Bioinformatics Recipe Cookbook
All Projects

Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in just 60 seconds.

This recipe is based on a fun diversion that I show during lectures. The goal of the recipe is to demonstrate that, when properly documented it is possible to reproduce major scienific findings with relative ease t and sometimes under a minute.

This recipe reproduces the main results published in the work:

On a properly set up system, and depending on bandwidth, the recipe completes under a minute. This includes getting the data, references, aligning and calling variants! The results even include annotations of the variant effects relative to the features on the genome.

The best way to enjoy this analysis is to have the following video playing while the analyis is running:

You win and save the world if you can finish running the analysis before the music stops.

Note how this theme song makes even the otherwise bland analysis feel super exciting.

Recipe Code
Recipe Interface
Interface Preview
Interface preview shows the resulting view of the combined interface elements.
Interface specification
Interface element specification. Shows the code and the resulting interface element.
Double click on an element to insert it into the interface.
Integer values
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
Float values
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
Text box
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
Dropdown menu
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
Check box
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
Upload Field
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
Pick Data
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
Radio Buttons
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
Edit Recipe
Recipe display name
Unique identifier for the recipe.

Determines who can run a recipe.

A detailed explanation of what the recipe does (markdown OK).
Image :
Optional image for the recipe ( 500px Maximum ).
Used to order recipes (optional).

Powered by the release 2.1