Citizen Science/The Urinomics Project

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The Urinomics Project

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INTERACTIVOS?09: Garage Science Workshop-Seminar Application Form

Title: The Urinomics Project

Team

Project Summary

Different Levels
Different Levels

We propose 'Urinomics' as the science of piss; the study of urine and the information it can reveal. We'll call this information the 'Urinome'. A 'urinoscope' is the device that translates urine to data using spectrophotoscopy, and we've built a first prototype. In this project, we want to Sense, Store, Share and Show both our individual and collective urinome. The result will be a collection of urinoscopes, a data-set accessible to everyone, and an installation that visualises this data.

Project description

Overview:

Urinomics project overview
Urinomics project overview


The Urinoscope

First prototype
First prototype

Spectrophotometer, first prototype on YouTube

We've build the first prototype of a simple spectrophotometer using an Arduino, some LED's and other cheap, accessible components. The spectrometer measures the absorption of light at various wavelengths, in our case the 'colour' of the 5 LED's. We will use it to create a data-portrait out of people's urine.

UV/visible spectrophotometry is an essential tool in the identification and quantification of a very broad range of chemical and biological substances. It relies on the measurement of radiation intensity absorption at various spectral wavelength. It has proved particularly useful in biochemical analysis, and is of vital importance in the clinical laboratory where various components of blood and/or urine samples, are determined and monitored on a 24h basis. Building a cheap and accessible (simple) spectrometer can empower and open up possibilities for Citizen Science.

The Urinome Open Dataset

After collection (take a urine sample and run a spectrography), the data will be stored in an open database on the internet. The data differs for each urine sample but isn't analytical, it won't tell anything about the urine or person. The database will contain the spectrophotometer-data and whatever data we want to add to it: the time and place of urination, ... . We call this meta-data.

We'll build an (open) dataplatform using the Google App framework (similar to Django). It provides an easy to develop SDK as well as database resources. We'll make sure the platform and formats we use are compatible with those used within the scientific community. Crossing these boundaries can provide benefit for scientists and citizens as both can engage with the same data: experimenting with new way of using, aggregating or visualising ...

Urinome Visualisation and more

Because the data from the spectrophotometer feeds into Processing, it opens up a huge amount of 'interactive' visualisation potential. We want to make use of this potential in the design/art community to experiment with new ways of visualising this scientific data. On the other hand, by complying with scientific formats for this data, we want to offer the opportunity to engage with the kind of data that normally isn't accessible.

Visualising this data will result in a shadow-play with spectrometer-data. The data isn't analytic but it is personal and will differ between people and over time, opening up space for interpretation. We imagine it will be like cloud-watching: comparing your urine-clouds with that one from the day before or those of others.

Project Installation

Urinomics project installation
Urinomics project installation

The Urinomics Installation will be the most physical of visualisations. It consists of a urinoscope and a matrix of fastgrowing, different coloured plants with a dripping installation on top of it. The data gathered by the urinoscope is translated into a 'dripping pattern' so which plants get watered depends on the urinome. The dripping patterns, visible in the pipets before the drops fall on the plant, reflect the individual Urinome. Over time, the growth and colour patern of the plants will reflect the collective Urinome.

Project technical requirements

The Urinomics project touches on a wide range of topics: Hardware, Software and Visualisation.

Urinoscope requirements

The Urinoscope is an Open Source Hardware spectrophotometer. It is suggested to build the Urinoscope from an Arduino microcontroller as well as LED technologies. It should be cheap and reliable.

The Urinoscope should also generate spectral data complying with defined scientific data format. Along with spectral data, it will be possible to add metadata to the measurement such as: time, location, and free tagging keywords.

Urinome Open Dataset requirements

The Urinome dataset will be implemented using Open Source Software solutions such as DJango. The data format of the repository will comply with existing scientific spectroscopic data standard.

The Urinome Dataset should also provide an Open API to submit and query Urinome data so future services could be implemented in the future.

In order to extend the connectivity of the Urinome Open Dataset, it is suggested to implement a variety of interface with existing Web services (Twitter, Flickr, or Facebook).

Installation requirements

Materials / components needed: spectroscope, standard transparant lab pipets, tubes, vibration motors, controller (e.g. arduino from spectroscope), standard electrical components, plants, soil, square pots, steel / wood to build frame, coloured water, ... The installation mainly requires workshop-work.

Other project requirements, with estimated budget (optional)

Urinoscope budget

The Urinoscope will be based on an Arduino microcontroller and some other easy to find electronic components. It is estimated that the overall cost for a urine spectrophotometer will be under 50 euros. The production of five urinoscopes is planned in order to enable data collection for the final installation (5 Urinoscopes = 250 euros).

Urinome Open Dataset budget

The Urinome database will be develop from Open Source Software. No dedicated budget is required for this part of the project.

Installation budget

The Urinomics installation requires an estimated budget of 300 euros.

Project schedule

Over the 2 weeks that last the workshop, we plan to develop 3 distinct and interconnected parts to support this Urinomics project: Urinoscope, Collective Urinome OpenDatabase, Visualisation and installation.

>>> Week 1 deliverables

  • Urinoscope-related:
    • Finalised Urinoscope hardware design + prototype testing/calibration.
    • Finalised Arduino-software to enable the Urinoscope to be 'SpectroML' format compatible.
    • Urinoscope documentation (an 'Instructables' for example)
  • Collective Urinome OpenDataset-related:
    • Implementation of a 'SpectroML' + Metadata compatible database
    • Implementation of a data entry interface to submit data to Urinome OpenDataset.
    • Urinome Dataset documentation on OpenWetWare
  • Installation-related:
    • Hardware:
      • Construction of a water dripping system controlled by an Arduino
      • 'SpectroML' file format to Processing software code

>>> Week 2 deliverables

  • Urinoscope-related:
    • Production and testing of 4 additional Urinoscope
    • Data collection
  • Collective Urinome OpenDataset-related:
    • Implementation of a output interface to query/retreive data from the Urinome OpenDataset
    • Urinome Dataset documentation on OpenWetWare
  • Installation-related:
    • Integration of the different Urinomics parts
    • Fabrication of the water-dripping/plant watering system.

Project documentation (optional)

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