Journal:Open source data logger for low-cost environmental monitoring

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Full article title Open source data logger for low-cost environmental monitoring
Journal Biodiversity Data Journal
Author(s) Baker, Ed
Author affiliation(s) The Natural History Museum - London
Primary contact edwbaker at gmail dot com
Editors Caithness, Neil
Year published 2014
Volume and issue 2
Page(s) e1059
DOI 10.3897/BDJ.2.e1059
ISSN 1314-2828
Distribution license Creative Commons Attribution 4.0 International
Website http://bdj.pensoft.net/articles.php?id=1059
Download Click the "PDF" button on the website.

Abstract

The increasing transformation of biodiversity into a data-intensive science has seen numerous independent systems linked and aggregated into the current landscape of biodiversity informatics. This paper outlines how we can move forward with this program, incorporating real-time environmental monitoring into our methodology using low-power and low-cost computing platforms.

Keywords: Arduino, open source, open hardware, environmental monitoring, big data, internet of things, temperature, humidity, Ethernet

Introduction

Low power and cheap computational projects such as Arduino and Raspberry Pi have brought the use of small computers and micro-controllers to the masses, and their use in fields related to biodiversity science is increasing (e.g. Hirafuji shows the use of Arduino in agriculture[1]). There is a large amount of potential in using automated tools for monitoring environments and identifying species based on these emerging hardware platforms, but to be truly useful we must integrate the data they generate with our existing systems. This paper describes the construction of an open-source environmental data logger based on the Arduino platform and its integration with the web content management system Drupal which is used as the basis for Scratchpads[2] among other biodiversity tools. The Drupal platform uses familiar open-source standards while the Arduino hardware uses the emerging open hardware licenses (see below). It is assumed that most biodiversity scientists are not familiar with the construction of electronic devices, so this paper is presented more in the style of a "how to guide" rather than a straightforward functional description. It is hoped that people will make use of the technologies described here and adapt them to the needs of their own interests and projects.

Open hardware?

The open source hardware movement extends the familiar licenses of open-access and open-source software to physical objects. The aim is to create an ecosystem of projects and products much like the community that develops around open-source software. To be open hardware, all materials needed to construct the hardware (schematics, printed circuit board (PCB) layouts, bills of materials) and the software required (on device and ideally to interface with the device) must be released under a permissive "copyleft" license. More information about open hardware can be found at the Open Source Hardware Association.[3]

Citizen engineers

The introduction of easy-to-use micro-controller devices such as the Arduino brought working with digital electronics to a broader audience. The Arduino project[4] (and similar initiatives) has generated a number of books and a plethora of web pages detailing the basic use of the devices and the use of sensors (ideal for data-logging), writing to SD cards (Secure Digital: a format of memory card widely used in digital cameras) and interfacing with the internet.[5][6] Additionally, there are a wide range of books describing the basics of electronics; Scherz's Practical Electronics for Inventors[7] is recommended as a reference text due to its comprehensive approach and detailed theory, but one of the many electronics "primer" books may be a better introduction. There is great potential for the biodiversity community if we collaborate with knowledgeable "hackers" and "makers" as citizen engineers in the same way we interact with knowledgeable amateur natural historians as citizen scientists.

Project description

Design description

The device constructed is intended both as a functional device capable of generating useful environmental datasets and also as a demonstration to the biodiversity community of what is possible using the Arduino system as a base. This project aims to be as easy as possible to construct and use for those with no experience in electronic devices, and for this reason we have steered away from the use of custom PCBs or other materials. The use of a prototyping board rather than a custom PCB also allows for the project to be extended more easily and assembled without soldering. The author would encourage anybody who wishes to release a custom PCB layout for this project to do so.

Funding

This project was supported by the European Union funded ViBRANT project (Contract no. RI-261532).

Web location (URLs)

Homepage: http://ebaker.me.uk/project-role/open-source-data-logger

Bug database: https://github.com/edwbaker/environment-data-logger/issues

Technical specification

Platform: Arduino / Drupal

Programming language: C / PHP

Operating system: Arduino / Linux (can also run on Windows/OS X)

Repository

Type: Git

Browse URL: https://github.com/edwbaker/environment-data-logger

Usage rights

Use license: Other IP rights notes: The Drupal code and Arduino code are released under the GNU General Public License version 2 or later.

Implementation

The requirements for the device, and the server software (Drupal) that receives the data were specified as follows:

Data logger

  • Be able to record the temperature and humidity at a regular time interval (e.g. every five minutes)
  • Record the data collected to a micro-SD card
  • Submit data collected automatically and in real time to a Drupal website (using an Ethernet connection)
  • Have a real time clock (RTC) – the Arduino internal clock counts milliseconds since the micro-controller was turned on, we need to record the actual time of measurement
  • Use standard and readily-available components
  • Be able to run off readily-available batteries (e.g. AA) for at least eight hours

Server software

  • Be able to receive data from a device or more than one device and save it as a Drupal node (content item)
  • Be able to generate code for the Arduino to assist others in using this software to post data

Audience

This project should be useful to a wide range of biodiversity scientists. Some possible study scenarios include:

  • using a single device alongside a light, malaise or pitfall trap to collect abiotic data over the study period
  • using multiple devices to study small climatic differences between different micro-habitats
  • using devices over a long period to compliment studies on organism phenology

It is hoped that the publication of this device will encourage biodiversity scientists to collaborate outside of their discipline, whether it be with citizen engineers or professional academics. A work by Baker, Bennett and Chesmore (University of York) in 2013 (in prep) expands the concept of using electronic devices from monitoring environments to automated species identification using the acoustics of orthoptera.[8] Where reliable identification of species can be performed by machines, the potential for collecting high quality, high precision and long-term datasets on species abundance alongside environmental variables becomes a possibility.


References

  1. Hirafuji, M. (2013). "Comprehensive Data Collection by Sensor Network and Optical Sensor for Agricultural Big Data" (PDF). APAN. http://archive.apan.net/meetings/Daejeon2013/Session/Agri/Hirafuji-APAN_Daejeon2013.pdf. 
  2. Smith, V.S.; Rycroft, S.D.; Brake, I. et al. (2011). "Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science". ZooKeys 150: 53–70. doi:10.3897/zookeys.150.2193. PMC PMC3234431. PMID 22207806. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=PMC3234431. 
  3. "Open Source Hardware Association". Open Source Hardware Association. http://www.oshwa.org/. 
  4. "Arduino - Home". Arduino, LLC. http://arduino.cc/. 
  5. McRoberts, M. (2010). Beginning Arduino. Apress Media, LLC. pp. 472. ISBN 9781430232407. http://www.apress.com/9781430232407. 
  6. McEwen, A.; Cassimally, H. (2013). Designing the Internet of Things. John Wiley & Sons. pp. 336. ISBN 9781118430620. http://www.wiley.com/WileyCDA/WileyTitle/productCd-111843062X.html. 
  7. Scherz, P.; Monk, S. (2013). Practical Electronics for Inventors (3rd ed.). McGraw-Hill Education. pp. 1040. ISBN 9780071771337. 
  8. Bennett, W.; Chesmore, D.; Baker, E. (6 December 2013). "Speckled Bush Cricket Data Logger - Project Report". University of York. pp. 29. doi:10.6084/m9.figshare.1430094. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. In many cases what were originally inline external links were turned into proper citations. A few references were mentioned but not directly cited; citations were added to fill those gaps.