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project:openfooddna [2015/06/05 12:10] – created alog | project:openfooddna [2015/06/06 16:30] (current) – heluc | ||
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===== Open Food DNA ===== | ===== Open Food DNA ===== | ||
- | (screenshots or sketches up here) | + | The basic idea is to carry out a citizen science project to compile an open dataset of DNA information about food and beverages. |
- | Brief description goes here. Add sections below if you need more room. | + | Many more details about the project on the dedicated wiki [[http:// |
- | Include links to your demo and/ | + | Take beer. The assumption is that the DNA content (genetic or genomic information about every single living organism that was present during the brewing) may correlate with the type and taste of the brew. |
+ | |||
+ | Somebody else (working for a [[http:// | ||
+ | |||
+ | ===== Team ===== | ||
+ | |||
+ | * [[user: | ||
+ | * [[user: | ||
+ | * Soraia Binz, designer [[https:// | ||
+ | * [[user: | ||
+ | |||
+ | Disclaimer: Luc Henry and Gianpaolo Rando run the BeerDeCoded project at the open laboratory Hackuarium in Renens and came to get input about data analysis. | ||
===== Data ===== | ===== Data ===== | ||
- | * List and link your actual and ideal data sources. | + | In this project, genetic |
- | ===== Team ===== | + | ==== Random data generation |
- | | + | Since we do not have data yet, we generated a random dataset using this Octave/ |
- | | + | (generates a table containing random binary data for 10 samples and 30 parameters and calculate the euclidian distance matrix) |
+ | |||
+ | < | ||
+ | # | ||
+ | % lines : beer samples | ||
+ | li = 10; | ||
+ | % columns : species and sub species | ||
+ | co = 30; | ||
+ | M = round(rand(li, | ||
+ | O = zeros(li); | ||
+ | for i = 1:li | ||
+ | for j = 1:i | ||
+ | O(i,j) = norm( M(:, | ||
+ | endfor | ||
+ | endfor | ||
+ | O | ||
+ | </ | ||
+ | |||
+ | We did not plot this data yet. | ||
+ | |||
+ | ==== Metadata ==== | ||
+ | |||
+ | We searched for metadata to add to the data generated and making it look more real. Few of our findings: | ||
+ | |||
+ | | ||
+ | |||
+ | Webpage of [[http:// | ||
+ | |||
+ | Download data [[http:// | ||
+ | |||
+ | ==== Workflow ==== | ||
+ | |||
+ | Starting from a table containing m samples (S1-Sm) | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | The metadata entries (M1-Mn) can be attached to this matrix and used to generate a plot that contains sample points with associated characteristics. This plot contains every single sample present in the database. | ||
+ | |||
+ | A user friendly interface has to be built in order for the beer lover to choose the beers they know, and compare this " | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | ===== Prototype ===== | ||
+ | |||
+ | We " | ||
+ | |||
+ | We have a main display with three visualisation types you can switch from: Plot (display beer samples based on Euclidian distance), Tree (same but in a tree fashion), Rank (forget distances and rank based on metadata, such as alcohol %, bitterness). | ||
+ | |||
+ | Here is the Plot: | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | Here is the Tree (can switch from linear to circular representation): | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | Here is the Plot being transformed into a Rank: | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | Transformation from Plot to Rank was taken from the following example: | ||
+ | http:// | ||
===== Links ===== | ===== Links ===== | ||
- | * Relevant documentation ... | + | The original pad where we worked is here (many more info from web searches) |
- | * Blog or forum posts ... | + | * https:// |
- | * Tools you used ... | + | |
- | + | The kickstarter campaign of the BeerDeCoded project is here: | |
- | {{tag> | + | * https://www.kickstarter.com/ |
+ | |||
+ | The wiki of the DIY biology Hackuarium association is here: | ||
+ | * http:// | ||
+ | {{tag> |