Table 1 test_simulation pseudocode
From: The Multiscale Systems Immunology project: software for cell-based immunological simulation
procedure Initialize(n0) | ▹ Number of leukocytes. |
DBConnStr ← (user, dbname, host, port, password) | ▹ Initialize database. |
DBMaker ← DBMaker::Instance(DBConnStr) | |
Environment ← DBMaker.CreateEnvironment("testenv") | |
Source1 ← DBMaker.CreateCell("source") | ▹ Creating and adding point sources to Environment. |
Source1.SetPosition(x1, y1, z1) | |
Environment.AddProp(Source1) | |
Source2 ← DBMaker.CreateCell("source") | |
Source2.SetPosition(x2, y2, z2) | |
Environment.AddProp(Source2) | |
Source3 ← DBMaker.CreateCell("source") | |
Source3.SetPosition(x3, y3, z3) | |
Environment.AddProp(Source3) | |
TNF ← DBMaker.CreateSolfac("tnf") | ▹ Creating and adding soluble factors to environment. |
Environment.AddSolfac(TNF) | |
STNFR ← DBMaker.CreateSolfac("stnfr") | |
Environment.AddSolfac(TNF) | |
MCP1 ← DBMaker.CreateSolfac("mcp1") | |
Environment.AddSolfac(TNF) | |
Vasculature ← DBMaker.CreateVasculature("testvessel") | |
Environment.AddVasculature(Vasculature) | |
for i ← 1, n0 do | ▹ Creating and adding leukocytes to environment. |
Cell ← DBMaker.CreateCell("macrophage") | |
Cell.SetPosition(Random(Environment.Bounds)) | |
Environment.AddCell(Cell) | |
end for | |
end procedure | |
procedure Main(dt, numsteps) | |
Initialize(n0) | |
Simulation ← new Simulation(Environment) | |
for i ← 1, numsteps do | |
Simulation.Step(dt) | |
Log(i, Simulation) | ▹ Log of simulation results. |
end for | |
end procedure |