Libraries of Modules in Systems Biology

In a Systems biology scenario modules can represent basic regulatory mechanisms or regulatory motifs in cellular systems that appear recurrently involving different molecular species interacting according to characteristic rates in specific locations of the cells. For example, the following basic library defines modules representing positve, negative and constitutive gene expression as well as some basic transcriptional regulatory motifs in bacterial systems as negative autoregulation (NAR) and incoherent feedforward loop (IFFL):

libraryOfModules transcriptionalMotifs

   Const({X},{c_1},{l}) =
   {
       r1: [ geneX ]_l -c_1-> [ geneX + rnaX ]_l
   }

   PosReg({X,Y},{c_1,c_2,c_3},{l}) =
   {
       r1: [ proteinX + geneY ]_l -c_1-> [ proteinX_geneY ]_l
       r2: [ proteinX_geneY ]_l -c_2-> [ proteinX + geneY ]_l
       r3: [ proteinX_geneY ]_l -c_3-> [ proteinX_geneY + rnaY ]_l
   }

   NegReg({X,Y},{c_1,c_2},{l}) =
   {
       r1: [ proteinX + geneY ]_l -c_1-> [ proteinX_geneY ]_l
       r2: [ proteinX_geneY ]_l -c_2-> [ proteinX + geneY ]_l
   }

   PostTransc({X},{c_1,c_2,c_3},{l}) =
   {
       r1: [ rnaX ]_l -c_1-> [ ]_l
       r2: [ rnaX ]_l -c_2-> [ rnaX + proteinX ]_l
       r3: [ proteinX ]_l -c_3-> [ ]_l
   }

   NAR({X},{c_1,c_2},{l}) =
   {
       NegReg({X,X},{c_1,c_2},{l}) from this
   }

   IFFL({X,Y,Z},{c_1,c_2,c_3,c_4,c_5,c_6,c_7,c_8},{l}) =
   {
       PosReg({X,Y},{c_1,c_2,c_3},{l}) from this
       PosReg({X,Z},{c_4,c_5,c_6},{l}) from this
       NegReg({Y,Z},{c_7,c_8},{l}) from this
    }

endLibraryOfModules