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    Archived pages: 10 . Archive date: 2014-06.

  • Title: FAME - the Flux Analysis and Modeling Environment
    Descriptive info: .. F A M E.. Welcome to FAME, the Flux Analysis and Modeling Environment!.. FAME is your one stop shop for stoichiometric modeling and flux balance analysis.. It features FBA model construction, model execution, results visualization, and friendly elephants.. RUN/EDIT EXISTING MODEL.. BUILD NEW MODEL.. MERGE MODELS.. ONLY VISUALIZE.. LOST YOUR MODEL?.. VIEW MANUAL.. TUTORIAL.. If you are unsure what to do, have a look at the.. tutorial.. and/or.. manual.. , and you'll be on your way soon.. If you can come up with questions or unexpected results that the manual didn't count on, please let me know by email:.. j.. boele@vu.. nl.. FAME is under constant development.. If you encounter any malfunctions, bugs, etc.. in FAME, please be so kind as to inform me by.. email.. , so that I can fix the application if necessary.. Please also send me an email (with a snippet of your model's SBML) if you cannot get your model to load properly.. 2011-2014 Joost Boele / VU University Amsterdam -.. disclaimer, license, and info.. Last update: January 9th, 2014.. The future of FBA visualization is here.. Head over to.. http://f-a-m-e.. org/synechocystis/.. to check it out!.. The full publication can be found here:.. Maarleveld TR, Boele J, Bruggeman FJ, Teusink B (2014) A Data Integration And Visualization Resource for the Metabolic Network of.. Synechocystis.. sp.. PCC 6803.. Plant Phys 2014 pp.. 113.. 224394.. (epub ahead of print).. If you use FAME in your research, please cite:.. Boele J, Olivier BG, Teusink B (2012) FAME, the Flux Analysis and Modeling Environment.. BMC Syst Biol.. 6.. :8.. Import an existing model.. New:.. to save upload time, you can also upload zipped model files.. Uploaded zip files must have a file name ending in.. zip, may contain only one file, and that file must be a.. xml file.. 1.. Select your file.. OR: enter file URL.. (include http://) (filename must end in.. xml).. 2.. Set the default rate for new reactions (when unsure, just leave these values).. Max rate (normal reactions):.. Max rate (boundaries):.. 3.. Was this model generated or processed using.. FAME.. ?.. This is a.. model (also select this if you use SBML level 3 with FBC extension).. This is.. NOT.. a.. model.. 4.. All set?.. -- or just click here to load a demo model!.. Build new model.. Please select a species:.. aae - Aquifex aeolicus.. aau - Arthrobacter aurescens.. aav - Acidovorax avenae.. aba - Candidatus Koribacter versatilis.. abc - Acinetobacter baumannii ACICU.. abm - Acinetobacter baumannii SDF.. abo - Alcanivorax borkumensis.. abu - Arcobacter butzleri.. aby - Acinetobacter baumannii AYE.. acb - Acinetobacter baumannii ATCC 17978.. ace - Acidothermus cellulolyticus.. aci - Acinetobacter sp.. ADP1.. acl - Acholeplasma laidlawii.. acr - Acidiphilium cryptum JF-5.. ade - Anaeromyxobacter dehalogenans 2CP-C.. aeh - Alkalilimnicola ehrlichei.. afm - Aspergillus fumigatus.. afu - Archaeoglobus fulgidus.. afw - Anaeromyxobacter sp.. Fw109-5.. aga - Anopheles gambiae (mosquito).. ago - Ashbya gossypii (Eremothecium gossypii).. aha - Aeromonas hydrophila.. ajs - Acidovorax sp.. JS42.. ama - Anaplasma marginale St.. Maries.. amr - Acaryochloris marina.. amt - Alkaliphilus metalliredigens.. ana - Anabaena sp.. PCC7120.. ang - Aspergillus niger.. ani - Aspergillus nidulans.. aoe - Alkaliphilus oremlandii.. aor - Aspergillus oryzae.. apa - Actinobacillus pleuropneumoniae AP76 (serotype 7).. ape - Aeropyrum pernix.. aph - Anaplasma phagocytophilum.. apj - Actinobacillus pleuropneumoniae JL03 (serotype 3).. apl - Actinobacillus pleuropneumoniae L20 (serotype 5b).. art - Arthrobacter sp.. FB24.. asa - Aeromonas salmonicida.. asu - Actinobacillus succinogenes.. ath - Arabidopsis thaliana (thale cress).. atu - Agrobacterium tumefaciens C58.. ava - Anabaena variabilis.. ayw - Phytoplasma AYWB.. azc - Azorhizobium caulinodans.. azo - Azoarcus sp.. BH72.. bab - Buchnera aphidicola Bp.. bac - Burkholderia ambifaria MC40-6.. bad - Bifidobacterium adolescentis.. baf - Borrelia afzelii.. bam - Burkholderia cepacia.. ban - Bacillus anthracis Ames.. bar - Bacillus anthracis Ames 0581.. bas - Buchnera aphidicola Sg.. bat - Bacillus anthracis Sterne.. bav - Bordetella avium.. bay - Bacillus amyloliquefaciens FZB42.. bba - Bdellovibrio bacteriovorus.. bbk - Bartonella bacilliformis.. bbr - Bordetella bronchiseptica.. bbt - Bradyrhizobium sp.. BTAi1.. bbu - Borrelia burgdorferi B31.. bca - Bacillus cereus ATCC 10987.. bcc - Buchnera aphidicola Cc.. bce - Bacillus cereus ATCC 14579.. bch - Burkholderia cenocepacia HI2424.. bci - Baumannia cicadellinicola.. bcl - Bacillus clausii.. bcm - Burkholderia cenocepacia MC0-3.. bcn - Burkholderia cenocepacia AU1054.. bcs - Brucella canis.. bcy - Bacillus cytotoxis NVH 391-98.. bcz - Bacillus cereus ZK.. bfl - Candidatus Blochmannia floridanus.. bfr - Bacteroides fragilis YCH46.. bfs - Bacteroides fragilis NCTC9343.. bga - Borrelia garinii.. bha - Bacillus halodurans.. bhe - Bartonella henselae.. bid - Beijerinckia indica.. bja - Bradyrhizobium japonicum.. bld - Bacillus licheniformis DSM13.. bli - Bacillus licheniformis ATCC 14580.. blj - Bifidobacterium longum DJO10A.. blo - Bifidobacterium longum NCC2705.. bma - Burkholderia mallei ATCC 23344.. bmb - Brucella abortus 9-941.. bmc - Brucella abortus S19.. bme - Brucella melitensis bv.. 1 16M.. bmf - Brucella melitensis biovar Abortus.. bml - Burkholderia mallei NCTC 10229.. bmn - Burkholderia mallei NCTC 10247.. bms - Brucella suis 1330.. bmt - Brucella suis ATCC 23445.. bmu - Burkholderia multivorans ATCC 17616 (JGI).. bmv - Burkholderia mallei SAVP1.. bmy - Brugia malayi (filaria).. bov - Brucella ovis.. bpa - Bordetella parapertussis.. bpd - Burkholderia pseudomallei 668.. bpe - Bordetella pertussis.. bph - Burkholderia phymatum.. bpl - Burkholderia pseudomallei 1106a.. bpm - Burkholderia pseudomallei 1710b.. bpn - Candidatus Blochmannia pennsylvanicus.. bps - Burkholderia pseudomallei K96243.. bpt - Bordetella petrii.. bpu - Bacillus pumilus.. bqu - Bartonella quintana.. bra - Bradyrhizobium sp.. ORS278.. bsu - Bacillus subtilis.. bta - Bos taurus (cow).. bte - Burkholderia thailandensis.. bth - Bacteroides thetaiotaomicron.. btk - Bacillus thuringiensis 97-27.. btl - Bacillus thuringiensis Al Hakam.. btr - Bartonella tribocorum.. buc - Buchnera aphidicola APS.. bur - Burkholderia sp.. 383.. bvi - Burkholderia vietnamiensis.. bvu - Bacteroides vulgatus.. bwe - Bacillus weihenstephanensis.. bxe - Burkholderia xenovorans.. cab - Chlamydophila abortus.. cac - Clostridium acetobutylicum ATCC 824.. cak - Caulobacter sp.. K31.. cal - Candida albicans.. cau - Chloroflexus aurantiacus.. cba - Clostridium botulinum A ATCC 19397.. cbb - Clostridium botulinum B1 Okra.. cbd - Coxiella burnetii Dugway 5J108-111.. cbe - Clostridium beijerinckii.. cbf - Clostridium botulinum F Langeland.. cbh - Clostridium botulinum A Hall.. cbk - Clostridium botulinum B Eklund 17B.. cbl - Clostridium botulinum A3 Loch Maree.. cbo - Clostridium botulinum A ATCC 3502.. cbs - Coxiella burnetii RSA 331.. cbu - Coxiella burnetii RSA 493.. cca - Chlamydophila caviae.. cch - Chlorobium chlorochromatii.. cco - Campylobacter concisus 13826.. ccr - Caulobacter crescentus CB15.. ccv - Campylobacter curvus.. cdf - Clostridium difficile 630.. cdi - Corynebacterium diphtheriae.. cef - Corynebacterium efficiens.. cel - Caenorhabditis elegans (nematode).. cfa - Canis familiaris (dog).. cfe - Chlamydophila felis.. cff - Campylobacter fetus.. cgb - Corynebacterium glutamicum ATCC 13032 (Bielefeld).. cgl - Corynebacterium glutamicum ATCC 13032 (Kyowa Hakko).. cgr - Candida glabrata.. cgt - Corynebacterium glutamicum R.. cha - Campylobacter hominis ATCC BAA-381.. cho - Cryptosporidium hominis.. chu - Cytophaga hutchinsonii.. chy - Carboxydothermus hydrogenoformans.. cja - Cellvibrio japonicus.. cjd - Campylobacter jejuni subsp.. doylei 269.. 97.. cje - Campylobacter jejuni NCTC11168.. cjj - Campylobacter jejuni 81-176.. cjk - Corynebacterium jeikeium.. cjr - Campylobacter jejuni RM1221.. cju - Campylobacter jejuni 81116.. ckl - Clostridium kluyveri DSM 555.. cko - Citrobacter koseri ATCC BAA-895.. cma - Caldivirga maquilingensis.. cme - Cyanidioschyzon merolae.. cmi - Clavibacter michiganensis subsp.. michiganensis.. cms - Clavibacter michiganensis subsp.. sepedonicus.. cmu - Chlamydia muridarum.. cnb - Cryptococcus neoformans B-3501A.. cne - Cryptococcus neoformans JEC21.. cno - Clostridium novyi.. cpa - Chlamydophila pneumoniae AR39.. cpb - Chlorobium phaeobacteroides BS1.. cpe - Clostridium perfringens 13.. cpf - Clostridium perfringens ATCC 13124.. cph - Chlorobium phaeobacteroides DSM 266.. cpj - Chlamydophila pneumoniae J138.. cpn - Chlamydophila pneumoniae CWL029.. cpr - Clostridium perfringens SM101.. cps - Colwellia psychrerythraea.. cpt - Chlamydophila pneumoniae TW183.. cpv - Cryptosporidium parvum.. cpy - Clostridium phytofermentans.. cre - Chlamydomonas reinhardtii.. crp - Candidatus Carsonella ruddii.. csa - Chromohalobacter salexigens.. csc - Caldicellulosiruptor saccharolyticus.. cta - Chlamydia trachomatis A/HAR-13.. ctb - Chlamydia trachomatis L2/434/Bu.. ctc - Clostridium tetani E88.. cte - Chlorobaculum tepidum.. cth - Clostridium thermocellum.. cti - Cupriavidus taiwanensis.. ctl - Chlamydia trachomatis L2b/UCH-1/proctitis.. ctr - Chlamydia trachomatis D/UW-3/CX.. cur - Corynebacterium urealyticum.. cvi - Chromobacterium violaceum.. cya - Synechococcus sp.. JA-3-3Ab.. cyb - Synechococcus sp.. JA-2-3B'a(2-13).. cyt - Cyanothece sp.. ATCC 51142.. dac - Delftia acidovorans.. dar - Dechloromonas aromatica.. dau - Candidatus Desulforudis audaxviator.. dbmo - Bombyx mori (silkmoth).. dde - Desulfovibrio desulfuricans G20.. ddi - Dictyostelium discoideum (cellular slime mold).. deb - Dehalococcoides sp.. BAV1.. deh - Dehalococcoides sp.. CBDB1.. det - Dehalococcoides ethenogenes.. dfru - Fugu rubripes (Japanese puffer fish).. dge - Deinococcus geothermalis.. dha - Debaryomyces hansenii.. dkwa - Kluyveromyces waltii.. dme - Drosophila melanogaster (fruit fly).. dno - Dichelobacter nodosus.. dol - Candidatus Desulfococcus oleovorans.. dola - Oryzias latipes (Japanese medaka).. dpo - Drosophila pseudoobscura pseudoobscura.. dps - Desulfotalea psychrophila.. dra - Deinococcus radiodurans.. dre - Danio rerio (zebrafish).. drm - Desulfotomaculum reducens.. dsba - Saccharomyces bayanus.. dsh - Dinoroseobacter shibae.. dsmi - Saccharomyces mikatae.. dsy - Desulfitobacterium hafniense Y51.. dtni - Tetraodon nigroviridis (green spotted pufferfish).. dvl - Desulfovibrio vulgaris DP4.. dvu - Desulfovibrio vulgaris Hildenborough.. eba - Aromatoleum aromaticum EbN1.. eca - Pectobacterium atrosepticum.. ecc - Escherichia coli O6:K2:H1 CFT073 (UPEC).. ecd - Escherichia coli K-12 DH10B.. ece - Escherichia coli O157:H7 EDL933 (EHEC).. ech - Ehrlichia chaffeensis.. eci - Escherichia coli O18:K1:H7 UTI89 (UPEC).. ecj - Escherichia coli K-12 W3110.. ecl - Escherichia coli C ATCC 8739.. ecm - Escherichia coli SMS-3-5 (environmental).. ecn - Ehrlichia canis.. eco - Escherichia coli K-12 MG1655.. ecp - Escherichia coli O6:K15:H31 536 (UPEC).. ecs - Escherichia coli O157:H7 Sakai (EHEC).. ecu - Encephalitozoon cuniculi.. ecv - Escherichia coli O1:K1:H7 (APEC).. ecw - Escherichia coli O139:H28 E24377A (ETEC).. ecx - Escherichia coli O9 HS (commensal).. efa - Enterococcus faecalis.. ehi - Entamoeba histolytica.. eli - Erythrobacter litoralis.. ent - Enterobacter sp.. 638.. erg - Ehrlichia ruminantium Gardel.. eru - Ehrlichia ruminantium Welgevonden (South Africa).. erw - Ehrlichia ruminantium Welgevonden (France).. esa - Cronobacter sakazakii.. esi - Exiguobacterium sibiricum.. eta - Erwinia tasmaniensis.. fal - Frankia alni.. fgr - Fusarium graminearum.. fjo - Flavobacterium johnsoniae.. fma - Finegoldia magna.. fno - Fervidobacterium nodosum.. fnu - Fusobacterium nucleatum.. fph - Francisella philomiragia.. fps - Flavobacterium psychrophilum.. fra - Frankia sp.. CcI3.. fre - Frankia sp.. EAN1pec.. fta - Francisella tularensis subsp.. holarctica FTNF002-00.. ftf - Francisella tularensis subsp.. tularensis FSC 198.. fth - Francisella tularensis subsp.. holarctica OSU18.. ftl - Francisella tularensis subsp.. holarctica LVS.. ftm - Francisella tularensis subsp.. mediasiatica FSC147.. ftn - Francisella novicida U112.. ftu - Francisella tularensis subsp.. tularensis SCHU S4.. ftw - Francisella tularensis subsp.. tularensis WY96-3418.. gbe - Granulibacter bethesdensis.. gdi - Gluconacetobacter diazotrophicus PAl 5 (Brazil).. gfo - Gramella forsetii.. gga - Gallus gallus (chicken).. gka - Geobacillus kaustophilus.. gla - Giardia lamblia.. glo - Geobacter lovleyi.. gme - Geobacter metallireducens.. gox - Gluconobacter oxydans.. gsu - Geobacter sulfurreducens.. gtn - Geobacillus thermodenitrificans.. gur - Geobacter uraniumreducens.. gvi - Gloeobacter violaceus.. hac - Helicobacter acinonychis.. hal - Halobacterium sp.. NRC-1.. har - Herminiimonas arsenicoxydans.. hau - Herpetosiphon aurantiacus.. hbu - Hyperthermus butylicus.. hch -  ...   haemolyticus.. she - Shewanella sp.. MR-4.. shl - Shewanella halifaxensis.. shm - Shewanella sp.. MR-7.. shn - Shewanella sp.. ANA-3.. shw - Shewanella sp.. W3-18-1.. sil - Silicibacter pomeroyi.. sit - Ruegeria sp.. TM1040.. slo - Shewanella loihica.. sma - Streptomyces avermitilis.. smd - Sinorhizobium medicae.. sme - Sinorhizobium meliloti 1021.. smg - Candidatus Sulcia muelleri GWSS.. sml - Stenotrophomonas maltophilia K279a.. smr - Staphylothermus marinus.. smu - Streptococcus mutans UA159.. son - Shewanella oneidensis.. spa - Streptococcus pyogenes MGAS10394 (serotype M6).. spb - Streptococcus pyogenes MGAS6180 (serotype M28).. spc - Shewanella putrefaciens.. spd - Streptococcus pneumoniae D39 (virulent serotype 2).. spe - Serratia proteamaculans.. spf - Streptococcus pyogenes Manfredo (serotype M5).. spg - Streptococcus pyogenes MGAS315 (serotype M3).. sph - Streptococcus pyogenes MGAS10270 (serotype M2).. spi - Streptococcus pyogenes MGAS10750 (serotype M4).. spj - Streptococcus pyogenes MGAS2096 (serotype M12).. spk - Streptococcus pyogenes MGAS9429 (serotype M12).. spl - Shewanella pealeana.. spm - Streptococcus pyogenes MGAS8232 (serotype M18).. spn - Streptococcus pneumoniae TIGR4 (virulent serotype 4).. spo - Schizosaccharomyces pombe (fission yeast).. spq - Salmonella enterica subsp.. enterica serovar Paratyphi B.. spr - Streptococcus pneumoniae R6 (avirulent).. sps - Streptococcus pyogenes SSI-1 (serotype M3).. spt - Salmonella enterica subsp.. enterica serovar Paratyphi A ATCC9150.. spu - Strongylocentrotus purpuratus (purple sea urchin).. spv - Streptococcus pneumoniae Hungary19A 6.. spw - Streptococcus pneumoniae CGSP14 (serotype 14).. spy - Streptococcus pyogenes SF370 (serotype M1).. spz - Streptococcus pyogenes MGAS5005 (serotype M1).. sru - Salinibacter ruber.. ssa - Streptococcus sanguinis.. ssc - Sus scrofa (pig).. sse - Shewanella sediminis.. ssn - Shigella sonnei.. sso - Sulfolobus solfataricus.. ssp - Staphylococcus saprophyticus.. ssu - Streptococcus suis 05ZYH33.. ssv - Streptococcus suis 98HAH33.. stc - Streptococcus thermophilus CNRZ1066.. ste - Streptococcus thermophilus LMD-9.. sth - Symbiobacterium thermophilum.. stl - Streptococcus thermophilus LMG18311.. stm - Salmonella enterica subsp.. enterica serovar Typhimurium LT2.. sto - Sulfolobus tokodaii.. stp - Salinispora tropica.. stt - Salmonella enterica subsp.. enterica serovar Typhi Ty2.. sty - Salmonella enterica subsp.. enterica serovar Typhi CT18.. sul - Sulfurihydrogenibium sp.. YO3AOP1.. sun - Sulfurovum sp.. NBC37-1.. sus - Candidatus Solibacter usitatus.. swd - Shewanella woodyi ATCC 51908.. swi - Sphingomonas wittichii.. swo - Syntrophomonas wolfei.. syc - Synechococcus elongatus PCC6301.. syd - Synechococcus sp.. CC9605.. sye - Synechococcus sp.. CC9902.. syf - Synechococcus elongatus PCC7942.. syg - Synechococcus sp.. CC9311.. syn - Synechocystis sp.. PCC6803.. syp - Synechococcus sp.. PCC7002.. syr - Synechococcus sp.. RCC307.. syw - Synechococcus sp.. WH8102.. syx - Synechococcus sp.. WH7803.. tac - Thermoplasma acidophilum.. tan - Theileria annulata.. tbd - Thiobacillus denitrificans.. tbr - Trypanosoma brucei.. tca - Tribolium castaneum (red flour beetle).. tcr - Trypanosoma cruzi.. tcx - Thiomicrospira crunogena.. tde - Treponema denticola.. tdn - Sulfurimonas denitrificans.. tel - Thermosynechococcus elongatus.. ter - Trichodesmium erythraeum.. tet - Tetrahymena thermophila.. tex - Thermoanaerobacter sp.. X514.. tfu - Thermobifida fusca.. tko - Thermococcus kodakaraensis.. tle - Thermotoga lettingae.. tma - Thermotoga maritima.. tme - Thermosipho melanesiensis.. tne - Thermoproteus neutrophilus.. tpa - Treponema pallidum subsp.. pallidum Nichols.. tpd - Thermoanaerobacter pseudethanolicus.. tpe - Thermofilum pendens.. tpp - Treponema pallidum subsp.. pallidum SS14.. tpt - Thermotoga petrophila.. tpv - Theileria parva.. trq - Thermotoga sp.. RQ2.. tte - Thermoanaerobacter tengcongensis.. tth - Thermus thermophilus HB27.. ttj - Thermus thermophilus HB8.. tva - Trichomonas vaginalis.. tvo - Thermoplasma volcanium.. twh - Tropheryma whipplei Twist.. tws - Tropheryma whipplei TW08/27.. uma - Ustilago maydis.. upa - Ureaplasma parvum serovar 3 ATCC 27815.. uur - Ureaplasma parvum serovar 3 ATCC 700970.. vch - Vibrio cholerae O1.. vco - Vibrio cholerae O395.. vei - Verminephrobacter eiseniae.. vfi - Vibrio fischeri.. vha - Vibrio harveyi.. vok - Candidatus Vesicomyosocius okutanii.. vpa - Vibrio parahaemolyticus.. vpo - Vanderwaltozyma polyspora.. vvu - Vibrio vulnificus CMCP6.. vvy - Vibrio vulnificus YJ016.. wbm - Wolbachia wBm.. wbr - Wigglesworthia glossinidia.. wol - Wolbachia wMel.. wpi - Wolbachia pipientis.. wsu - Wolinella succinogenes.. xac - Xanthomonas axonopodis pv.. citri 306.. xau - Xanthobacter autotrophicus.. xcb - Xanthomonas campestris pv.. campestris 8004.. xcc - Xanthomonas campestris pv.. campestris ATCC 33913.. xcv - Xanthomonas campestris pv.. vesicatoria.. xfa - Xylella fastidiosa 9a5c.. xfm - Xylella fastidiosa M12.. xfn - Xylella fastidiosa M23.. xft - Xylella fastidiosa Temecula1.. xla - Xenopus laevis (African clawed frog).. xom - Xanthomonas oryzae MAFF311018.. xoo - Xanthomonas oryzae KACC10331.. xtr - Xenopus tropicalis (western clawed frog).. yen - Yersinia enterocolitica subsp.. enterocolitica 8081.. yli - Yarrowia lipolytica.. ypa - Yersinia pestis Antiqua (biovar Antiqua).. ype - Yersinia pestis CO92 (biovar Orientalis).. ypg - Yersinia pestis Angola.. ypi - Yersinia pseudotuberculosis IP31758 (serotype O:1b).. ypk - Yersinia pestis KIM 10 (biovar Mediaevalis).. ypm - Yersinia pestis 91001 (biovar Microtus).. ypn - Yersinia pestis Nepal516 (biovar Antiqua).. ypp - Yersinia pestis Pestoides F.. yps - Yersinia pseudotuberculosis IP32953 (serotype I).. ypy - Yersinia pseudotuberculosis YPIII.. zmo - Zymomonas mobilis.. Please select any number of pathways to include in the model:.. Pathway options will appear here when you select a species.. Choose a name for your model and default max rates for reactions.. You can change the rates for individual reactions later.. Model Name:.. Would you like some fixes?.. Include?.. MAX objective?.. ATP.. ATP + H2O -> ADP + Pi.. 1 DNA + 50 PPi">DNA.. 1 DNA + 50 PPi">DNA synthesis from dNTPs.. 1 RNA + 183 PPi">RNA.. 1 RNA + 183 PPi">RNA synthesis from NTPs.. MALICENZYME.. Malic enzyme w/ NADP+/NADPH.. R00835.. R00835 (fixes PPP).. FRUCTOSE.. FRUCTOSE (fixes PPP).. BIOMASS reaction.. OXPHOS.. P/O:.. 9 CoA + 8 ADP + 8 Pi + 16 NADP + 1 Lipid">LIPIDS.. UTP + G1P = UDP-Glc + PPi; UDP-Glc = Glycogen.. Inorganic Pyrophosphatase (3.. 6.. 1).. PPi + H2O -> 2 Pi.. Use FBC extension? (under development!).. No!.. Yes.. 5.. Ready to go?.. Merge models.. Use this form to merge two models.. Objectives from the slave model are ignored, constraints from the slave model are overwritten by those of the master model.. Note that if you have deleted reactions from either model, they may still exist in the other.. Select your model files.. Master model:.. Slave model:.. Set the default rate for reactions (when unsure, just leave these values).. These will not affect reactions currently in the models.. Lost your model?.. If you have lost your model or would like to retrieve an old session, enter the model ID here to get the latest version of your model that was kept on our server.. You can find your model ID in the XML in the following line:.. model id="MODEL-ID" name="MODEL-ID".. Enter your model ID:.. Only visualize.. To visualize data on KEGG-like maps, enter your data in the box below and select the appropriate KEGG maps.. Make sure your data are of the form.. KEGG-ID,value.. and only enter one key-value pair per line.. Enter your data.. Select pathways.. 01100 - Visualize on full map.. 00010 - Glycolysis / Gluconeogenesis.. 00020 - Citrate cycle (TCA cycle).. 00030 - Pentose phosphate pathway.. 00040 - Pentose and glucuronate interconversions.. 00051 - Fructose and mannose metabolism.. 00052 - Galactose metabolism.. 00053 - Ascorbate and aldarate metabolism.. 00061 - Fatty acid biosynthesis.. 00062 - Fatty acid elongation in mitochondria.. 00071 - Fatty acid metabolism.. 00072 - Synthesis and degradation of ketone bodies.. 00100 - Steroid biosynthesis.. 00120 - Primary bile acid biosynthesis.. 00130 - Ubiquinone and other terpenoid-quinone biosynthesis.. 00140 - Steroid hormone biosynthesis.. 00230 - Purine metabolism.. 00232 - Caffeine metabolism.. 00240 - Pyrimidine metabolism.. 00250 - Alanine, aspartate and glutamate metabolism.. 00251 - Alanine, aspartate and glutamate metabolism.. 00253 - Tetracycline biosynthesis.. 00260 - Glycine, serine and threonine metabolism.. 00270 - Cysteine and methionine metabolism.. 00271 - Cysteine and methionine metabolism.. 00280 - Valine, leucine and isoleucine degradation.. 00281 - Geraniol degradation.. 00290 - Valine, leucine and isoleucine biosynthesis.. 00300 - Lysine biosynthesis.. 00310 - Lysine degradation.. 00311 - Penicillin and cephalosporin biosynthesis.. 00330 - Arginine and proline metabolism.. 00331 - Clavulanic acid biosynthesis.. 00340 - Histidine metabolism.. 00350 - Tyrosine metabolism.. 00351 - 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation.. 00360 - Phenylalanine metabolism.. 00361 - gamma-Hexachlorocyclohexane degradation.. 00362 - Benzoate degradation via hydroxylation.. 00363 - Bisphenol A degradation.. 00364 - Fluorobenzoate degradation.. 00380 - Tryptophan metabolism.. 00400 - Phenylalanine, tyrosine and tryptophan biosynthesis.. 00401 - Novobiocin biosynthesis.. 00402 - Benzoxazinoid biosynthesis.. 00410 - beta-Alanine metabolism.. 00430 - Taurine and hypotaurine metabolism.. 00440 - Phosphonate and phosphinate metabolism.. 00450 - Selenoamino acid metabolism.. 00460 - Cyanoamino acid metabolism.. 00471 - D-Glutamine and D-glutamate metabolism.. 00472 - D-Arginine and D-ornithine metabolism.. 00473 - D-Alanine metabolism.. 00480 - Glutathione metabolism.. 00500 - Starch and sucrose metabolism.. 00520 - Amino sugar and nucleotide sugar metabolism.. 00521 - Streptomycin biosynthesis.. 00522 - Biosynthesis of 12-, 14- and 16-membered macrolides.. 00523 - Polyketide sugar unit biosynthesis.. 00524 - Butirosin and neomycin biosynthesis.. 00540 - Lipopolysaccharide biosynthesis.. 00550 - Peptidoglycan biosynthesis.. 00561 - Glycerolipid metabolism.. 00562 - Inositol phosphate metabolism.. 00564 - Glycerophospholipid metabolism.. 00565 - Ether lipid metabolism.. 00590 - Arachidonic acid metabolism.. 00591 - Linoleic acid metabolism.. 00592 - alpha-Linolenic acid metabolism.. 00600 - Sphingolipid metabolism.. 00601 - Glycosphingolipid biosynthesis - lacto and neolacto series.. 00603 - Glycosphingolipid biosynthesis - globo series.. 00604 - Glycosphingolipid biosynthesis - ganglio series.. 00620 - Pyruvate metabolism.. 00621 - Biphenyl degradation.. 00622 - Toluene and xylene degradation.. 00623 - 2,4-Dichlorobenzoate degradation.. 00624 - 1- and 2-Methylnaphthalene degradation.. 00625 - Tetrachloroethene degradation.. 00626 - Naphthalene and anthracene degradation.. 00627 - 1,4-Dichlorobenzene degradation.. 00628 - Fluorene degradation.. 00629 - Carbazole degradation.. 00630 - Glyoxylate and dicarboxylate metabolism.. 00631 - 1,2-Dichloroethane degradation.. 00632 - Benzoate degradation via CoA ligation.. 00633 - Trinitrotoluene degradation.. 00640 - Propanoate metabolism.. 00641 - 3-Chloroacrylic acid degradation.. 00642 - Ethylbenzene degradation.. 00643 - Styrene degradation.. 00650 - Butanoate metabolism.. 00660 - C5-Branched dibasic acid metabolism.. 00670 - One carbon pool by folate.. 00680 - Methane metabolism.. 00710 - Carbon fixation in photosynthetic organisms.. 00720 - Reductive carboxylate cycle (CO2 fixation).. 00730 - Thiamine metabolism.. 00740 - Riboflavin metabolism.. 00750 - Vitamin B6 metabolism.. 00760 - Nicotinate and nicotinamide metabolism.. 00770 - Pantothenate and CoA biosynthesis.. 00780 - Biotin metabolism.. 00785 - Lipoic acid metabolism.. 00790 - Folate biosynthesis.. 00791 - Atrazine degradation.. 00830 - Retinol metabolism.. 00860 - Porphyrin and chlorophyll metabolism.. 00900 - Terpenoid backbone biosynthesis.. 00901 - Indole alkaloid biosynthesis.. 00902 - Monoterpenoid biosynthesis.. 00903 - Limonene and pinene degradation.. 00904 - Diterpenoid biosynthesis.. 00905 - Brassinosteroid biosynthesis.. 00906 - Carotenoid biosynthesis.. 00908 - Zeatin biosynthesis.. 00909 - Sesquiterpenoid biosynthesis.. 00910 - Nitrogen metabolism.. 00920 - Sulfur metabolism.. 00930 - Caprolactam degradation.. 00940 - Phenylpropanoid biosynthesis.. 00941 - Flavonoid biosynthesis.. 00942 - Anthocyanin biosynthesis.. 00943 - Isoflavonoid biosynthesis.. 00944 - Flavone and flavonol biosynthesis.. 00945 - Stilbenoid, diarylheptanoid and gingerol biosynthesis.. 00950 - Isoquinoline alkaloid biosynthesis.. 00960 - Tropane, piperidine and pyridine alkaloid biosynthesis.. 00965 - Betalain biosynthesis.. 00966 - Glucosinolate biosynthesis.. 00970 - Aminoacyl-tRNA biosynthesis.. 00980 - Metabolism of xenobiotics by cytochrome P450.. 00981 - Insect hormone biosynthesis.. 00982 - Drug metabolism - cytochrome P450.. 00983 - Drug metabolism - other enzymes.. 01040 - Biosynthesis of unsaturated fatty acids.. 01051 - Biosynthesis of ansamycins.. 01053 - Biosynthesis of siderophore group nonribosomal peptides.. Top.. 2011-2014.. Joost Boele.. / VU University Amsterdam.. All rights reserved -..

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    Descriptive info: FAME, the Flux Analysis and Modeling Environment.. Copyright Joost Boele / VU University Amsterdam 2011 - 2013.. All Rights Reserved.. LICENSE AGREEMENT.. The Author, Joost Boele, hereby grants to you, the User a non-exclusive license to use the Flux Analysis and Modeling Environment software (furthermore FAME) and accompanying documentation on the terms below.. The User may use the Software on any computer.. It may not be included as a part of any commercial package, or used or distributed in support of a commercial service without prior express written permission from the Author.. The User may not permit other individuals to use the Software except under the terms listed above.. To translate, reverse engineer, decompile, disassemble the Software; rent or lease the Software; or remove any proprietary notices on the Software is prohibited.. THIS SOFTWARE IS PROVIDED " AS IS " AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  ...   any problems that may be encountered in using it.. Title, ownership rights, and intellectual property rights in and to the Software shall remain in the Author.. The Software is protected by the copyright laws of the Netherlands and international copyright treaties.. DISCLAIMER.. The authors of this program accept no responsibility for damages resulting from the use of this software and makes no warranty, either express or implied, including, but not limited to, any implied warranty of fitness for a particular purpose.. This software is provided as it is, and you, its user, assume all risks when using it.. INFORMATION FROM KEGG.. FAME makes use of information from the Kyoto Encyclopedia of Genes and Genomes (KEGG).. This information is free for academic, non-commercial use as described on.. this page.. ICONS.. The FAME elephant icon/species icon:.. http://www.. visualpharm.. com/.. The boundaries/customs and lost-and-found icons:.. thenounproject.. Command prompt (batch run) icon by.. Deleket @ DeviantArt.. SOURCE CODE.. FAME is open source, and its source code will be provided upon request.. To obtain the source code of FAME, please send your request to.. CITING FAME.. If you use FAME in your research, we request that you cite..

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