JSim Kegg Models Page
This page allows users to run about 12,000 biochemical models from the Kegg Pathways Database under JSim. To run these models online, you must have a Java plugin installed in your WWW browser. To run them in JSim on your own computer, download the model code and the JSim application. Either way, see Running JSim for instructions on how to use JSim. Since these models do not specify simulation time length or delta, these must be set by the user before running the model.
Return to complete JSim model archives.
Species for which models are available
- Bordetella bronchiseptica (bbr)
- Escherichia coli CFT073 (UPEC) (ecc)
- Bacillus cereus ATCC 10987 (bca)
- Streptococcus mutans (smu)
- Listeria innocua (lin)
- Thermoanaerobacter tengcongensis (tte)
- Bacteroides thetaiotaomicron (bth)
- Lactobacillus plantarum (lpl)
- Synechococcus sp. WH8102 (syw)
- Yersinia pestis CO92 (ype)
- Candidatus Blochmannia floridanus (bfl)
- Caulobacter crescentus (ccr)
- Porphyromonas gingivalis (pgi)
- Aquifex aeolicus (aae)
- Phytoplasma OY (poy)
- Prochlorococcus marinus SS120 (pma)
- Agrobacterium tumefaciens C58 (Cereon) (atc)
- Vibrio vulnificus CMCP6 (vvu)
- Staphylococcus aureus MW2 (sam)
- Streptomyces coelicolor (sco)
- Streptococcus agalactiae 2603 (serotype V) (sag)
- Buchnera aphidicola APS (buc)
- Mycoplasma mycoides (mmy)
- Borrelia burgdorferi (bbu)
- Campylobacter jejuni NCTC11168 (cje)
- Chlorobium tepidum (cte)
- Chlamydophila pneumoniae TW183 (cpt)
- Bordetella pertussis (bpe)
- Archaeoglobus fulgidus (afu)
- Wolbachia wMel (wol)
- Homo sapiens (human) (hsa)
- Streptococcus pneumoniae R6 (spr)
- Streptococcus agalactiae NEM316 (serotype III) (san)
- Lactococcus lactis subsp. lactis IL1403 (lla)
- Yersinia pestis KIM (ypk)
- Staphylococcus aureus N315 (sau)
- Nitrosomonas europaea (neu)
- Brucella melitensis (bme)
- Vibrio parahaemolyticus (vpa)
- Agrobacterium tumefaciens C58 (UWash/Dupont) (atu)
- Rattus norvegicus (rat) (rno)
- Salmonella enterica serovar Typhi CT18 (sty)
- Mesorhizobium loti (mlo)
- Helicobacter hepaticus (hhe)
- Aeropyrum pernix (ape)
- Pyrococcus abyssi (pab)
- Shigella flexneri 301 (serotype 2a) (sfl)
- Mycoplasma pneumoniae (mpn)
- Helicobacter pylori J99 (hpj)
- Streptococcus pyogenes SF370 (serotype M1) (spy)
- Streptococcus pyogenes SSI (sps)
- Streptococcus pyogenes MGAS315 (serotype M3) (spg)
- Bacillus subtilis (bsu)
- Bacillus anthracis Ames (ban)
- Mycobacterium bovis AF2122/97 (mbo)
- Bacillus cereus ATCC 14579 (bce)
- Saccharomyces cerevisiae (sce)
- Clostridium acetobutylicum (cac)
- Treponema denticola (tde)
- Thermoplasma acidophilum (tac)
- Escherichia coli K (ecj)
- Sinorhizobium meliloti (sme)
- Methanococcus jannaschii (mja)
- Escherichia coli O157 EDL933 (EHEC) (ece)
- Streptococcus pyogenes MGAS8232 (serotype M18) (spm)
- Neisseria meningitidis MC58 (serogroup B) (nme)
- Oceanobacillus iheyensis (oih)
- Thermoplasma volcanium (tvo)
- Mycobacterium avium paratuberculosis (mpa)
- Tropheryma whipplei Twist (twh)
- Streptomyces avermitilis (sma)
- Chlamydophila pneumoniae AR39 (cpa)
- Leptospira interrogans serovar lai (lil)
- Vibrio vulnificus YJ016 (vvy)
- Photorhabdus luminescens (plu)
- Synechocystis sp. PCC6803 (syn)
- Brucella suis (bms)
- Sulfolobus tokodaii (sto)
- Sulfolobus solfataricus (sso)
- Synechococcus elongatus PCC6301 (syc)
- Pseudomonas syringae pv. tomato DC3000 (pst)
- Haemophilus ducreyi (hdu)
- Lactobacillus johnsonii (ljo)
- Caenorhabditis elegans (nematode) (cel)
- Corynebacterium diphtheriae (cdi)
- Rickettsia conorii (rco)
- Vibrio cholerae (vch)
- Yersinia pestis Mediaevails (ypm)
- Corynebacterium glutamicum ATCC 13032 (Kyowa Hakko) (cgl)
- Escherichia coli O157 Sakai (EHEC) (ecs)
- Plasmodium falciparum (pfa)
- Clostridium perfringens 13 (cpe)
- Ralstonia solanacearum (rso)
- Chlamydophila caviae (cca)
- Shigella flexneri 2457T (serotype 2a) (sfx)
- Prochlorococcus marinus MIT9313 (pmt)
- Anabaena sp. PCC7120 (ana)
- Bacillus halodurans (bha)
- Haemophilus influenzae (serotype d) (hin)
- Pseudomonas aeruginosa PAO1 (pae)
- Salmonella enterica serovar Typhi Ty2 (stt)
- Escherichia coli K (eco)
- Corynebacterium efficiens (cef)
- Rhodopirellula baltica (rba)
- Deinococcus radiodurans (dra)
- Chlamydia trachomatis serovar D (ctr)
- Neisseria meningitidis Z2491 (serogroup A) (nma)
- Methanopyrus kandleri (mka)
- Xylella fastidiosa Temecula1 (xft)
- Mycobacterium tuberculosis H37Rv (mtu)
- Xanthomonas axonopodis (xac)
- Fusobacterium nucleatum (fnu)
- Xylella fastidiosa 9a5c (xfa)
- Methanobacterium thermoautotrophicum (mth)
- Bordetella parapertussis (bpa)
- Thermotoga maritima (tma)
- Bifidobacterium longum (blo)
- Mycoplasma genitalium (mge)
- Streptococcus pneumoniae TIGR4 (spn)
- Nanoarchaeum equitans (neq)
- Pyrobaculum aerophilum (pai)
- Helicobacter pylori 26695 (hpy)
- Methanococcus maripaludis S2 (mmp)
- Buchnera aphidicola Sg (bas)
- Geobacter sulfurreducens (gsu)
- Mycoplasma pulmonis (mpu)
- Staphylococcus epidermidis ATCC 12228 (sep)
- Buchnera aphidicola Bp (bab)
- Pyrococcus horikoshii (pho)
- Thermosynechococcus elongatus (tel)
- Wigglesworthia glossinidia (wbr)
- Clostridium tetani E88 (ctc)
- Mycobacterium tuberculosis CDC1551 (mtc)
- Methanosarcina mazei (mma)
- Shewanella oneidensis (son)
- Drosophila melanogaster (fruit fly) (dme)
- Enterococcus faecalis (efa)
- Chlamydophila pneumoniae J138 (cpj)
- Methanosarcina acetivorans (mac)
- Pasteurella multocida (pmu)
- Bdellovibrio bacteriovorus (bba)
- Pseudomonas putida (ppu)
- Chlamydia muridarum (cmu)
- Encephalitozoon cuniculi (ecu)
- Rhodopseudomonas palustris CGA009 (rpa)
- Ureaplasma urealyticum (uur)
- Treponema pallidum (tpa)
- Chlamydophila pneumoniae CWL029 (cpn)
- Listeria monocytogenes EGD (lmo)
- Mycoplasma penetrans (mpe)
- Tropheryma whipplei TW08/27 (tws)
- Pyrococcus furiosus (pfu)
- Mycoplasma gallisepticum (mga)
- Bradyrhizobium japonicum (bja)
- Mus musculus (mouse) (mmu)
- Prochlorococcus marinus MED4 (pmm)
- Wolinella succinogenes (wsu)
- Coxiella burnetii (cbu)
- Thermus thermophilus HB27 (tth)
- Schizosaccharomyces pombe (spo)
- Mycobacterium leprae (mle)
- Xanthomonas campestris pv. campestris ATCC 33913 (xcc)
- Halobacterium sp. NRC (hal)
- Chromobacterium violaceum (cvi)
- Staphylococcus aureus Mu50 (sav)
- Gloeobacter violaceus (gvi)
- Arabidopsis thaliana (thale cress) (ath)
- Salmonella typhimurium LT2 (stm)
- Rickettsia prowazekii (rpr)
[This page was last modified 03Mar08, 3:11 pm.]
Model development and archiving support at physiome.org provided by the following grants: NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.
