Sample Tracker: A web-based application for tracking and!managing environmental research samples !

Gerard Devine*, Catriona Macdonald, Vinod Kumar!

The HIE Sample Tracker is a web-based inventory and management system for tracking environmental samples, such as soils, leaves and ecological material, at the Hawkesbury Institute for the Environment at the University of Western Sydney. Sample metadata, including the experimental conditions under which it has been sampled, characteristics of the sample, and its eventual storage location, is captured in a centralised database. A web front-end allows research scientists to efficiently enter information about samples they have collected, using either web forms or through spreadsheet upload of multiple sample information. In addition, scientists have the ability to discover samples held within the inventory for possible re-use. Research facility managers, on the other hand, can monitor sampling activity being carried out at their particular field site and thus ensure proper sampling procedures and documentation practices are being adhered to. Automated barcode generation combined with unique identifiers on each sample allow tracking of the sample through the lab analysis phase, and in the future will enable datasets arising from such samples to be augmented with high quality sample metadata.

Overview!

Background!The Hawkesbury Institute for the Environment (HIE) at the University of Western Sydney is a leading centre of excellence in research into ecosystem function and environmental responses to changing climates. Key to this research is the sampling of a physical environment (namely soils, leaves, and organic material) that is undergoing a range of modified climatic conditions across a number of large field facilities. These samples thus provide insight into future ecosystem response to enhanced climatic scenarios. The uniqueness of the experiments as well as the cost of running such facilities means that the collected samples are extremely valuable, both for current research and for potential reuse in future experiments.   To date, information about each sample (which number in the thousands) has typically been recorded in spreadsheets saved locally on researcher’s desktops, with very limited centralisation. Backup, discoverability and retrieval of samples has therefore been difficult. Off-the-shelf inventory management systems, while satisfying some of the necessary requirements, do not provide an ideal solution, most notably as they do not lend themselves well to the structure and typical transactions of an environmental research facility.

The Application!In response to this, the HIE Sample Tracker was developed. This is a Ruby on Rails web application that captures the lifecycle of a collected sample, from initial sampling request, through to deposit in storage. The Sample Tracker enables researchers and facility staff at HIE to manage, document and search for environmental samples collected at various sampling field sites. In particular, it: - allows research scientists to set up a batch of samples to be sampled at a particular facility - allows field facility staff to monitor what samples are being collected at a particular facility, on what dates, and under which scientific project - automatically creates sample information templates to be used in the field as well as sample barcodes for easy sample identification - enables researchers to enter details of single samples using web forms, or multiple samples through batch spreadsheet upload   Unique identifiers on each sample allow tracking of the sample through the lab analysis phase. In the future it is planned that the Sample Tracker is linked to the institution’s data management platform and ultimately enable datasets derived from such samples to be augmented with sample metadata, thus enhancing the scientific record.

Ability to provide sample information for each sample individually through webform entry or for multiple samples through pre-rendered spreadsheet templates

Easy requesting of new sample sets from a specific field facility. A seperate admin interface is available for the management of facilities, projects, users etc.

Detailed information about each sample is held within the system including the experimental conditions under which sampling was carried out, location and type of sample, as well as analyses that the sample will be/has been subjected to. QR codes are automatically created for attaching to each sample OR at a ‘container’ level for multiple samples

Sample database can be queried using a number of search parameters for easy discovery of existing samples, thus reducing the time and effort required for resampling •  Application now live at https://hie-sampletracker.uws.edu.au

•  Github: https://github.com/gdevine/sampleTracker

Schematic showing a typical walkthrough of the Sample

Tracker workflow

QR codes are automatically generated for each sample to uniquely identify it. These QR codes can be printed individually or as a batch of codes associated with a Sample Set. QR codes are also generated for ‘containers’ which hold multiple sample vials that are too small to be tagged with individual QR codes. You can use standard smartphone software to scan the adjacent code.

Hawkesbury Institute for the Environment, University of Western Sydney!* g.devine@uws.edu.au!