Winter Software Challenge 2018-2019

Summary: Biomaker is inviting applications for the Winter 2018-9 Challenge. Applicants will develop software nodes for integrating hardware with a new graphical programming interface, XOD. With a short-form application, all successful applicants will receive a hardware starter kit, document their projects on the Hackster platform, exhibit their results in February 2019, and be in the running for fabulous prizes.

The Challenge:

Develop XOD nodes for code-free programming of scientific instruments and real-world tools for biology.

We will provide teams with a low-cost development platform based on the Open-Smart Rich UNO R3 board, which contains a variety of embedded components. The board is Arduino compatible, and can be programmed directly from the graphical programming environment XOD (C++ source code available). XOD nodes can be programmed using C++ (https://xod.io/docs/guide/#making-your-own-nodes), or composed from low-level XOD nodes (e.g. I2C device support, https://xod.io/libs/xod/i2c/)

Potential projects might involve the production of code for new i2C devices, serial communication routines for use with programmable touch screens or integration and documentation of existing nodes for scientific use.

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What is Biomaker? The Biomaker Challenge is an interdisciplinary team-based opportunity to explore the intersection of electronics, 3D printing, sensor technology, low cost DIY instrumentation and biology. The Biomaker Challenge aims to promote collaboration between disciplines, tapping into commodity electronics and open technologies for instrumentation to build research skills and collaborations. Whether you’re a biologist looking to optimise your protocols and pick up some electronics knowledge; an engineer looking to apply your skills and gain experience of practical biology or you’re just curious and interested to participate, we’re keen to recruit you.

Simple hardware for computing: We have chosen Arduino-based hardware (www.arduino.cc) as our starting point. The Arduino community has established open standards and rich ecosystem of resources for simple microcontrollers, first established to simplify programming and physical computing for designers and artists. Arduino circuit boards can be plugged into the USB port of any laptop, and a simple cross-platform programming environment used to program the board. A program is simply loaded to non-volatile memory on the Arduino board, which will execute this program loop whenever the board is powered on - behaving as a dedicated appliance or instrument. Arduino boards include many input/output ports, and are intended to interface with sensors and actuators. The Arduino system provides a simple environment for learning programming and hardware skills, and developing real-world laboratory tools for biologists. Further, the Biomarker Challenge provides a direct route for other scientists and engineers to get hands-on experience with biological systems.

Visual programming: We have adopted XOD as a simple platform for programming Arduino-based hardware. XOD is an open source platform that allows the graphical layout and assembly of software through connection of a series of nodes. XOD allows a hierarchical and dataflow driven approach, avoids the complexities of text management and syntax, and can be used to directly programme Arduino boards. We use XOD for our training programmes. The software can be downloaded from (https://xod.io). In order to get started with XOD - head to https://xod.io/docs/tutorial/install/

A starter kit of parts: We will provide an extended Arduino board, components, small prototyping board and programmable display. It is based on the Open-Smart Rich UNO R3 board, which contains a variety of embedded components, including sensors, 7-segment 4 digit display, real-time clock, touch sensors, buzzer, mp3 player with microSD card holder and expansion shield. Importantly, the connections to the embedded components can be turned off using a DIP switch. The board is Arduino UNO compatible, and can be programmed directly from XOD. Click here to download the board manual (4.9 MB PDF). The Starter kit includes a wide variety of addition components that allow the addition of new inputs and outputs.

Programmable interface: The Biomaker Starter Kit contains a 4D Systems 3.2" gen4 touch-responsive programmable display (with memory card, Arduino interface and programmer), with information about programming environments. An Arduino library for direct serial communication with the display is available - along with more sophisticated Workshop4 development tools, including ViSi-Genie, a graphical programming tool that allows simple access to a wide range of display widgets like gauges, switches, sliders, readouts, etc., for creating customised interfaces for Arduino-based instruments. The programmable displays can be easily adapted for Raspberry Pi board computers.

We are recruiting teams for the Winter Challenge, running information sessions and mixer events in Cambridge and Norwich. Up to 50 teams are funded over the winter, and we are extending the competition internationally. Contact Alexandra Ting (synbio@hermes.cam.ac.uk) for more information.

Starter Kit

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The Starter Kit will contain an extended Arduino board, components, small prototyping board and programmable display. It is based on the Open-Smart Rich UNO R3 board, which contains a variety of embedded components, including sensors, 7-segment 4 digit display, real-time clock, touch sensors, buzzer, mp3 player with microSD card holder and expansion shield. Importantly, the connections to the embedded components can be turned off using a DIP switch. The board is Arduino UNO compatible, and can be programmed directly from XOD. Click here to download the board manual (4.9 MB PDF).

Further, the board is available as a kit of components that includes a wide range of sensors and displays. The kit includes: the Arduino board and: IO Shield, Voltage sensor, Ultrasonic sensor, Touch sensor, Water sensor, PIR motion sensor, Rocker switch, NTC sensor, Light sensor, Slide Potentiometer, Vibration motor, Passive buzzer, Speaker, 8 LED bar, Eagle eyes LED, I2C 1602 LCD, 4-Digit display, microSD card (256MB), CR1220 button battery (40mAh), Infrared Remote Control (with one CR2032 battery), Micro SD card adapter, Infrared emitter, 40pin female to female cable, USB cable (50cm).

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The extended kit provides a wide range of sensors, actuators and displays that are programmable from XOD and can form the basis for an extended set of tutorials - as well as provide parts for applications.

We wil also provide a programmable touchscreen, such as the 4D Systems Gen4 µLCD 3.2” resistive touch screen. This intelligent display provides a microcontroller and touch screen that can be customised to display user interface elements for visualisation of data (e.g. gauges) or graphical input (e.g. switches, sliders). Graphical elements can be laid out using the free 4D Systems Workshop4 IDE, and downloaded to the display, which can then interact with an Arduino board via serial connection.

Click to download the spec sheet for the 4D Systems Gen4-µLCD-32DT touch screen (2.5 MB PDF)

Click to download an introduction to codeless programming of the intelligent display (3.6 MB PDF).

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Eligibility

Applicants and teams:

  • Primary applicants should be students or staff at the University of Cambridge, John Innes Centre the Earlham Institute, though external team members are welcome and encouraged. If you are not from a participating institute but would like to join a team, post on our Hackster discussion page and we'll help match people and projects!

  • Teams can be any size, including individuals if all other eligibility criteria are met. All team members will be provided a Starter Kit.

  • Teams which span Norwich and Cambridge are highly encouraged.

Proposals:

  • All proposals must lead to a publicly documented and open hardware design and prototype which demonstrates interdisciplinary thinking.

  • Except for Cambridge-Norwich team travel, the discretionary budget can only be spent on hardware, materials, consumables and biological reagents.

Application Process

Please submit an application form to biomaker@hermes.cam.ac.uk in an editable format such as .odt or Word .docx (not PDF) and attach any images separately to the email.

Applications should include:

  1. Team details, including contact details and hardware or programming experience

  2. Project title and brief abstract

  3. Description of the intended challenge.

  4. Expected outcomes and benefits

The full application should be no more than 2 pages, excluding any figures, photos and diagrams which can be inserted at the end of the document and referenced in the text.

Applications are invited from Monday November 26th, and will be evaluated on a rolling basis until applications close on Sunday December 16th. (Cambridge undergraduates may be able to pick up their Starter Kits before the end of term, otherwise these will be mailed).


Questions?

Please contact biomaker@hermes.cam.ac.uk with any enquiries.

The Biomaker Challenge is organised by:

  • OpenPlant (Cambridge) and the Synthetic Biology SRI: Alexandra Ting; synbio@hermes.cam.ac.uk

  • OpenPlant (Norwich): Dr Colette Matthewman; colette.matthewman@jic.ac.uk

 

The Biomaker Challenge is sponsored by BBSRC/EPSRC through OpenPlant Synthetic Biology Research Centre (www.openplant.org) and the University of Cambridge Research Policy Committee through the Synthetic Biology Strategic Research Initiative (www.synbio.cam.ac.uk).

Online suppliers:

Rich UNO R3 board and interface kit:
Current price: around £30/$40 per kit with international shipping.

DX-Dealextreme - https://www.dx.com/p/open-smart-rich-uno-r3-atmega328p-development-sensor-module-kit-472696#

AliExpress - https://www.aliexpress.com/item/Rich-UNO-R3-Atmega328P-Development-Board-Sensor-Module-Kit-for-Arduino-with-IO-Shield-MP3-DS1307/32822090848.html

4D Systems Gen4 µLCD 3.2” resistive touch screen:
Current Price: around £50/$70 per kit

RS online: https://uk.rs-online.com/web/p/lcd-colour-displays/12580202

Additional information:

Arduino Learning review:
http://arduinolearning.com/hardware/look-open-smart-rich-uno-r3-atmega328p-development-kit.php

Arduino.cc - setting up the Rich UNO R3
https://forum.arduino.cc/index.php?topic=541297.0