Under construction
The Biomaker site is being expanded to cover new approaches to low code programming and improved hardware. The old site with extensive resources that employ XOD as a visual programming environment is linked here as an archive. Revised material that describes new tools and projects will be compiled here (biomaker.org) and at openrig.science
The Biomaker platform...
Biomaker is free resource for open source tools and information that helps to enable researchers, students, and hobbyists to build scientific instruments and experimental setups using off-the-shelf components and open source software. Biomaker includes a training platform that has been based on a series of microcontroller boards including support for a variety of hardware components, such as microcontrollers, sensors, and actuators, as well as a set of software tools and libraries for programming and controlling these components. We have been using a visual programming language for Arduino-compatible microcontrollers, XOD (xod.io) which provides a dataflow model for programming interactive devices. However, recent years have seen the emergence of more powerful hardware and disruption of the development of XOD. The organisers, Matt Wayland and Jim Haseloff in Cambridge are developing updated resources for Biomaker, which are described on this website (biomaker.org), and a new site at openrig.science
The aims of these updates to Biomaker are to (i) support modern ESP32 microcontrollers which provide dual benefits of improved performance and low cost; (ii) adopt a free environment that allows no-code/low-code visual programming and a pathway to Python and use of AI assistants; and (iii) integrated development of graphical interfaces for producing touchscreen-based user interfaces.
Jim Haseloff has recently retired from his academic role at the University of Cambridge, and is focusing on demonstration projects to produce low cost tools for open science. For example, key projects are:
Air-flow driven microtube reactors for isothermal DNA modification, assembly, and LAMP reactions, and thermocycling PCR amplification
Particle inflow gene gun for plant transformation
Custom optical systems for whole plant observation.
Sensor and control systems for plant propagation
The shift in emphasis from training to the implementation of practical devices is documented here, and comes with a more personal viewpoint, as these projects are aligned with work developing free tools for bioengineering in plants (details can be found at marchantia.org). Online updates can be found on Bluesky (@jimhaseloff).
History of Biomaker hardware for training and prototyping
Biomaker has aimed to bring together organised training materials and electronic building blocks for design and assembly of bioinstrumentation. An important part of this has been to bring people together in seasonal workshops and challenges. These activities have been funded by funding from the UK Research Councils. Beginning in 2017, we have been collecting and distributing base kits to provide foundations for prototyping work.
The base kits have evolved from simple Arduino UNO boards with breadboard and components to higher powered microcontrollers with integrated sensor and actuator devices
Mk I Biomaker Kit
The Biomaker kit (2017) contained a large prototyping breadboard along with an Arduino UNO board and several kits of parts including Seeedstudio Grove boards and other discrete components, and a programmable touchscreen from 4D Systems.
Mk II Biomaker Kit
The (2019/2020) Biomaker kit was upgraded to contain a multi-purpose Arduino-compatible Rich UNO board from Open Smart and several sets of parts and breakout boards for expansion including a programmable touchscreen from 4D Systems.
Mk III Biomaker Kit
The Biomaker kit was updated to an Arduino UNO compatible multifunction board - the Seeedstudio Grove Beginner board. A multi-stage training scheme was devised, starting with a Beginner's kit, adding an expansion kit and then Seeedstudio Wio Terminal with integrated screen and wireless communications.
Mk IV Biomaker Kit
This kit included the Seeedstudio Wio Terminal (ATSAMD51 microcontroller-based device with Realtek RTL8720DN BLE 5.0 & Wi-Fi 2.4G/5G Dev Board with a 2.4” LCD Screen and onboard sensors with Grove connectors for expansion
Rapid improvements in hardware and software are continuing to arrive, especially as AI tools improve and become more accessible. We think that a careful selection of tools will facilitate the hands-on use of electronic sensors, control and communications by biologists - making custom builds easier for our experiments. This website is intended to provide a window into ongoing developments, and regular updates can be found at the Bluesky link below.
The next generation of Biomaker hardware
Matt Wayland and I have been surveying new hardware devices that would (i) take advantage of the ESP32 family of high performance, low cost microcontrollers, (ii) offer well supported alternative to XOD for visual and low-code programming, preferably with a pathway to a conventional coding language such as Python, (iii) with good support for existing hardware and flexibility for the future including use of AI tools, (iv) tools for interactive design and programming of touchscreen user interfaces, and (v) all this accessible at reasonable price and availability.
After numerous trials, we have gravitated to M5Stack hardware, well-engineered devices based on ESP32- S3 and ESP32-P4 microcontrollers, available with integrated touchscreens and Grove-compative connectors for expansion. The Core family is comprised of 5x5cm modules that can be stacked on each other via a custom M5 electronic bus for communication. A number of different functions can be plugged together to create hybrid multi-function devices. In addition the Tab5 device is available that provides a larger touchscreen and is based on the ESP-P4 (with an ESP32-C3 for wireless communications). The M5Stack Core3 and Tab5 have support for new AI tools like prompt-based coding via ESP-Claw. Perhaps most importantly from the perspective of Biomaker, M5Stack provides access to a web based programming environment UiFlow2 that gives (i) a Blockly interface for visual programming, teamed with (ii) a linked Micropython editor to allow combined approaches to coding. (iii) There is good built-in support for the wide variety of M5Stack devices, including small Atom and Stamp devices and peripherals. There is also support for Seeedstudio Xiao and Arduino Nesso ESP32 based devices. (iv) UiFlow2 includes a special integrated interface for programming their touchscreens, and allows seamless switching back and forth between the programming environments. In this way, user interfaces can be developed and tested quickly.
biomaker.org