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project:openfooddna [2015/06/06 12:33] – heluc | project:openfooddna [2015/06/06 16:27] – heluc | ||
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===== Open Food DNA ===== | ===== Open Food DNA ===== | ||
- | The basic idea is to create | + | The basic idea is to carry out a citizen science project to compile |
+ | |||
+ | Many more details about the project on the dedicated wiki [[http:// | ||
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. | 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. | ||
- | We want to build a data workflow from sampling | + | Somebody else (working for a [[http:// |
- | Somebody else (at a [[http:// | + | ===== Team ===== |
- | ===== Prototype ===== | + | * [[user: |
- | + | * [[user: | |
- | Interface - or how to present the data? | + | * 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 ===== | ||
- | | + | In this project, genetic data will initially be qualitative sequencing data. The idea is to transform this sequencing data into binary data about the presence=1/ |
+ | |||
+ | ==== 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:// | Webpage of [[http:// | ||
Download data [[http:// | Download data [[http:// | ||
- | ===== Team ===== | ||
- | * [[user: | + | ==== Workflow ==== |
- | * [[user:randogp|Gianpaolo Rando]], scientist [[https://twitter.com/randogp|@randogp]] | + | |
- | * Soraia Binz, designer [[https://twitter.com/supsi|@supsi]] | + | Starting from a table containing m samples (S1-Sm) and a [m x n] matrix of binary data (D1-Dn species are either present or not) for each sample, we can build a [m x m] matrix of Euclidian distances between the samples. |
- | * [[user:alog|Antoine Logean]], engineer [[https://twitter.com/ecolix|@ecolix]] | + | |
- | * and other team members | + | {{ :project: |
+ | |||
+ | 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 " | ||
+ | |||
+ | {{ :project: | ||
+ | |||
+ | ===== 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: | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | The sidebar should contain a search space (with autofilling) and then items can be either added as " | ||
+ | |||
+ | 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://work.interactivethings.com/nzz-swiss-maps/ | ||
===== Links ===== | ===== Links ===== | ||
+ | The original pad where we worked is here (many more info from web searches) | ||
* https:// | * https:// | ||
- | * Relevant documentation ... | + | |
- | * Blog or forum posts ... | + | The kickstarter campaign of the BeerDeCoded project is here: |
- | * Tools you used ... | + | * https://www.kickstarter.com/ |
- | + | ||
+ | The wiki of the DIY biology Hackuarium association is here: | ||
+ | * http://wiki.hackuarium.ch | ||
{{tag> | {{tag> |