rough sketch with some examples

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "reveal.js"]
+	path = reveal.js
+	url = git@github.com:hakimel/reveal.js.git

Makefile

@@ -3,7 +3,12 @@
 INPUT = sketch.md.lhs
 
 pdf: $(INPUT)
-	pandoc -f markdown+lhs+smart+emoji -o documentation.pdf $(INPUT)
+	pandoc -f markdown+lhs+smart+emoji -H make-code-footnotesize.tex \
+	-o documentation.pdf $(INPUT)
+
+slides: $(INPUT)
+	pandoc -f markdown+lhs+smart+emoji -t revealjs --self-contained --incremental \
+	-o documentation.html $(INPUT)
 
 
 run: $(INPUT)

README.md

@@ -8,3 +8,12 @@ References:
 - [Moore et al (2013): Explaining intraspecific diversity in plant secondary metabolites in an ecological context](https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.12526)
 - [Firn, Jones (2003): Natural products – a simple model to explain chemical diversity](http://www.caryinstitute.org/sites/default/files/public/reprints/Firn_&_Jones_2003_Natural_RSC_Nat_Prod_Rep_20_382-391.pdf)
 
+## Creating slideshow
+
+The slides are created with revealjs which has to be present. A simple
+
+```bash
+git submodule update --init
+```
+
+pulls all dependencies and `make slides` then works as expected.

make-code-footnotesize.tex

@@ -0,0 +1 @@
+\renewenvironment{Shaded} {\footnotesize} {}

reveal.js

@@ -0,0 +1 @@
+Subproject commit 65bdccd5807b6dfecad6eb3ea38872436d291e81

sketch.md

@@ -0,0 +1 @@
+sketch.md.lhs

sketch.md.lhs

@@ -1,22 +1,38 @@
 ---
 title: Sketch for simulating chemodiversity
 author: Stefan Dresselhaus
-date: 2018-09-21
+date: \today
 format: markdown+lhs
 
+papersize: a4
+fontsize: 10pt
+documentclass: scrartcl
+
+width: 1920
+height: 1080
+margin: 0.2
+theme: solarized
+slideNumber: true
+
 ...
 
-= (rough) sketch components responsible for chemodiversity
+(rough) sketch components responsible for chemodiversity
+========================================================
 
-== Genes
+---
+
+Genes
+-----
 
 - define which enzymes are produced in which quantities
-    - list in fig. 1 in [1]
+    - list in fig. 1 in [[1](git@github.com:hakimel/reveal.js.git)]
 - can be scaled down/inactivated (i.e. when predators leave for generations)
     - easy to ramp up production as long as the genes are still there
 - plants can survive without problems with inactive PSM-cycles when no
   adversaries are present.
 
+---
+
 === Inheritance & Mutation
 
 - via whole-genome and local-genome duplication
@@ -26,6 +42,8 @@ format: markdown+lhs
     - need to classify products by "chemical distance" for simulation
     - **TODO**: Map/Markov-Chain of mutations that may occur here?
 
+---
+
 === Evolutional strategies
 
 - "Bet-hedging": reduce variations of fitness over time
@@ -40,16 +58,21 @@ format: markdown+lhs
       adversarial traits in the population
         - Keyword: Frequency-dependent-selection (FDS)
 
-== Pathways to produce chemical compounds
+---
+
+Pathways to produce chemical compounds
+--------------------------------------
 
 - 40k+ compounds just stem from compounds of the calvin-cycle taking the
   MEP-pathway or from the krebs-cycle taking the MVA-pathway
     - both yield the same intermediate product that forms the basis.
 - 10k+ compounds are amino-acid-derivatives
-- Chapter VI in [1] exemplary describes 4 complete different pathways that yield
+- Chapter VI in [[1](git@github.com:hakimel/reveal.js.git)] exemplary describes 4 complete different pathways that yield
   compounds.
     - similar compounds/pathways should be found in the simulation
 
+---
+
 === Consequences of producing compounds
 
 - taking away parts of the calvin/krebs cycle puts pressure on those
@@ -57,7 +80,10 @@ format: markdown+lhs
 - **TODO**: where do amino-acids come from? How much impact has the diversion of
   these components?
 
-== Maintaining chemical diversity
+---
+
+Maintaining chemical diversity
+------------------------------
 
 === + screening hypothesis
 
@@ -76,9 +102,11 @@ format: markdown+lhs
   evolution suggesting they got rid of them when no pressure to maintain them
   was applied
 
-==== questions resulting from this that should be answered in the simulation
+---
 
-- details in chapter VIII of [1]
+=== questions resulting from this that should be answered in the simulation
+
+- details in chapter VIII of [[1](git@github.com:hakimel/reveal.js.git)]
 - how quick can lost diversity be restored?
 - how expensive is it to keep producing many inactive substances while also
   producing active deterrents? Does this lead to a single point-of-failure due
@@ -91,20 +119,287 @@ format: markdown+lhs
     - adaptation in the qualitative & quantitative evolution in response to
       changed pressure? (i.e. those who cannot adapt quick enough die?)
 
-= Scenario
+---
 
-== Plants
+Scenario
+========
 
-> data Foo = Bar
+As this is literate Haskell first a bit of throat-clearing:
 
-== Enzymes
+> {-# LANGUAGE RecordWildCards #-}
+> 
+> import Data.Functor        ((<$>))
+> import Control.Applicative ((<*>))
+> import Control.Monad       (forM_)
+> import Data.List           (permutations, subsequences)
 
-== Herbivores
+Then some general aliases to make everything more readable:
 
-== Environment
+> type Probability = Float
+> type Quantity = Int
+> type Activation = Float
+> type Amount = Float
 
-== Fitness
+---
 
-== Mating & Creation of diversity
+Nutrients & Compounds
+---------------------
+
+Nutrients are the basis for any reaction and are found in the environment of the
+plant.
+
+> data Nutrient = Sulfur
+>               | Phosphor
+>               | Nitrate
+>               | Photosynthesis
+>      deriving (Show, Enum, Bounded, Eq)
+>
+> data Component = PP
+>                | FPP
+>      deriving (Show, Enum, Bounded, Eq)
+
+Compounds are either direct nutrients or already processed components
+
+> data Compound = Substrate Nutrient
+>               | Produced Component
+>      deriving (Show, Eq)
+
+This simple definition is only a brief sketch.
+
+---
+
+Enzymes
+-------
+
+Enzymes are the main reaction-driver behind synthesis of intricate compounds.
+
+> data Enzyme = Enzyme
+>        { enzymeName            :: String
+>          -- ^ Name of the Enzyme. Enzymes with the same name are supposed
+>          --   to be identical.
+>        , substrateRequirements :: [(Nutrient,Amount)]
+>          -- ^ needed for reaction to take place
+>        , substrateIntolerance  :: [(Nutrient,Amount)]
+>          -- ^ inhibits reaction if given nutrients are above the given concentration
+>        , synthesis             :: [(Compound,Amount)] -> [(Compound,Amount)]
+>          -- ^ given x in amount a, this will produce y in amount b
+>        , dominance             :: Maybe Amount
+>          -- ^ in case of competition for nutrients this denotes the priority
+>          --   Nothing = max possible
+>        }
+> 
+> instance Show Enzyme where
+>   show (Enzyme{..}) = enzymeName
+>
+> instance Eq Enzyme where
+>   a == b = enzymeName a == enzymeName b
+
+---
+
+Example "enzymes" could be:
+
+> pps :: Enzyme -- uses Phosphor from Substrate to produce PP
+> pps = Enzyme "PPS" [(Phosphor,1)] [] syn Nothing
+>  where
+>    syn compAvailable = [(Substrate Phosphor,i*(-1)),(Produced PP,i)]
+>      where
+>        i = getAmountOf (Substrate Phosphor) compAvailable
+>
+> fpps :: Enzyme -- PP -> FPP
+> fpps = Enzyme "FPPS" [] [] syn Nothing
+>  where
+>    syn compAvailable = [(Produced PP,i*(-1)),(Produced FPP,i*0.5)]
+>      where
+>        i = getAmountOf (Produced PP) compAvailable
 
 
+---
+
+Environment
+-----------
+
+In the environment we have predators that impact the fitness of our plants and
+may be resistant to some compounds the plant produces. They can also differ in
+their intensity.
+
+> data Predator = Predator { resistance    :: [Component]
+>                            -- ^ list of components this predator is resistant to
+>                          , fitnessImpact :: Amount
+>                            -- ^ impact on the fitness of a plant
+>                            --   (~ agressiveness of the herbivore)
+>                          } deriving (Show, Eq)
+
+Exemplatory:
+
+> greenfly :: Predator         -- 20% of plants die to greenfly, but the fly is
+> greenfly = Predator [PP] 0.2 -- killed by any Component not being PP
+
+---
+
+The environment itself is just the soil and the predators. Extensions would be
+possible.
+
+> data Environment =
+>      Environment
+>    { soil      :: [(Nutrient, Amount)]
+>      -- ^ soil is a list of nutrients available to the plant.
+>    , predators :: [(Predator, Probability)]
+>      -- ^ Predators with the probability of appearance in this generation.
+>    } deriving (Show, Eq)
+
+Example:
+
+> exampleEnvironment :: Environment
+> exampleEnvironment =
+>   Environment
+>     { soil = [ (Nitrate, 2)
+>              , (Phosphor, 3)
+>              , (Photosynthesis, 10)
+>              ]
+>     , predators = [ (greenfly, 0.1) ]
+>     }
+
+---
+
+Plants
+------
+
+Plants consist of a Genome responsible for creation of the PSM and also an
+internal state how many nutrients and compounds are currently inside the plant.
+
+> type Genome = [(Enzyme, Quantity, Activation)]
+>
+> data Plant = Plant
+>      { genome            :: Genome
+>        -- ^ the genetic characteristic of the plant
+>      , absorbNutrients   :: Environment -> [(Nutrient,Amount)]
+>        -- ^ the capability to absorb nutrients given an environment
+>      }
+> instance Show Plant where
+>   show p = "Plant with Genome " ++ show (genome p)
+> instance Eq Plant where
+>   a == b = genome a == genome b
+
+---
+
+The following example yields in the example-environment this population:
+
+    *Main> printPopulation [pps, fpps] plants
+    Population:
+    PPS     ______oöö+++______oöö+++____________oöö+++oöö+++
+    FPPS    ____________oöö+++oöö+++______oöö+++______oöö+++
+
+> plants :: [Plant]
+> plants = (\g -> Plant g defaultAbsorption) <$> genomes
+>  where
+>    enzymes = [pps, fpps]
+>    quantity = [1,2] :: [Quantity]
+>    activation = [0.7, 0.9, 1]
+>
+>    genomes = do
+>      e <- permutations enzymes
+>      e' <- subsequences e
+>      q <- quantity
+>      a <- activation
+>      return $ (,,) <$> e' <*> [q] <*> [a]
+>
+>    defaultAbsorption (Environment s _) = limit Phosphor 2
+>                                        . limit Nitrate 1
+>                                        . limit Sulfur 0
+>                                        <$> s
+>    -- custom absorbtion with helper-function:
+>    limit :: Nutrient -> Amount -> (Nutrient, Amount) -> (Nutrient, Amount)
+>    limit n a (n', a')
+>      | n == n'   = (n, min a a') -- if we should limit, then we do ;)
+>      | otherwise = (n', a')
+
+---
+
+Fitness
+-------
+
+The fitness-measure is central for the generation of offspring and the
+simulation. It evaluates the probability for passing on genes given a plant in
+an environment.
+
+> type Fitness = Float
+>
+> fitness :: Environment -> Plant -> Fitness
+> fitness e p = survivalRate
+>    where
+>      nutrients = absorbNutrients p e
+>      products = produceCompounds p nutrients
+>      survivalRate = deterPredators (predators e) products
+
+
+---
+
+> produceCompounds :: Plant -> [(Nutrient, Amount)] -> [Compound]
+> produceCompounds (Plant genes _) = undefined
+>   -- this will take some constrained linear algebra-solving
+
+> deterPredators :: [(Predator, Probability)] -> [Compound] -> Probability
+> deterPredators ps cs = sum $ do
+>       c <- cs -- for every compound
+>       (p,prob) <- ps -- and every predator
+>       return (if c `notin` (resistance p) -- if the plant cannot deter the predator
+>                  then prob * fitnessImpact p -- impact it weighted by probability
+>                  else 0)
+>    where
+>      (Produced a) `notin` b = all (/=a) b
+>      _ `notin`_             = False
+
+
+Mating & Creation of diversity
+------------------------------
+
+TODO
+
+---
+
+Running the simulation
+----------------------
+
+> main = do
+>   putStrLn "Environment:"
+>   print exampleEnvironment
+>   putStrLn "Example population:"
+>   printPopulation [pps, fpps] plants
+
+    runhaskell sketch.md.lhs
+    Environment:
+    Environment { soil = [(Nitrate,2.0),(Phosphor,3.0),(Photosynthesis,10.0)]
+                , predators = [(Predator {resistance = [PP], fitnessImpact = 0.2},0.1)]}
+    Example population:
+    Population:
+    PPS     ______oöö+++______oöö+++____________oöö+++oöö+++
+    FPPS    ____________oöö+++oöö+++______oöö+++______oöö+++
+
+
+---
+
+Utility Functions
+-----------------
+
+> getAmountOf :: Compound -> [(Compound, Amount)] -> Amount
+> getAmountOf c = sum . fmap snd . filter ((== c) . fst)
+>
+> printPopulation :: [Enzyme] -> [Plant] -> IO ()
+> printPopulation es ps = do
+>   let padded i str = take i $ str ++ repeat ' '
+>   putStrLn "Population:"
+>   forM_ es $ \e -> do
+>     putStr $ padded 8 (show e)
+>     forM_ ps $ \(Plant g _) -> do
+>       let curE = sum $ map (\(_,q,a) -> (fromIntegral q)*a) 
+>                      . filter (\(e',_,_) -> e == e')
+>                      $ g
+>           plot x
+>            | x > 2     = "O"
+>            | x > 1     = "+"
+>            | x > 0.7   = "ö"
+>            | x > 0.5   = "o"
+>            | x > 0     = "."
+>            | otherwise = "_"
+>       putStr (plot curE)
+>     putStrLn ""