ChemChains sandbox
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(Redirected from Chemchains sandbox)
ChemChains is an awesome chunk of software simulating cell biology in a boolean network.
This page is the ChemChains sandbox, where Omaha Dynamic Language Users Group folk are messing around with various implementations of ChemChains in whatever programming languages fit their mood. You too can play along at home:
$ mkdir ChemChains
$ svn co --username odynug --password odynugmathbio \
http://mathbio.unomaha.edu/svn/chemchains/perl/trunk/ ChemChains/perl
$ svn co --username odynug --password odynugmathbio \
-r{20080702} \
http://mathbio.unomaha.edu/svn/chemchains/cpp/trunk/ ChemChains/cpp
$ cd ChemChains/perl
$ perl chemchains.pl 10
Congrats -- you just simulated cell biology. :)
Email questions / concerns to our mailing list, or to jay(at)jays(dot)net.
Links
- ChemChains
- Official cpp/ tutorial
- Jay's YAPC::NA 2008 lightning talk abstract and slides.
Regression Testing
4 C++ versions of ChemChains exist. You can regression test them all with perl/trunk/TAP. This tests that each version outputs the same results as ChemChains1.0_clean when running a simple network.
# Get all releases from svn svn co http://mathbio.unomaha.edu/svn/chemchains/ chemchains/svn # Get tarball releases mkdir chemchains/tarballs cd chemchains/tarballs/ wget http://www.bioinformatics.org/download.php?fileid=450 tar xvzf ChemChains1.0.tar.gz # Compile all C++ versions cd ChemChains1.0_clean make cd ../../svn/cpp/branches/CC1_0-rc1 make cd ../MathbioRelease make cd ../../trunk make # Run the test suite cd ../../perl/trunk prove -r 2>/dev/null
Current prove output: --Jhannah 20:44, 24 August 2008 (UTC)
TAP/000_mkdir..............ok
TAP/CC1_0-rc1..............ok
TAP/ChemChains1.0_clean....ok
TAP/MathbioRelease.........FAILED tests 3-5, 7-9, 11-13, 15-17, 19-21, 23-25, 27-29, 31-33, 35-37, 39-41, 43-45, 47-49, 51-53, 55-57, 59-61, 63-65, 67-69, 71-73, 75-77, 79-81, 83-85, 87-89, 91-93, 95-97, 99
Failed 73/99 tests, 26.26% okay
TAP/trunk..................ok
Failed Test Stat Wstat Total Fail List of Failed
-------------------------------------------------------------------------------
TAP/MathbioRelease.t 99 73 3-5 7-9 11-13 15-17 19-21 23-25 27-
29 31-33 35-37 39-41 43-45 47-49
51-53 55-57 59-61 63-65 67-69 71-73
75-77 79-81 83-85 87-89 91-93 95-97
99
Failed 1/5 test scripts. 73/399 subtests failed.
Files=5, Tests=399, 1 wallclock secs ( 0.60 cusr + 0.17 csys = 0.77 CPU)
The network repeats?
In my Perl version it looks like the network repeats after T+16: back to 13,14,15,16, then again 13,14,15,16, etc. Even running out to 1000 iterations shows this same pattern, apparently. Have you seen this is the C++ version?
The output below shows each node in the network (sorted by node name, ASCII sort). The underscores are the Input nodes, which are not iterated after the initial state (T+0).
Over on the far right is a new counter I added tonight which tracks all states of the network that have been seen before (whether or not the string of zeros and ones is unique). When a state is novel it assigns a new number for that state. When a state has been seen before, it prints the number of that state. So apparently T+17 is NOT unique, it is exactly the same state as T+13, etc.
... Come to think of it I think the way my code currently works any loop back to any previous state will always cause such a loop. I suppose this may no longer be true once I add Chaos and Delay nodes?
Just curious if you've seen this before in C++. --Jhannah 05:20, 17 August 2008 (UTC)
Hannah-Mac-Mini:~/src/ChemChains/perl jhannah$ perl chemchains.pl 30 Reading node configuration... 139 nodes memorized. T+0000 1000000000000000000000001101000000000000000000000000000001000000110000010100000000100000000001000000000100000000010000000000000000000000000 0 T+0001 0001000000000011000010__00_10000000000011_010000000000000110010100011011000000001000100000000000001000000000000101_00001000000_0_0_0_000100 1 T+0002 0010001001000011011000__10_10000000000011_000000000000000100011100011110010001001010000000000000001000000010000001_00000000000_0_0_0_000100 2 T+0003 0011000000000011011011__10_10001000000011_010000000010000110011100011001101001001000000000010000101100000010000110_00000000000_0_0_0_000100 3 T+0004 0011000001000000011110__10_00000000000001_001000000000000100001100001111110001000100000000000000100110010000010001_00010000000_0_0_0_000000 4 T+0005 0001000000000000000010__10_00000000000001_010000000010000110001110011110111001001100000000010000111110010000000010_00001000100_0_0_0_000100 5 T+0006 0001000001000000000110__10_00001000000001_011000000000000100011110001111110001001100000000000000010010010000000011_00010000000_0_0_0_001000 6 T+0007 0001000001000001000010__10_00001000000001_011000000000000110011110011110111001001100000000010000011000010000010011_00001000100_0_0_0_000100 7 T+0008 0001001001000000000110__10_00000000000001_011000000000000100011110011111110001001100000000010000011000010000010011_00011000000_0_0_0_000100 8 T+0009 0001001001000000000010__10_00000000000001_011000000000000110011110011110111001001100000000010000011000010000000011_00001000100_0_0_0_000100 9 T+0010 0001001001000001000110__10_00001000000001_011000000000000100011110011111110001001100000000010000011000010000000011_00011000000_0_0_0_000100 10 T+0011 0001001001000001001010__10_00001000000001_011000000000000110011110011110111001001100000000010000011000010000010011_00001000100_0_0_0_000100 11 T+0012 0001001001000000000110__10_00000000000001_011000000000000100011110011111110001001100000000010000011000010000010010_00011000000_0_0_0_000100 12 T+0013 0001001001000000000010__10_00000000000001_011000000000000110011110001110111001001100000000010000011000010000000011_00010000000_0_0_0_001000 13 T+0014 0001001001000001000110__10_00001000000001_011000000000000100011110011111110001001100000000010000011000010000000011_00001000100_0_0_0_000100 14 T+0015 0001001001000001001010__10_00001000000001_011000000000000110011110011110111001001100000000010000011000010000010011_00011000000_0_0_0_000100 15 T+0016 0001001001000000000110__10_00000000000001_011000000000000100011110011111110001001100000000010000011000010000010010_00001000100_0_0_0_000100 16 T+0017 0001001001000000000010__10_00000000000001_011000000000000110011110001110111001001100000000010000011000010000000011_00010000000_0_0_0_001000 13 T+0018 0001001001000001000110__10_00001000000001_011000000000000100011110011111110001001100000000010000011000010000000011_00001000100_0_0_0_000100 14 T+0019 0001001001000001001010__10_00001000000001_011000000000000110011110011110111001001100000000010000011000010000010011_00011000000_0_0_0_000100 15 T+0020 0001001001000000000110__10_00000000000001_011000000000000100011110011111110001001100000000010000011000010000010010_00001000100_0_0_0_000100 16 T+0021 0001001001000000000010__10_00000000000001_011000000000000110011110001110111001001100000000010000011000010000000011_00010000000_0_0_0_001000 13 T+0022 0001001001000001000110__10_00001000000001_011000000000000100011110011111110001001100000000010000011000010000000011_00001000100_0_0_0_000100 14 T+0023 0001001001000001001010__10_00001000000001_011000000000000110011110011110111001001100000000010000011000010000010011_00011000000_0_0_0_000100 15 T+0024 0001001001000000000110__10_00000000000001_011000000000000100011110011111110001001100000000010000011000010000010010_00001000100_0_0_0_000100 16 T+0025 0001001001000000000010__10_00000000000001_011000000000000110011110001110111001001100000000010000011000010000000011_00010000000_0_0_0_001000 13 T+0026 0001001001000001000110__10_00001000000001_011000000000000100011110011111110001001100000000010000011000010000000011_00001000100_0_0_0_000100 14 T+0027 0001001001000001001010__10_00001000000001_011000000000000110011110011110111001001100000000010000011000010000010011_00011000000_0_0_0_000100 15 T+0028 0001001001000000000110__10_00000000000001_011000000000000100011110011111110001001100000000010000011000010000010010_00001000100_0_0_0_000100 16 T+0029 0001001001000000000010__10_00000000000001_011000000000000110011110001110111001001100000000010000011000010000000011_00010000000_0_0_0_001000 13 T+0030 0001001001000001000110__10_00001000000001_011000000000000100011110011111110001001100000000010000011000010000000011_00001000100_0_0_0_000100 14 All done. We're at T+30. Here are your final result: AA:0 AC:0 AND_3_4:0 ARF:1 ASK1:0 Actin:0 Akt:1 Arp_2_3:0 B_Arrestin:0 B_Parvin:1 Ca:0 CaM:0 CaMK:0 CaMKK:0 Cas:0 Cbp:1 Cdc42:0 Crk:0 Csk:0 DAG:1 DGK:1 DOCK180:0 ECM:0 (Input) EGF:0 (Input) EGFR:1 Erk:0 ExtPump:0 (Input) Fak:0 GCK:0 GRK:0 Ga_12_13:0 Gab1:1 Gai:0 Gaq:0 Gas:0 Gbg_12_13:0 Gbg_i:0 Gbg_q:0 Gbg_s:0 Graf:0 Grb2:1 IL1_TNF:0 (Input) IL1_TNFR:0 ILK:1 IP3:1 IP3R1:0 Integrins:0 MKK3:0 MKK6:0 MKK7:0 MKPs:0 MLCK:0 MLCP:0 MLK1:0 MLK2:0 MLK3:0 Mek:0 Mekk1:1 Mekk2:0 Mekk3:0 Mekk4:0 Myosin:1 NIK:1 Nck:1 PA:1 PAK:0 PDE4:0 PDK1:1 PI3K:1 PI4K:1 PI5K:1 PIP2_34:1 PIP2_45:1 PIP3_345:1 PIP_4:0 PKA:0 PKC:0 PKC_primed:1 PLA2:0 PLC_B:0 PLC_g:1 PLD:1 PP2A:0 PTEN:0 PTP1b:0 PTPPEST:0 PTPa:0 Palpha_12_13_R:0 Palpha_i_R:0 Palpha_q_R:0 Palpha_s_R:0 Pix_Cool:1 RGS:0 RKIP:0 Rac:0 Raf:0 Raf_DeP:0 Raf_Loc:1 Raf_Rest:1 Ral:0 RalBP1:0 RalGDS:0 Rap1:0 Ras:1 RasGRF_GRP:0 Rho:0 RhoGDI:0 RhoK:0 SAPK:0 SHP2:0 Sek1:0 Shc:0 Sos:1 Src:1 Stress:0 (Input) TAK1:0 TAO_1_2:0 Tab_1_2:0 Talin:0 Tiam:1 Tpl2:0 Trafs:0 Trx:0 Vinc:1 WASP:0 alpha_12_13_R:0 alpha_12_13_lig:0 (Input) alpha_i_R:0 alpha_i_lig:0 (Input) alpha_q_R:0 alpha_q_lig:0 (Input) alpha_s_R:0 alpha_s_lig:0 (Input) cAMP:0 p115RhoGEF:0 p120RasGAP:0 p190RhoGAP:1 p38:0 p90RSK:0
