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.
Note: Models of this page require JSim version 1.6.84 or above.
Return to complete JSim model archives.
Species for which models are available
- Aquifex aeolicus (aae)
- Archaeoglobus fulgidus (afu)
- Anabaena sp. PCC7120 (ana)
- Aeropyrum pernix (ape)
- Agrobacterium tumefaciens C58 (Cereon) (atc)
- Arabidopsis thaliana (thale cress) (ath)
- Agrobacterium tumefaciens C58 (UWash/Dupont) (atu)
- Buchnera aphidicola Bp (bab)
- Bacillus anthracis Ames (ban)
- Buchnera aphidicola Sg (bas)
- Bdellovibrio bacteriovorus (bba)
- Bordetella bronchiseptica (bbr)
- Borrelia burgdorferi (bbu)
- Bacillus cereus ATCC 10987 (bca)
- Bacillus cereus ATCC 14579 (bce)
- Candidatus Blochmannia floridanus (bfl)
- Bacillus halodurans (bha)
- Bradyrhizobium japonicum (bja)
- Bifidobacterium longum (blo)
- Brucella melitensis (bme)
- Brucella suis (bms)
- Bordetella parapertussis (bpa)
- Bordetella pertussis (bpe)
- Bacillus subtilis (bsu)
- Bacteroides thetaiotaomicron (bth)
- Buchnera aphidicola APS (buc)
- Clostridium acetobutylicum (cac)
- Coxiella burnetii (cbu)
- Chlamydophila caviae (cca)
- Caulobacter crescentus (ccr)
- Corynebacterium diphtheriae (cdi)
- Corynebacterium efficiens (cef)
- Caenorhabditis elegans (nematode) (cel)
- Corynebacterium glutamicum ATCC 13032 (Kyowa Hakko) (cgl)
- Campylobacter jejuni NCTC11168 (cje)
- Chlamydia muridarum (cmu)
- Chlamydophila pneumoniae AR39 (cpa)
- Clostridium perfringens 13 (cpe)
- Chlamydophila pneumoniae J138 (cpj)
- Chlamydophila pneumoniae CWL029 (cpn)
- Chlamydophila pneumoniae TW183 (cpt)
- Clostridium tetani E88 (ctc)
- Chlorobium tepidum (cte)
- Chlamydia trachomatis serovar D (ctr)
- Chromobacterium violaceum (cvi)
- Drosophila melanogaster (fruit fly) (dme)
- Deinococcus radiodurans (dra)
- Escherichia coli CFT073 (UPEC) (ecc)
- Escherichia coli O157 EDL933 (EHEC) (ece)
- Escherichia coli K (ecj)
- Escherichia coli K (eco)
- Escherichia coli O157 Sakai (EHEC) (ecs)
- Encephalitozoon cuniculi (ecu)
- Enterococcus faecalis (efa)
- Fusobacterium nucleatum (fnu)
- Geobacter sulfurreducens (gsu)
- Gloeobacter violaceus (gvi)
- Halobacterium sp. NRC (hal)
- Haemophilus ducreyi (hdu)
- Helicobacter hepaticus (hhe)
- Haemophilus influenzae (serotype d) (hin)
- Helicobacter pylori J99 (hpj)
- Helicobacter pylori 26695 (hpy)
- Homo sapiens (human) (hsa)
- Leptospira interrogans serovar lai (lil)
- Listeria innocua (lin)
- Lactobacillus johnsonii (ljo)
- Lactococcus lactis subsp. lactis IL1403 (lla)
- Listeria monocytogenes EGD (lmo)
- Lactobacillus plantarum (lpl)
- Methanosarcina acetivorans (mac)
- Mycobacterium bovis AF2122/97 (mbo)
- Mycoplasma gallisepticum (mga)
- Mycoplasma genitalium (mge)
- Methanococcus jannaschii (mja)
- Methanopyrus kandleri (mka)
- Mycobacterium leprae (mle)
- Mesorhizobium loti (mlo)
- Methanosarcina mazei (mma)
- Methanococcus maripaludis S2 (mmp)
- Mus musculus (mouse) (mmu)
- Mycoplasma mycoides (mmy)
- Mycobacterium avium paratuberculosis (mpa)
- Mycoplasma penetrans (mpe)
- Mycoplasma pneumoniae (mpn)
- Mycoplasma pulmonis (mpu)
- Mycobacterium tuberculosis CDC1551 (mtc)
- Methanobacterium thermoautotrophicum (mth)
- Mycobacterium tuberculosis H37Rv (mtu)
- Nanoarchaeum equitans (neq)
- Nitrosomonas europaea (neu)
- Neisseria meningitidis Z2491 (serogroup A) (nma)
- Neisseria meningitidis MC58 (serogroup B) (nme)
- Oceanobacillus iheyensis (oih)
- Pyrococcus abyssi (pab)
- Pseudomonas aeruginosa PAO1 (pae)
- Pyrobaculum aerophilum (pai)
- Plasmodium falciparum (pfa)
- Pyrococcus furiosus (pfu)
- Porphyromonas gingivalis (pgi)
- Pyrococcus horikoshii (pho)
- Photorhabdus luminescens (plu)
- Prochlorococcus marinus SS120 (pma)
- Prochlorococcus marinus MED4 (pmm)
- Prochlorococcus marinus MIT9313 (pmt)
- Pasteurella multocida (pmu)
- Phytoplasma OY (poy)
- Pseudomonas putida (ppu)
- Pseudomonas syringae pv. tomato DC3000 (pst)
- Rhodopirellula baltica (rba)
- Rickettsia conorii (rco)
- Rattus norvegicus (rat) (rno)
- Rhodopseudomonas palustris CGA009 (rpa)
- Rickettsia prowazekii (rpr)
- Ralstonia solanacearum (rso)
- Streptococcus agalactiae 2603 (serotype V) (sag)
- Staphylococcus aureus MW2 (sam)
- Streptococcus agalactiae NEM316 (serotype III) (san)
- Staphylococcus aureus N315 (sau)
- Staphylococcus aureus Mu50 (sav)
- Saccharomyces cerevisiae (sce)
- Streptomyces coelicolor (sco)
- Staphylococcus epidermidis ATCC 12228 (sep)
- Shigella flexneri 301 (serotype 2a) (sfl)
- Shigella flexneri 2457T (serotype 2a) (sfx)
- Streptomyces avermitilis (sma)
- Sinorhizobium meliloti (sme)
- Streptococcus mutans (smu)
- Shewanella oneidensis (son)
- Streptococcus pyogenes MGAS315 (serotype M3) (spg)
- Streptococcus pyogenes MGAS8232 (serotype M18) (spm)
- Streptococcus pneumoniae TIGR4 (spn)
- Schizosaccharomyces pombe (spo)
- Streptococcus pneumoniae R6 (spr)
- Streptococcus pyogenes SSI (sps)
- Streptococcus pyogenes SF370 (serotype M1) (spy)
- Sulfolobus solfataricus (sso)
- Salmonella typhimurium LT2 (stm)
- Sulfolobus tokodaii (sto)
- Salmonella enterica serovar Typhi Ty2 (stt)
- Salmonella enterica serovar Typhi CT18 (sty)
- Synechococcus elongatus PCC6301 (syc)
- Synechocystis sp. PCC6803 (syn)
- Synechococcus sp. WH8102 (syw)
- Thermoplasma acidophilum (tac)
- Treponema denticola (tde)
- Thermosynechococcus elongatus (tel)
- Thermotoga maritima (tma)
- Treponema pallidum (tpa)
- Thermoanaerobacter tengcongensis (tte)
- Thermus thermophilus HB27 (tth)
- Thermoplasma volcanium (tvo)
- Tropheryma whipplei Twist (twh)
- Tropheryma whipplei TW08/27 (tws)
- Ureaplasma urealyticum (uur)
- Vibrio cholerae (vch)
- Vibrio parahaemolyticus (vpa)
- Vibrio vulnificus CMCP6 (vvu)
- Vibrio vulnificus YJ016 (vvy)
- Wigglesworthia glossinidia (wbr)
- Wolbachia wMel (wol)
- Wolinella succinogenes (wsu)
- Xanthomonas axonopodis (xac)
- Xanthomonas campestris pv. campestris ATCC 33913 (xcc)
- Xylella fastidiosa 9a5c (xfa)
- Xylella fastidiosa Temecula1 (xft)
- Yersinia pestis CO92 (ype)
- Yersinia pestis KIM (ypk)
- Yersinia pestis Mediaevails (ypm)
[This page was last modified 19Aug08, 3:25 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.
