From c9f4066c014ffd7440fbbd50c6f270bcb526f2d3 Mon Sep 17 00:00:00 2001 From: alex patrie Date: Fri, 16 Feb 2024 19:06:09 -0500 Subject: [PATCH] feat: added Min1 publication to test suite examples --- .../smoldyn/Andrews-Min1-PUBLICATION.omex | Bin 0 -> 3952 bytes .../Andrews-Min1-PUBLICATION/manifest.xml | 6 + .../Andrews-Min1-PUBLICATION/metadata.rdf | 57 +++++++ .../Andrews-Min1-PUBLICATION/model.txt | 115 ++++++++++++++ .../Andrews-Min1-PUBLICATION/simulation.sedml | 147 ++++++++++++++++++ 5 files changed, 325 insertions(+) create mode 100644 examples/smoldyn/Andrews-Min1-PUBLICATION.omex create mode 100644 examples/smoldyn/Andrews-Min1-PUBLICATION/manifest.xml create mode 100644 examples/smoldyn/Andrews-Min1-PUBLICATION/metadata.rdf create mode 100644 examples/smoldyn/Andrews-Min1-PUBLICATION/model.txt create mode 100644 examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION.omex b/examples/smoldyn/Andrews-Min1-PUBLICATION.omex new file mode 100644 index 0000000000000000000000000000000000000000..482bf4c59b3564b77e7ffe09aa3e24523b07deb7 GIT binary patch literal 3952 zcmZ{nXHXN~w#5?!DFFcq2%_{Vy-G(zk=~T5AP_=tLO=nj1|bl7N170d8oCHlqzOcN zZ;6pEN{0Z_AOCrG-o4kEcg}}1d(K&3_MZ8jwTyJHkb(gu01Ci(g@%RVFT0{%QUKtH z8UUaK0016d4ls97_zQTh`46u}S?ZAZb1Go4OEpj3cX($DHCBXB(NHWj%C=el8ajsb zu5qx~wXSImNp(MRieY>G$y05YTkx3soy~|U3wa}~gfa#(!d59+AJhgsa$DK5x=Z*gk{4#MP&RqEZ+0o<=t^=Kt<5SOvw z0X^ZkY?ASQ|%2Hc}&m`mgD?60q4^qHC`6_0XFUigSZs>w3rrB_>i$ zdw-qB=S?>4Gs(X?hW1POQn~fqzeRlJaHHSxi=SUR7%7~%9v4df^0elRd9zTYMCEZn zUX+FLa*%-aX954*9Z52TRHzIYLZpq;hV7Fb@pN}+tpDz$PG4b_A55OkXTl;lH^#BDwM{ZJuRRCkUjTSZ-ZQox-kz*ZrhAbA};GFFG}|2 z5gSsjCq4ZK3%>A2`BBk`g>H`gzyl0ZpyzqKp_!UV`k11?o6C9~i42YE#)-_l4!l zeym$_OizA-A1?#VI*M98hwiWZQdns=BhaMUm0Hjkt1Y(#1Y1gKl}N?~Kpl^?rqB_4 zwUyJ&WK`t4Rh`72Ri*bfkX3oxo5&2UY`@Lv#7&(& zV}Elo$W2_F4JWGEtwJB>hwn3)xmOp3e4jq6_Zrg5v|!|C3fItgi2tDba|L4m^9bD= z=}=aSue%mVkuzL@TGsw^!Y1ZMawci_d*Kl2?7AdMi57ra@hU*y{hjdkbI34zAT$FMg>E`sR8lg*Vv+xmQpTpS)xO4BgX`lu?yuyq|`^>fA_+ z@4q0W+5!rCr)Gviw316xIWur+v1^P54I6sl>z=_=cnk}*ijR9xCn?X8s?mP|?+q-- z`Sc0^a9w6i}B)F{M`>CL9%@%W&jow|f|cjCO5(_DC2rjEqxpH5dO zqBHx*7(YmyMt;fp63H%Vs3~Eo7XnxmT99ZS3sgpNK^2$R_1>HMvqlOOyq*RsI>to8Zu9oWGX%5S~a;7FTkI#SC!eowGhWn`p8IMqLvNn zERc+};XgKm7C(2-@8YVaglhet+9Wb{7|}k7dOEi za^Zin6DU`uTKNMlC!E|u(g%3H?I1uOzvcUK_KBj_0SU>2al;y(UX=7qmGzv6vQSc0 z*KfX;>6=t;r)d<0Rq1zzngm#_fs>Nf%O&q*!>DzqcVX>}cyG*>|Ln%j&d&NyM;-2{ z>A6=C^4YUcK2_PRth+yn*OhEFc2M*gZR76l0drVQ0=~HGVi3P*lBt9c3KAliwR4>J zI3=ekO4m_8H1B(XG`I^eHr9ik8-LWmzjYXdaS^3$QsjAe;E=8f;^Kt9%?AGo7|V;j z)%HOZIlkpvPpt4e|KR58t3G?rLsPpv`jb@n=NARhzC@t3;}_XAYW|h^9PyRN0nC#E zFvniCox<%MWxDyt9O7O<%4%IXm9c|Bm)^yC!<;hSyc9wHmnBsk1Zf9g&Ch^LPn^>Y zb@B~{^!kqY@Z{C?P3Lgn?Q`bDR(r^QV|7j*r;u5i|O{YAx4MSujkYU zQr=fiq8s-XR1Z$38*f37{w%kF7Dq;t zlV3NXA)_#?XMx_LsdqYuyqrya{xeN z(!{05AdvF8R^2mCq^NJBmj18$iWWl|>Y?=>EU~*W{hn!XW=vi*zL!4=lX<0O?L%-O zN9(a#e#QwPM8%2$azGy_3I3xso$>bAIgWW&ZM8G;FzXj**a&C^(71z9C5GqI&e8b- zTD-3zRL6E>KR# zZ`!X%*2axW({#v1Luox<1d34;0wAp{s$u1e=iC$O)p5YIMC-*TlPgNuybMXN7L>vg z(tA-ZP8DV8bzH=d_0e9)AKt~eu4O)VgIL;=TK};@gH?(!mm+ZqkM1fz6Utr}jmVMv z4whF>3{|+2rAVESdM2__&19L$*Yu?O8j~OG6In(v z@8xApj^C2LzLO?MY%{TwjUHT|F$cHN=D!sRf?Z}tGKzG?KdceuYr!{~@g>RO_LC^=NA4RgRqf8kaR z+_Q9G5b%dc)m8-Dw(Mqk3mFsbSf`?Qd_}QGt#TLF8R)r^;mZ*8cCqAeRQ}5VwNx{C zNDy)=gMC4)wezsh2o9>d5oH$$ZU2~LeL@v~JXIMuYxG()O{4pnK|n_D!Xx&`Z96*6 zaJRw(T-)${cA8+4L=jC;#s0+crxq24hC(sV1O7@~?#(eRDKo&7r>);-^hHyiRV|^^ zf6|2BYeQ)kd#m;GkfGX>!_0VR8BDzOrxa;YMbMs28|q7)%U8Ck*YX7>dU#4qlq zSSze`W6|ke5KSIgOS-hSm_9gnlrP4HH(no3R^Bl9y$Rxm2b&Ma7jgWQq`kwe`iKl3 z^?|0;JG12Ck%_Tl_ZwqRf5$TGml*4p)&7l?Ik~9$aa54Z)An_Eo4Zf)%+f6EsaCqi zwkv4ts|sV5K=FIqw(GZ-9D`V2t5KEqfDJC(9t0@CsV=q~u#H(;G9r883*kI>6HUM0 z{(OU}_Is)+D{nr2a-LC~ndmtP9aq`RW;hw&8HsWdEab^5UQ!65(kcu72@$}bS~MJWb|}VN9;UZ9AUn2(H9=>xk*Dhq!QFoTYF$$^DHwjE~(nm{gTpspzE88$dcRH zsQxc4-&JD@Kno&>(=Q1;osPw5LbZ=@075YsL{%%KvT{Zt*3@&(Cj0O%xMTm@3Ui`H zoz@CHL4AcBTG%5j@wI!ncr#9jcvH$XZ=~*1?dY(3JR(n&B2%IGs(H;vjLx!>GznvZ zcHf->$UBGSK1nf|-0dM;E+=uM*G^M5;sbL@@+s$!{%_sXF~Xop`UriLZAF9JXtF__ zBQZ5Z;G)3-bl5{IHT~^lts^k`xVrIp`|12q@{M6J+_jaH`jX8nM!G-}0O0?RoR_Tu zT(;(4>;D4i-?G1r+duFBSGIEr>A!8<-|D|%{% + + + + + diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/metadata.rdf b/examples/smoldyn/Andrews-Min1-PUBLICATION/metadata.rdf new file mode 100644 index 0000000..6e6ab32 --- /dev/null +++ b/examples/smoldyn/Andrews-Min1-PUBLICATION/metadata.rdf @@ -0,0 +1,57 @@ + + + + + + + E. coli Min system, based on Huang, Meir, Wingreen (HMW) with surface diffusion. + + Motivation: Smoldyn is a spatial and stochastic biochemical simulator. + It treats each molecule of interest as an individual particle in continuous space, + simulating molecular diffusion, molecule-membrane interactions and chemical reactions, + all with good accuracy. + + + 2024-01-15 + + + 2024-02-05 + E. coli Min system based on Huang, Meir, Wingreen (Andrews, 2009) + + + Steven Andrews + Steven Andrews + + + + Alex Patrie + + Alex Patrie + + + + smoldyn:S99_more/Min/Min1.txt + + + + Steven S Andrews. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 33, 5 (2017). + + + + GPL-3.0-only + + + diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/model.txt b/examples/smoldyn/Andrews-Min1-PUBLICATION/model.txt new file mode 100644 index 0000000..f59251b --- /dev/null +++ b/examples/smoldyn/Andrews-Min1-PUBLICATION/model.txt @@ -0,0 +1,115 @@ +# File Min1.txt, by Steve Andrews, 11/2009. +# E. coli Min system, based on Huang, Meir, Wingreen (HMW) +# This file is HMW system exactly, plus surface diffusion +# units are micron, second + +define D_D 2.5 # MinD diffusion coefficient (um^2/s) +define D_E 2.5 # MinE diffusion coefficient (um^2/s) +define D_d 0.01 # MinD_ATP(front) diff. coeff. (um^2/s) +define D_de 0.01 # MinDMinE(front) diff. coeff. (um^2/s) +define SIGMA_D_D2T 1 # MinD phosphorylation rate (s^-1) +define SIGMA_D 0.025 # MinD_ATP adsorption coeff. (um/s) +define SIGMA_dD 0.0015 # cooperative adsorption coeff. (um^3/s) +define SIGMA_de 0.7 # desorption rate of MinDMinE (s^-1) +define SIGMA_E 0.093 # MinE binding to surface-bound MinD (um^3/s) + +define UNBINDRAD 0.01 # MinD separation on surface (um) + +define R 0.5 # cell radius +define L_PARAM 2 # half of cell length +define L_PARAM2 1.5 # half of cell length minus radius + +define NUMBER_MIND 4000 # number of MinD in cell +define NUMBER_MINE 1400 # number of MinE in cell + +define TIME_STOP 10 # stopping time + +#define KICK_START 1 # start with MinD_ATP at an end + +random_seed 1 + +#graphics opengl +#graphic_iter 100 + +#tiff_name movie/MinMovie +#tiff_iter 200 +#tiff_min 1 +#tiff_max 200 + +dim 3 +boundaries 0 -L_PARAM L_PARAM +boundaries 1 -R R +boundaries 2 -R R +frame_thickness 0 +time_start 0 +time_stop TIME_STOP +time_step 0.002 # 2 millisecond time step + +accuracy 5 +molperbox 4 + +species MinD_ATP +species MinD_ADP +species MinE +species MinDMinE + +molecule_lists list1 list2 list3 list4 list5 +mol_list MinD_ATP(soln) list1 +mol_list MinD_ATP(front) list2 +mol_list MinD_ADP(all) list3 +mol_list MinE(all) list4 +mol_list MinDMinE(all) list5 + +difc MinD_ATP(solution) D_D +difc MinD_ATP(front) D_d +difc MinD_ADP(solution) D_D +difc MinE(solution) D_E +difc MinDMinE(front) D_de + +color MinD_ATP(soln) 0 0 0.6 # MinD_ATP(solution) is dark blue +color MinD_ATP(front) 0 0.6 0 # MinD_ATP(front) is dark green +color MinD_ADP(soln) 0.4 0.6 1 # MinD_ADP is light blue +color MinE(soln) 1 0 0 # MinE is red +color MinDMinE(front) 0.2 1 0.2 # MinDMinE is bright green +display_size all(solution) 2 +display_size all(front) 4 + +start_surface membrane +action both all reflect +rate MinD_ATP fsoln front SIGMA_D # reaction 1a +polygon both edge +panel cylinder -L_PARAM2 0 0 L_PARAM2 0 0 -R 20 10 cyl0 +panel hemi -L_PARAM2 0 0 -R 1 0 0 20 5 hemi0 +panel hemi L_PARAM2 0 0 -R -1 0 0 20 5 hemi1 +neighbors cyl0 hemi0 hemi1 +neighbors hemi0 cyl0 +neighbors hemi1 cyl0 +end_surface + +start_compartment cell +surface membrane +point 0 0 0 +end_compartment + +reaction rxn1b MinD_ATP(fsoln) + MinD_ATP(front) -> MinD_ATP(front) + MinD_ATP(front) SIGMA_dD +product_placement rxn1b unbindrad UNBINDRAD +reaction rxn1c MinD_ATP(fsoln) + MinDMinE(front) -> MinD_ATP(front) + MinDMinE(front) SIGMA_dD +product_placement rxn1c unbindrad UNBINDRAD +reaction rxn2 MinE(fsoln) + MinD_ATP(front) -> MinDMinE(front) SIGMA_E +reaction rxn3 MinDMinE(front) -> MinD_ADP(fsoln) + MinE(fsoln) SIGMA_de +reaction rxn4 MinD_ADP -> MinD_ATP SIGMA_D_D2T + +ifundefine KICK_START + surface_mol NUMBER_MIND MinD_ATP(front) membrane all all +else + surface_mol NUMBER_MIND MinD_ATP(front) membrane hemi hemi1 +endif +compartment_mol NUMBER_MINE MinE cell + + +output_files modelout.txt +cmd i 0 TIME_STOP 2 executiontime modelout.txt +cmd i 0 TIME_STOP 2 listmols modelout.txt + +end_file + diff --git a/examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml b/examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml new file mode 100644 index 0000000..396e498 --- /dev/null +++ b/examples/smoldyn/Andrews-Min1-PUBLICATION/simulation.sedml @@ -0,0 +1,147 @@ + + + + + + + + + + + + + + + + + variable_time + + + + + + + + variable_count_species_MinD_ADP + + + + + + + + variable_count_species_MinD_ADP_compartment_cell + + + + + + + + variable_count_species_MinD_ADP_surface_membrane + + + + + + + + variable_count_species_MinD_ATP + + + + + + + + variable_count_species_MinD_ATP_compartment_cell + + + + + + + + variable_count_species_MinD_ATP_surface_membrane + + + + + + + + variable_count_species_MinDMinE + + + + + + + + variable_count_species_MinDMinE_compartment_cell + + + + + + + + variable_count_species_MinDMinE_surface_membrane + + + + + + + + variable_count_species_MinE + + + + + + + + variable_count_species_MinE_compartment_cell + + + + + + + + variable_count_species_MinE_surface_membrane + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +