C SBML Model Name:  Repressilator Model
C
C Generated by MathSBML 2.2.1-beta-9 (25 Nov 2003)
C Creation Time: 26-November-2003 10:40:20.585419
C User:          jamestkirk
C Machine:       DHCP-52-160
C Processor:     PowerPC
C Machine type:  PowerMac
C Oper. System:  MacOSX
C --------------------------------------------------------
C
C lsodi compliant SBML model
C Reference: http://netlib.org/alliant/ode/prog/lsodi.f
C
C --------------------------------------------------------
C
C This file contains the following modules:
C
C Module Name       Description                            
C ----------------- ---------------------------------------
C addp (subroutine) Add A to any matrix - required by lsodi
C init (subroutine) Set initial conditions
C jac (subroutine)  Compute Jacobian - required by lsodi
C res (subroutine)  Calculate Residuals - required by lsodi
C
C --------------------------------------------------------
C
      subroutine res(neq,t,y,s,r,ires)
      double precision r,s,t,y
C
C This is subroutine res for lsodi
C This function computes the residuals r(i)=g(t,y)- A(t,y)(dy/dt)
C for the linear-implicit system system (A)*(dy/dt)=g(t,y)
C where A is a constant, possibly singular, matrix.
C
C Here A is diagonal with (restriction imposed by SBML, not lsodi)
C       A(i,i)=1, i=1,...,m, where m=# of odes in the SBML Model
C       A(i,i)=0, i=m+1,...,m+nrules, where nrules =# of algebraic rules
C       A(i,i)=0, i=nrules+1,...,nvars, where nvars is the total number
C                 of variables in the system and nvars-nrules-m>0 is the
C                 number of variables controlled purely by events
C
C If the system is purely differential
C the right-hand side of the system dydt = g(y,t) will 
C be returned if s is zero-filled.
C
C Representation of Model Variables by the array y
C ------------------------------------------------
C y(1) = px
C y(2) = py
C y(3) = pz
C y(4) = x
C y(5) = y
C y(6) = z
C
      dimension r(6),s(6),y(6)
      r(1)=-s(1) + 5.*(-y(1) + y(4))
      r(2)=-s(2) + 5.*(-y(2) + y(5))
      r(3)=-s(3) + 5.*(-y(3) + y(6))
      r(4)=-s(4) + 250./(1. + y(3)**2.1) - 1.*y(4)
      r(5)=-s(5) + 250./(1. + y(1)**2.1) - 1.*y(5)
      r(6)=-s(6) + 250./(1. + y(2)**2.1) - 1.*y(6)
      return
      end
C
C
C --------------------------------------------------------
C
      subroutine addp(neq, t, y, ml, mu, p, nrowp)
C
C Subroutine addp required by lsodi
C
      double precision p, t, y
      dimension y(6), p(nrowp,6)
      integer i
      Do i = 1,6
         p(i,i) = p(i,i)+1
      End Do
      return
      end
C
C --------------------------------------------------------
C
      subroutine jac (neq,t,y,s,ml,mu,p,nrowp)
C
C Subroutine jac required by lsodi, computes jacobian
C
      dimension y(6), s(6),p(nrowp,6)

      p(1,1)=-5.
      p(1,2)=0
      p(1,3)=0
      p(1,4)=5.
      p(1,5)=0
      p(1,6)=0
      p(2,1)=0
      p(2,2)=-5.
      p(2,3)=0
      p(2,4)=0
      p(2,5)=5.
      p(2,6)=0
      p(3,1)=0
      p(3,2)=0
      p(3,3)=-5.
      p(3,4)=0
      p(3,5)=0
      p(3,6)=5.
      p(4,1)=0
      p(4,2)=0
      p(4,3)=(-525.*y(3)**1.1)/(1. + y(3)**2.1)**2
      p(4,4)=-1.
      p(4,5)=0
      p(4,6)=0
      p(5,1)=(-525.*y(1)**1.1)/(1. + y(1)**2.1)**2
      p(5,2)=0
      p(5,3)=0
      p(5,4)=0
      p(5,5)=-1.
      p(5,6)=0
      p(6,1)=0
      p(6,2)=(-525.*y(2)**1.1)/(1. + y(2)**2.1)**2
      p(6,3)=0
      p(6,4)=0
      p(6,5)=0
      p(6,6)=-1.

      return
      end
C
C --------------------------------------------------------
C
      Subroutine init(neq,y)
      double precision y
      dimension y(6)
      y(1)=5.
      y(2)=Indeterminate
      y(3)=15.
      y(4)=Indeterminate
      y(5)=Indeterminate
      y(6)=Indeterminate
      return
      end