03f6e8dc491a2cb9198faf3bfc18739d *DESCRIPTION
784d7dc7357bd924e8d5642892bf1b6b *LICENSE
d4e1f1d253cf4acae12d6a38c54fab1b *NAMESPACE
90ecac75949618855d37c9257cd3f6ba *R/addAlgorithm.R
8308e92d9fa5642ee9c53541989b0161 *R/addExchReact.R
8481f7f4447aed5f32f2c11729e29a5b *R/addReact.R
b6fc85a91c57ad8233c9065711aaaf00 *R/addSolver.R
2a1c0a2be52da03b060fcb34af46ac2a *R/blockedReact.R
2c645acea7585b67c1d1820a1baee4fe *R/bracket_pairs.R
38743161b198e109f7c0a1f9657228d1 *R/ceilValues.R
ef427931942d9332a49254a720da8a23 *R/changeBounds.R
8f4d03faa34f40d81b9001264fbe222b *R/changeGPR.R
45f775f7c87d97030186555701ebd1a2 *R/changeObjFunc.R
4a76a6d8aae7c018117bec725b850c12 *R/checkAlgorithm.R
e3a4d2f9fd12ef86b792f5915813ae95 *R/checkDefaultMethod.R
afcf332a2a1832a6e6e8aa17890e8e03 *R/checkEmptyField.R
3fdc8bfb51a143f19e4fc66b62ac367d *R/checkReactId.R
1a025d46fa4f48abacbd0c3b73f59919 *R/check_brackets.R
a39db8a0d3043f200383baa7f49842eb *R/checksolClass.R
37cbc341d4ad73c05681b0d41960bf5e *R/createReactionString.R
44f1ea333d3837da3a462d98925c7d4b *R/deadEndMetabolite.R
563bed0f47351cf36e30310efb0f9a0c *R/doInRound.R
9856be12647a6aa75e24be484a7e0892 *R/doubleFluxDel.R
72590deb1656a9260198796b2d461d67 *R/doubleGeneDel.R
9aecec52feaa5637fbd465c4d1496c8d *R/doubleReact.R
e4cc6e7aaed353eae3ef9cff55baa72c *R/editEnvir.R
d90269aa0cd1c7bd0525f345a1930b4e *R/findExchReact.R
6919dd17bfcfa206d62c6dc7008cb1fa *R/floorValues.R
b6dfb672da86a3dd67e3d9883ba10b2f *R/fluxDistributionClass.R
47be7ca4522a71d3fc7a213215f0fc33 *R/fluxVar.R
c91e6c927fa6174530a8bfa26a6c37a1 *R/geneDel.R
54155cafbd020f506529f1d3b09712db *R/geneDeletion.R
0991ea1d270faf4fb8c17a95b3f9d696 *R/generateFluxdels.R
6a9ec13e76ac04adcee61d137c8e04c4 *R/generateModKey.R
07a4f4bebbd1994115902a48654e71be *R/generateWT.R
b194e79805abc0ac31a8caf051affdcc *R/generics.R
161f081b5e0e4ab9c6760b6c10f68d68 *R/getsybilenv.R
c9871521aa40b4ff5ef0366e25b99d14 *R/makeLPcompatible.R
b24905241f5563f655ed8f4e42a271d8 *R/mod2irrev.R
48057c793465f42492bfa86e38eca2de *R/modelorg2ExPA.R
ff95c8bba67c0872032c138e21917198 *R/modelorg2text.R
0008835ef92bd9dfc6cdfcb1c1e37a8d *R/modelorg2tsv.R
07af49dad851a4b66ac788351a234695 *R/modelorgClass.R
8fe684fdc9b0ab7377f4d98aa0cd0791 *R/modelorg_irrevClass.R
261781f2a650538647dd3c6324c6d0ce *R/multiDel.R
c8162b0edd7997141a9593e2b7e9b7de *R/netFluxClass.R
6fa896a4d254f3712dd2d6d8b9e99836 *R/oneFluxDel.R
2108d061d378328fee160e9f34219b6a *R/oneGeneDel.R
7bdc0491ddfe80cf84232c80a279522d *R/onlyChangeGPR.R
2bf00b25107e3454ad17c4210d428ce9 *R/onlyCheckGPR.R
b9b397908dfcc9d0e67f3f5b11152d20 *R/optObjClass.R
1e2353b32882d92b998de47e4d75c261 *R/optObj_basicfunc.R
031717b9dd5f23ecd7ea9aff32d27c36 *R/optObj_clpAPIClass.R
9ef89d87cdc1352513d851312528d96a *R/optObj_cplexAPIClass.R
85ac1dfaf016d674471aae080132a1bd *R/optObj_glpkAPIClass.R
50c8e6e21f2cfe0d19282532c298029e *R/optObj_lpSolveAPIClass.R
6c54af969a8d735a0f2ab0efbb3847b6 *R/optObj_lpSolveAPIcompat.R
13d8595ffa2e6698dcbb24d7b1829ba1 *R/optObj_pointer.R
d6d5067479ef8669bec1ed3b017143e5 *R/optimizer.R
de4364012f1c8bf7cd102506e2dc9bd6 *R/optsolClass.R
d44617853b3fdaa5bcfc3970f5639658 *R/optsol_blockedReactClass.R
1305a4c4d7670148380769137faa0ab1 *R/optsol_fluxVarClass.R
4084b12497406ed203ee90c0d38a3974 *R/optsol_fluxdelClass.R
779410ed819ee7e293317d3166e4ec03 *R/optsol_genedelClass.R
ad77153623fb8016deacd79dddb92505 *R/optsol_optimizeProbClass.R
808e2febfbc830f8a675916093db1bd6 *R/optsol_phppClass.R
36484f89c9ae7b1d91e6ae2755211517 *R/optsol_robAnaClass.R
799fb75d943d423b9110c98244be0dad *R/parseBoolean.R
4bcfa4434e025e5cf8acaf833aa544b9 *R/phpp.R
905d0f1ed5511a890d3d4c7f99c9b521 *R/ppProcClass.R
f121516c97606ece165c12fb90c40c8f *R/ppProcessing.R
824360522eddac0a8f23671af4115cca *R/prepareSubSysMatrix.R
75de08d58a12bfb6c75e3ee4640f611b *R/printLogComment.R
3cdeb4684cdde1ad915dc908de501c3a *R/printNamedList.R
725991084b78416f2909dce9f7f4bcfd *R/progress.R
b195ff2a50e46bf7fd7536dc6acb70b7 *R/promptSysBiolAlg.R
269041de08bc3dad5c9c716587408166 *R/reactIdClass.R
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2e34eb29fd827974392ad2a369dd75e1 *R/readTEXTmod.R
9ae36b854ab4616e082ee1ebe2fe9984 *R/readTSVmod.R
2333f0e4415c6d759231f47091dbbf93 *R/reassignFwBwMatch.R
7be0d1c8f0aeb3ee77d934c87dfdb16e *R/recodeMatrix.R
882438c2933a405063c219109ace673b *R/rmReact.R
85ee480ef1164d83e4321ff56bac3aff *R/robAna.R
3a9e4c5e22775d5a36022717429ccf92 *R/settings.R
7021a4fdac1e26a687f3132087efc747 *R/singletonMetabolite.R
32671f31aeb7af2b401c2bf4f6fb1740 *R/summaryOptsolClass.R
474f5824d454b9e07b0828b7ef89a984 *R/sybilErrorClass.R
d9b5c25b4e3592096f8e8a55e2c2cc61 *R/sybilLogClass.R
d6d5eb8a09894326bb10f7132e757c2a *R/sybilStack.R
547334fde70a775ef646ec5913e603c3 *R/sysBiolAlgClass.R
2f995f47ac07359ba07824eb2e48ebcd *R/sysBiolAlg_fbaClass.R
cf0b1562804d4518145cee37e49b083b *R/sysBiolAlg_fbaEasyConstraintClass.R
6f9b45a4726bf832be14cc56118b2d28 *R/sysBiolAlg_fvClass.R
f910f8cc337b8cd369fe68588bed17fa *R/sysBiolAlg_lmomaClass.R
1e274ec357de9c6f3f660e91445e73d6 *R/sysBiolAlg_momaClass.R
086ed8679d6df46ea294beb9c4e88359 *R/sysBiolAlg_mtfClass.R
688b11570c03c34811fe58668a778857 *R/sysBiolAlg_mtfEasyConstraintClass.R
7486b073ca76fbb5b4d1eecf92d844c4 *R/sysBiolAlg_roomClass.R
0df4342509a6804d37e5c93df3e9ca71 *R/validmodelorg.R
581b6740b46f3230ea6b70225adb5baf *R/validoptsol.R
4bf1eb49479dde86718fc4257b3049d0 *R/validreactId.R
f9253acaee4e2dae34d57291e0471248 *R/validreactId_Exch.R
723c6b1fa7a331c280ca8b049396b6c8 *R/validsysBiolAlg.R
94eef6e16843a2cd6cf543132f24f8cd *R/ypd.R
33ac8ff1db54548242de00fad0a60f9c *R/zzz.R
a1cdc11fea5e3f6aa43c660756951fa8 *README.md
88b4f331f8e4f7de84f59ac54306d0a1 *build/vignette.rds
42f22e08da875977b8b30a0ae23fd493 *data/Ec_core.RData
dcb1bdb0b852efeed6c4633f10aa2fd0 *inst/CITATION
0874aaa386bfa7ad78e9e01771e0a6ac *inst/NEWS.Rd
23d1433e302a9eba8ef18916b190c9d2 *inst/doc/sybil.R
24e6cf8fb9f47f6aa6c8b7bdf3957ca5 *inst/doc/sybil.Rnw
a8a34a2ee5ab2f05246aea9860f7a9d2 *inst/doc/sybil.pdf
57349ddd1c5292698b4f40828fb0a4c8 *inst/extdata/Ec_core_desc.tsv
a087d5c12df926906688674ba133e6a9 *inst/extdata/Ec_core_met.tsv
5e592ee880a444834fca2de9f320367a *inst/extdata/Ec_core_react.tsv
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4f41e7139e58fdb7c41001f7ccdcdc99 *man/SYBIL_SETTINGS.Rd
a826597974a9a1d4ce075c5f73d4eef6 *man/addAlgorithm.Rd
14ab03155ccfdef3e08be59b7061eec4 *man/addCols-methods.Rd
32028c50acf4063033c93bba053971d0 *man/addColsToProb-methods.Rd
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474df63379b19a0b6909ad23f0feaa7d *man/addReact.Rd
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681e62367891edbbd46171d9435024ea *man/addRowsToProb-methods.Rd
67b79f0ca3381692bd8bf334d64e8bd1 *man/addSolver.Rd
3422f576308e3bd1a9e9886739fa0acc *man/applyChanges-methods.Rd
206d92669e7b3c9ac487e898f719a251 *man/backupProb-methods.Rd
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9f81284beebc224e7d079a2e4bc6d5be *man/changeBounds.Rd
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db51a9eb1effebbdddb3c7ef69c61190 *man/changeGPR.Rd
660f3123273b750f98b05704a820afb4 *man/changeMatrixRow-methods.Rd
8adb5b17afe732819b7b0ee48a91de50 *man/changeObjCoefs-methods.Rd
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c6958244524e3df2437c9172011c253c *man/changeRowsBnds-methods.Rd
38186ec69234adb184e6cd9e8c3589a8 *man/changeUptake-methods.Rd
be90e2b926190713bb9c386dbf3b3498 *man/checkAkgorithm.Rd
95ab37fb8517a99f4f3078e1f8098aa8 *man/checkDefaultMethod.Rd
c9b1a83ea04b88c8d6d27d2219e0bc84 *man/checkOptSol-methods.Rd
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5154a7d4e5f8ef19839dd3d5d65cd50e *man/checksol-class.Rd
9dcfb4d294e27e815c50754c609f4a98 *man/deadEndMetabolites-methods.Rd
9a89d92a9e698ac57c195a5aa110c717 *man/delProb-methods.Rd
ec9ee63fb5b374445346188c5e2d19ce *man/deprecated.Rd
5c845239985edd90703fec4eeb5867f6 *man/doubleFluxDel.Rd
7faefaf770ef8a36d24ff23410af994f *man/doubleGeneDel.Rd
190d26c7735a8efd4b0dbff8ce3757b1 *man/doubleReact.Rd
b8c5de342b4db848046419bb94ca5c0d *man/editEnvir.Rd
ec861b708294cecfbdef4a98638e5242 *man/findExchReact.Rd
262850c04c44fcd3b17c969832de2229 *man/fluxDistribution-class.Rd
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c73478cd0ae73a20f26ad40f908a0f8b *man/geneDel.Rd
38e181c869185cf8ff2fc55bc646e1e2 *man/geneDeletion.Rd
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9e97f12bbeaaaa8db31be0acbf932867 *man/getColsLowBnds-methods.Rd
39589ce5fc45a11a6053877cb8bb77d8 *man/getColsNames-methods.Rd
18a1103e42f8fe5ca6ba8c1109e3dee5 *man/getColsUppBnds-methods.Rd
cf7c199dcef57accf859fe33aae1d92d *man/getFluxDist-methods.Rd
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1b4108419e0864c4c9cc7c90a96b76f6 *man/getNumNnz-methods.Rd
f86f7df11c15c4250e935352bc54f9f9 *man/getNumRows-methods.Rd
11c3651fe989fecd339c1504474c01fe *man/getObjCoefs-methods.Rd
9124944b213a82b09c0f76522b4fbe44 *man/getObjDir-methods.Rd
cfec843eab5afcbb027ce51c23ea0e82 *man/getObjVal-methods.Rd
4bcc8313bc83932239c251013fb126c7 *man/getRedCosts-methods.Rd
ec9b2846fc044472aa79443462f78abf *man/getRowsLowBnds-methods.Rd
22519c54adee1532294a8fb70b0b44c0 *man/getRowsNames-methods.Rd
3f8186fa4d3f43ac661038ca2c9e18f5 *man/getRowsUppBnds-methods.Rd
5a0332ac47da86ce0a2d3acab24df721 *man/getSolStat-methods.Rd
2e7eb4ab98735451461ccb93ab524630 *man/getSolverParm-methods.Rd
70a2290d937401faa1381e2854a0b36b *man/getsybilenv.Rd
92329739fd82e345e4424bfaba459b74 *man/initProb-methods.Rd
55b7ffbf45d2007cdef95325d151e557 *man/loadLPprob-methods.Rd
125274e3486d2b8459e5e5f261a041af *man/loadQobj-methods.Rd
24478dc94580fa98c2303da7533f5348 *man/makeOptsolMO.Rd
9ee35d011ac095f088940edaefb1e6c9 *man/mod2irrev.Rd
70cd87b7277e0d99c4547d1502b4bb68 *man/modelorg-class.Rd
01d6f4fd04d931e153af3e2caa1d7110 *man/modelorg2ExPA.Rd
9639639a418f98f5055752005742de57 *man/modelorg2tsv.Rd
3cc63c2f14c5adcd42e7d34eb3216d6e *man/modelorg_irrev-class.Rd
9f49a83ad56a215a8a24c252e12dac6f *man/multiDel.Rd
b41163c826bceada7c1e3767e9eea0d4 *man/netFlux-class.Rd
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3783494dda5616ccde027e5208340058 *man/oneGeneDel.Rd
b09443c6928d52f8c982deb5dccf42db *man/onlyChangeGPR.Rd
36394c12b65368cb5b60e0412739f347 *man/onlyCheckGPR.Rd
6958b875328aeee4fc7347947978b77d *man/optObj-class.Rd
6a0a84a5d221ca8d78e41dda6a9f1797 *man/optObj.Rd
edd7081ec5bd5a020ceb6df6a4b4aaab *man/optObj_clpAPI-class.Rd
5745e158940880620ba307090b32dee1 *man/optObj_cplexAPI-class.Rd
154354e20cf41ed81f512b028215640b *man/optObj_glpkAPI-class.Rd
ea7e283b01696d16eb5aded865d399fe *man/optObj_lpSolveAPI-class.Rd
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dbde8099a11f2f82d21d733d7a73d576 *man/optimizer.Rd
3a6bfe2f8992e368b78ee9df0d284864 *man/optsol-class.Rd
5df0d34739b7b8d8a06c5ced541e6f0f *man/optsol_blockedReact-class.Rd
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2b591d7ccc1d844581ff3073154687c0 *man/optsol_fluxdel-class.Rd
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87aafc82d79ac41b64dfe349284e2329 *man/resetChanges-methods.Rd
2ddf34cdc419e1027efed130cd5e0e1a *man/rmReact.Rd
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7e4aafdf64ec5d192d182bc45bfdd12c *man/scaleProb-methods.Rd
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9fc7cef1024ae017ad94e1741ceaed13 *man/setRowsNames-methods.Rd
9fa263d6a651bca3f8fe7c59d2fabf63 *man/setSolverParm-methods.Rd
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8a42a208ff9cef2334fb7cb8749333bd *man/singletonMetabolites-methods.Rd
7c4d54ac3c37335066d64703b6d7ee2c *man/solveLp-methods.Rd
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7f7b5a4d8a297e2c5f175aedf805971d *man/sybil-internal.Rd
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7f30778ed4283b09f937b0be5cd68b6f *man/sybilError-class.Rd
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c69c80cd3c93a8bd543903a7baf66941 *man/sybilStack.Rd
91249ef7c6260d0575d24d5046832cfc *man/sysBiolAlg-class.Rd
2f052ecd118cdcc13039d59888d94b4a *man/sysBiolAlg.Rd
556088fea24b6d98e225f33ba171f78f *man/sysBiolAlg_fba-class.Rd
0915e690a98b59cc6674b1963e53f529 *man/sysBiolAlg_fbaEasyConstraint-class.Rd
5be2a6f5fcbb0aede2112bbb32df3363 *man/sysBiolAlg_fv-class.Rd
13df79590c229d6d08bb912088802810 *man/sysBiolAlg_lmoma-class.Rd
3582dc280c12bba765ec83623e2e008e *man/sysBiolAlg_moma-class.Rd
9991e8b05e83164ab5748341cbdf2887 *man/sysBiolAlg_mtf-class.Rd
6a53ae644d7fa977318c5627f432432c *man/sysBiolAlg_room-class.Rd
e758bd824a0b2985092a489b77b9e9ea *man/writeProb-methods.Rd
932a1a876bf6d10f4215b1bac95de6a3 *man/ypd.Rd
ceeeafbf54e3ec1ae03879b7fa70aef6 *vignettes/net-crop.pdf
dd206b0067ca7c1ee9142cc6c8d374c1 *vignettes/optObj-class.pdf
898aa3640f4a96f38f3c2d5d33743b33 *vignettes/optObj-const.pdf
b523ed39db8f4554bd02127af8e4b2a2 *vignettes/optsol-class.pdf
24e6cf8fb9f47f6aa6c8b7bdf3957ca5 *vignettes/sybil.Rnw
886fcb9c559cfa27bd841d8b5ecacd64 *vignettes/sybil.bib
341a4d54f6c30d3076500aff0dfc5212 *vignettes/sysBiolAlg-class.pdf
c2182e6dd340a228aba67b0dd3a1cb19 *vignettes/sysBiolAlg-const.pdf
bc149984e431c983d88b6f1c2fbb3e80 *vignettes/sysBiolAlg-init.pdf
