v=PNv7bEZTxiw&t=359s

Key Points:

The example uses the dht11-hygrometer node, which represents the temperature and humidity sensor on the board
Connect the tweak-pulse node to the update (UPD) pin – that will let us control when the sensor updates
Connect the temperature (Tc) and humidity (RH) outputs to the watch pins – that will let us see the outputs
Expand the watch nodes by pulling on the tab in the bottom right corner - that makes sure you can see the whole output
Set the PORT pin to D3 (this is the pin the temperature and humidity sensor is connected to)
Click ‘Upload and Debug’ (ladybird button) NOT ‘Upload’ (lightening button)
The watch nodes will display 0 (no reading) until you initiate a sensor update
‘Tweak’ the tweak node by clicking on it, then in the Inspector panel click the ‘Pulse’ button
Every time you click the pulse button the sensor will take a reading which you can see in the watch nodes

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Flip, Clock and

Count Nodes

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Play the video on this slide to demonstrate Task 4: Flip, Clock and Count Nodes. You can either narrate the video as it plays, or explain what will happen, then play the video. There are three parts to this video, one to demonstrate flip-n-times, one to demonstrate flip-flop, and one one to demonstrate clock and count. You may want to pause the video between parts to narrate. If you can not play the video from the slides you may want to demonstrate yourself, or play a recording from the Biomaker YouTube channel: https://www.youtube.com/watch?v=PNv7bEZTxiw&t=723s

Key Points:

Flip-n-times

Ton and Toff set the time spent in each state
N sets the number of times the node ‘flips’ – set this to 5
Connect the tweak-pulse node to SET, OUT to LUM and set PORT to D4
Upload and debug, then pulse the tweak-pulse node
The LED will flash 5 times.

Flip-flop

Replace flip-n-times with flip-flop and reconnect (tweak-pulse to TGL and MEM to LUM)
Upload and debug, then pulse the tweak-pulse node
The LED will turn on
Each time you pulse the tweak-pulse node the LED will switch between on and off

Clock and count

Replace the tweak node with a clock node (TICK to TGL)
Add a count and watch node to the LED (DONE to INC and output pin to watch node)
Upload and debug
The clock node will switch the LED between on and off every second, and the watch node will count up in unison
This is the ’work around’ to be able to watch the output from a pulse pin mentioned earlier

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Concat, Join and

Format-Number Nodes

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Play the video on this slide to demonstrate Task 5: Concat, Join and Format-Number Nodes. You can either narrate the video as it plays, or explain what will happen, then play the video. If you can not play the video from the slides you may want to demonstrate yourself, or play a recording from the Biomaker YouTube channel: https://www.youtube.com/watch?v=PNv7bEZTxiw&t=1113s (note: there is a mistake in the YouTube version of this video. It is explained in the video and has been corrected here).

Key Points:

The barometer-thermometer node represents the air-pressure sensor

You do not need to set a port/address for this node as the I2C address is incorporated into the node
Set UPD to continuously

Concat

Connect TEMP to the first input and set the second input to ‘oC’ using the Inspector
Connect the output to the watch node

Format-number and Join

Connect PRESS to NUM and STR to S1
Set D to be a space ‘ ‘ and S2 to ‘Pa’
Connect to watch node
Upload and debug
Watch the outputs and see how they’re formatted – e.g. number of decimal places, space between number and units

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Next Week’s Session

13:00 Welcome, Recap & Lesson 4: Building Devices

Learn how to make more complex programmes in XOD using logic nodes,

sequences and loops.

14:00 Break

14:20 Lesson 4 cont. & Lesson 5: Next Steps

Learn how to expand your programming and hardware building capabilities to start

building your own devices, and take a look at some previous projects.

15:55 Round-Up

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Thank You

More info:

www.biomaker.org

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Session 2

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Today’s Session

13:00 Welcome, Recap & Lesson 4: Building Devices

Learn how to make more complex programmes in XOD using logic nodes,

sequences and loops.

14:00 Break

14:20 Lesson 4 cont. & Lesson 5: Next Steps

Learn how to expand your programming and hardware building capabilities to start

building your own devices, and take a look at some previous projects.

15:55 Round-Up

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Last Week’s Session

1 The Grove Board (p6-7)

2 The Microcontroller (p8-11)

3 The XOD IDE (p12-15)

4 Turned the LED on using the button (p20-25)

5 Controlled the buzzer using the button and potentiometer (p26-29)

6 Learned about some useful nodes in XOD (p31-45)

Tweak, watch, flip, clock, count, concat, join and format-number

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Creating New Nodes

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Use this slide to introduce the concept of creating your own nodes.

Key points:

You can simplify your programme by encapsulating part of it in a new node
This is easier than it sounds
You create a patch like normal, but then add ‘terminal nodes’ (represented here) to let your new node communicate with other nodes
Terminals can be inputs (top row) or outputs (bottom row) and will become the pins of your new node
There are different terminals for different data types e.g. input-boolean, input-number, output-number, output-pulse etc.
The next task will demonstrate how to use these to create a node that writes text to the OLED display screen

At this point you should demonstrate Task 6 from the Beginner’s Guide. This will give them a practical example of using terminals to create a new node. Try to show both how you build the programme on your computer screen (using a projector or share screen) and what happens to your board when you upload (via physical demonstration or a video).

We suggest demonstrating the task, then getting participants to try themselves, working in groups of 3-5.

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Try it Yourself – 15min

1 Work though Task 6 in groups

2 Step-by-step instructions are in the Guide (p50-54)

3 Ask if you need help

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Using Buses

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Use this slide to introduce the concept of buses.

Key points:

Buses are a way to link pins ‘invisibly’
They can be used to reduce the number of intersecting links and make the dataflow easier to compartmentalize and visualize
There are only two bus node: ‘to-bus’ and ’from-bus’
They automatically take on the data type that they’re connected to
The ‘to-bus’ node connects to an output and sends information from that output to the bus
The ‘from-bus’ node connects to an input and retrieves that information
The to and from buses need to be given the same name to link them

After this you should demonstrate Task 7 from the Beginner’s Guide. This will give them a practical example of using buses. Try to show both how you build the programme on your computer screen (using a projector or share screen) and what happens to your board when you upload (via physical demonstration or a video).

If you have time in the session for participants to try the task then they can. Otherwise, you can get them to modify the the write-text-to-oled node from Task 6 so that the ssd1306-oled-i2c-device DEV pin is linked to each of the other DEV pins by a bus rather than by links.

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Try it Yourself – 15min

1 Work though Task 7 in groups

2 Step-by-step instructions are in the Guide (p56-59)

3 Ask if you need help

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Break

20min

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Logic Programmes

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Try it Yourself – 15min

1 Work though Task 8 in groups

2 Step-by-step instructions are in the Guide (p60-63)

3 Ask if you need help

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Sequences and Loops

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Try it Yourself – 15min

1 Work though Task 9 in groups

2 Step-by-step instructions are in the Guide (p64-70)

3 Ask if you need help

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Case Studies

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Open Source Microbial Bioreactor

Behavioural Chamber to Evaluate Rodent Forelimb Grasping

Camera for Monitoring Plant Pollination Events

eCO-SENSE: Soil Sensors Powered by Plant Photosynthesis

www.hackster.io/biomaker

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Discussion – 15min

1 Read through the case studies (p80-83)

2 Discuss in groups

3 Which of this devices is most relevant to your research?

4 What extra hardware or programming skills would you

need to create one of these devices?

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Expanding

Your Capacity

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Expanding Your Capacity

Wires

Shields

Breakout Boards

Use this slide to explain how participants can expand the use of their boards and create new devices using additional components.

Key Points:

You can add components to your board in many different ways – we will cover a few
Wiring

You can connect components using electronic wiring, either directly or via a breadboard.
This is the most basic method, but you need some level of electronics knowledge

Shields

Shields plug into the yellow header pins on the left and right edge of the central Grove board module
They can add capacity (such as internet connection shields) or allow you to easily plug in breakout boards

Breakout boards

Small PCBs with electronic components wired in.
Usually have one component per board e.g. light sensor, LED
Each of the Grove modules is an inbuilt breakout board
These are often the easiest option

You can also remove components from the board, or remove the central microcontroller portion to free-up the board

This is useful to avoid component clashes (i.e. plugging two components into the same pin)
Use a sharp craft knife or scalpel the cut components from the board
You can always plug them back in using the Grove sockets and wires

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Plug-and-Play Components

Plug directly into white sockets

on the board

Plug into Open Smart Expansion Shield

(or use JST PH to JST XH cables)

www.adafruit.com

> Products > STEMMA/STEMMA QT

www.open-smart.aliexpress.com

Plug directly (STEMMA 4 pin)

Plug with JST PH to JST SH cable (STEMMA QT 4 pin)

Use this slide to let them know about the different plug-and-play systems compatible with the Grove board

Key points:

Seeed Studio Grove Components

The Grove board is produced by Seeed
All of their Grove components can plug directly into the board
Plug Grove connector cables into the white plug sockets on each end

M5Stack Componets

All of their ’Units’ are directly compatible with the Grove board
Use Grove or M5Stack connector cables

Open Smart Easy Plug Components

They have a similar plug-and-play system
It is not directly compatible
You can make them compatible using the Open Smart easy-plug expansion shield
Or JST PH to JST XH cables

Adafruit STEMMA/STEMMA QT Components

STEMMA components are directly compatible with Grove (use Grove or JST PH cables)

Only 4-pin components are compatible

STEMMA QT component are compatible with Grove by using JST PH to JST SH cables

Only 4-pin components are compatible

Side note:

SparkFun Qwiic Components (not shown here)

Compatible with Grove by using JST PH to JST SH cables

Only 4-pin components are compatible

Directly compatible with STEMMA QT

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www.open-smart.aliexpress.com

Wired Breakout Boards

Connect using expansion shield or Grove-to-female wires (make sure pin labels match up)

www.adafruit.com

Solder pins to board. Connect using Grove-to-female wires (make sure pin labels match up)

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Finding XOD Nodes

www.xod.io/libs

www.forum.xod.io

Search using ‘reference designator’

e.g. BMP280 (barometer) or SSD1306 (OLED screen)

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Arduino IDE

Arduino provides it’s own free IDE software, which uses C++ coding language to programme the board.

www.arduino.cc/en/software

Converting Arduino libraries for use in XOD

bit.ly/arduino-to-xod

Combining XOD and Arduino IDE

XOD menu > Deploy > ‘Show Code for Arduino’

More complex programming

www.arduino.cc/en/Tutorial/HomePage

Use this slide to let them know about the Arduino IDE, and why they might want to use it.

Key points:

Not all components have XOD nodes – sometimes you may want or need to use the Arduino IDE instead
Arduino IDE is free and uses C++ programming language
Sometimes you can convert Arduino libraries for a component into XOD libraries – we have a tutorial on how to do this (you will need some basic C++ knowledge)
You can combine XOD and Arduino, i.e. by writing a programme in XOD, exporting it to C++, and adding to/adapting it in Arduino – you may want to do this if you have written code in XOD but want to add a component that doesn’t have a XOD node.

To do this – go to ’Deploy’ in the menu bar in XOD, then click ‘Show Code for Arduino’.

Some complex programmes may be more efficient if written in Arduino.
The Arduino website provides simple tutorials on how to use Arduino and learn simple C++ if you are interested.

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What would you build?

?

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Discussion – 10min

1 What instruments would be useful in your own research?

2 How would you go about building such a device?

3 What additional hardware/programming would you need?

4 Do some research – has something like this already been

done? Can you find the things you need?

Questions? Contact the Biomaker team: coordinator@synbio.cam.ac.uk

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Thank You

More info:

www.biomaker.org