Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.

News

Update History

Information

Introduction to BioCyc
5500 Databases
Guided Tour
Pathway Tools Software
Pathway Tools Blog
Publications
Linking to BioCyc
Webinars
Contact Us

Services

Subscribe to BioCyc
Metabolic Posters
Genome Posters
Software/Database Downloads
Registry
Web Services

News

Oct. 11  BioCyc.org 17.5 Released

BioCyc.org 17.5 contains 2988 Pathway/Genome Databases.

BioCyc Database Improvements

  • In MetaCyc [release notes] we curated 32 new microbial pathways mediating the biosynthesis of antibiotics, amino acids, sugars, nucleotide-activated sugars, and modified nucleosides in tRNAs, as well as the degradation of acrylonitrile, sugars and D-glucosaminate. We also added 14 new yeast pathways involved in fatty acid and lipid metabolism and the biosynthesis and salvage of thiamin. In animal metabolism we added the biosynthesis of steroid hormones and octopamine, and an opine fermentation pathway. In plant secondary metabolism we curated nevadensin, salvigenin and papaverine biosynthesis. We also implemented a a new type of glycan pathway diagram in Pathway Tools that utilizes symbols for glycan monomers and arrows to indicate enzyme cleavage sites.
  • In EcoCyc [release notes], we have added a pathway describing the formation of 5-(carboxymethoxy)uridine, a posttranscriptionally modified nucleotide in tRNAs. Updates in membrane protein biology include the identification of a new subunit of the terminal oxidase cytochrome bd-1 and the addition of several transmembrane transport reactions. New active forms of the transcriptional regulators LsrR and MetJ have been added.
  • In HumanCyc [release notes] , we added two new pathways, which cover the salvage of tetrahydrobioterin and purine nucleotides. We also revised 10 existing pathways including the malate aspartate shuttle, biosynthesis of the amino acids serine and glycine and NAD salvage. HumanCyc was upgraded by propagation of relevant data updates from MetaCyc.

Jun. 11  BioCyc.org 17.1 Released

BioCyc.org 17.1 contains 2988 Pathway/Genome Databases.

BioCyc Database Improvements

  • In MetaCyc [release notes] we added 26 new microbial pathways covering the biosynthesis of secondary metabolites and iron-sulfur clusters, carbohydrate degradation, and a new TCA cycle variant for acetogenic bacteria. We also reorganized our purine nucleotides biosynthesis and salvage pathways. In plant metabolism we added 19 new pathways for the biosynthesis and degradation of primary and secondary metabolites including sucrose, gibberellin GA3, pentacyclic triterpenoids, coenzyme Q6, flavones, anthocyanins and alkaloids. In animal metabolism we added the mammalian variants of sphingolipid biosynthesis, glycolysis and gluconeogenesis. We also added two engineered pathways that describe the production of 3-hydroxybutanoate, a precursor of the commercially important polyester polyhydroxyalkanoate. We also set up Twitter and Facebook accounts to allow users to keep up with the latest BioCyc news (https://www.facebook.com/BioCyc and https://twitter.com/biocyc).
  • Updates to EcoCyc [release notes] include the identification of an orphan enzyme in the menaquinone biosynthesis pathway, new functions for several membrane proteins, and revisions to the metabolic network that were motivated by flux-balance analysis (FBA) predictions and experimental growth observations.
  • In HumanCyc [release notes] we imported 5 new pathways from MetaCyc to HumanCyc, which covered nucleotide and deoxynucleotide biosynthesis. We also revised 4 existing pathways in HumanCyc. HumanCyc was upgraded by propagation of relevant data updates from MetaCyc.

Mar. 28  BioCyc.org 17.0 Released

BioCyc.org 17.0 contains 2920 Pathway/Genome Databases. Starting with this release we are integrating several new types of data into newly generated BioCyc PGDBs:

  • Protein features (e.g., phosphorylation sites, metal ion binding sites, enzyme active sites) derived from UniProt
  • Gene Ontology terms derived from UniProt
  • Protein localization information derived from PSORTDB
  • Database links from BioCyc genes and proteins to 15 bioinformatics databases

BioCyc Database Improvements

  • In MetaCyc [release notes] we added 34 new microbial pathways encompassing biosynthesis, degradation, recycling and detoxification. We also updated our coverage of pyrimidine nucleotides metabolism. In animal metabolism we added 10 new mammalian pathways. In plant metabolism added 35 new pathways for the biosynthesis and degradation of primary and secondary metabolites, including pathways from the model green alga Chlamydomonas reinhardtii. In the bioenergy area, we added 5 new pathways, including engineered pathways for the production of ethylene. We also set up Twitter and Facebook accounts to allow users to keep up with the latest BioCyc news (https://www.facebook.com/BioCyc and https://twitter.com/biocyc).
  • In EcoCyc [release notes] we added a new signal transduction pathway and two metabolic pathways and re-organized the pyrimidine nucleotide biosynthesis pathways. Information about three newly identified transcription factors and several newly characterized membrane proteins was added.
  • In HumanCyc [release notes] we curated 20 new pathways describing nucleotide/nucleoside phosphorylation, biosynthesis and degradation, phytol degradation, peroxisomal beta oxidation of fatty acids, resolvin and lipoxin biosynthesis. Also for this release, HumanCyc has been upgraded by propagation of the latest data updates from MetaCyc.

Nov. 15  BioCyc.org 16.5 Released

BioCyc.org 16.5 contains 2038 Pathway/Genome Databases.

BioCyc Database Improvements

  • In MetaCyc [release notes] we curated 12 new microbial pathways mediating biosynthesis, nitrification, resistance, salvage, utilization and degradation. In animal metabolism we added a new pathway for detoxification and two new fatty acid α-oxidation pathways imported from HumanCyc. In plant metabolism added 12 new biosynthetic pathways including a degradation pathway for furcatin. In the bioenergy area, we added 6 new pathways including two pathways for intermediates in lignin degradation and 2 biofuel related engineered pathways. Other new features in MetaCyc include glycan structure representation via Glycan Builder software and links to the CAZy database.
  • In EcoCyc [release notes] we added newly described functions to a number of previously uncharacterized proteins, including several membrane proteins and a translocation and assembly module spanning the inner and outer membrane. A fifth Phenotype Microarray dataset measuring respiration under aerobic conditions using the Biolog platform was added to our growth media page.
  • BsubCyc [release notes] has been updated to add protein feature information from UniProt.
  • In HumanCyc [release notes] we curated two new pathways that describe the peroxisomal α-oxidation of 3-methyl branched fatty acids and 2-hydroxylated straight chain fatty acids. We also imported a pathway from MetaCyc for the detoxification of 4-hydroxy-2-nonenal, a product of lipid peroxidation. Also for this release, HumanCyc has been upgraded by propagation of the latest data updates from MetaCyc.

BioCyc Web Site Improvements

  • Phenotype Microarrays and Other Growth Data: The displays of growth media, growth observations, and phenotype microarray data has been substantially revised.

  • Atom Mappings: MetaCyc now contains atom mapping data for 8281 reactions. Atom mappings define the correspondence between atoms in the reactants of a chemical reaction, and the atoms in the products of that reaction.

  • New representation of EC Numbers in Pathway Tools: Clicking on the EC number from a reaction page navigates to an EC-number page. The difference is more obvious if a reaction is associated with multiple EC numbers. In these cases all of the EC numbers, along with their names, comments, citations, etc., appear on the reaction page.

  • Many Web Groups Enhancements: Many new transformations have been added/renamed. New transformations include:
    • New regulation transformations for genes
    • Transform gene to upstream promoter
    • Transform protein to DNA sites it binds to
    • Transform compound to proteins that bind to or are activated or inhibited by that compound

  • Customize Pathway Diagram with Omics Data: The command Pathway → Customize Pathway Diagram now includes an option for painting omics data onto an individual pathway diagram.

  • Web Omics Viewer Displays Table of Pathways: The Cellular Omics Viewer (see Cellular Overview → Overlay Experimental Data) now includes an option previously present in the desktop version, namely to generate a table displaying omics data painted onto diagrams of individual pathways. This option can be selected from the "Show data:" selector in the Omics Viewer dialog.

July. 5  BioCyc.org 16.1 Website
BioCyc.org 16.1 contains 1,962 Pathway/Genome Databases, including 494 complete bacterial genomes from the Human Microbiome Project.
  • In MetaCyc [release notes] we curated new microbial biosynthetic pathways for several aminoglycoside antibiotics, multiple alkanes and olefins, tetrahydrobiopterin, pyrrolysine, theophylline, violacein, CDP-D-arabitol, lipoate, and bacterial protein glycosylation. In microbial degradation we added pathways for (-)-camphor, daidzein, nicotine, L-1,2-propanediol, and the mineralization of several aromatic ring-containing compounds. In the bioenergy area we added microbial degradation pathways for alginate, 1,5-anhydrofructose, furfural, 5-hydroxymethylfurfural, and the conversion of glycerol to butanol. We also curated an engineered pathway for the biosynthesis of methyl ketones. New eukaryotic pathways depict the visual cycles used by molluscs and insects to regenerate their chromophores, an insect pathway to generate the chromophore 11-cis-3-hydroxyretinal, the biosynthesis of very-long-chain fatty acids, and chitin biosynthesis in lower eukaryotes. In plant metabolism we added new biosynthetic pathways for (+)-camphor, and (-) camphor, and umbelliferone. PMN curators added two malate-oxaloacetate shuttle pathways, a pathway for the transient synthesis of the signaling molecule phosphatidate, and a minor shunt pathway for abscisic acid biosynthesis.
  • EcoCyc [release notes] has been updated to review and standardize the names of 450 membrane proteins. We have also added in newly identified transcription factors, new binding sites for 17 other transcription factors, and the usual updates from the E. coli literature.
Feb. 16  BioCyc.org 16.0 Website
BioCyc.org 16.0 contains 1,763 Pathway/Genome Databases, including 414 complete bacterial genomes from the Human Microbiome Project.
  • In MetaCyc [release notes] In MetaCyc we curated new microbial pathways for thiamin metabolism, ammonium assimilation, the biosynthesis of plastoquinol, several antibiotics and several deoxysugars, and the degradation of cholesterol, testosterone, androsterone, sitosterol, methylamine, trimethylamine, styrene, ricinine, L-ascorbate and chitin. A new eukaryotic pathway describes the repair of a non-active form of NADH, known as NADHX. In plant metabolism we added new biosynthetic pathways for methylbutenol, epoxy fatty acids, benzoxazinoid glucosides, (Z)-butanethiol-S-oxide , and the plant defense compounds kauralexin, zealexin, sophoraflavanone G, pyrethrin and L-N-acetylornithine. We also curated pathways for selenite metabolism, phenolic malonylglucosides metabolism, and the degradation of chlorophyll a . In the bioenergy area we added engineered pathways for the biosynthesis of isopropanol and butanol in Escherichia coli and cyanobacteria, and a pathway for xylose degradation by a thermophilic bacterium.
  • EcoCyc [release notes] EcoCyc has been updated with new enzyme functions and a range of metabolic updates in accordance with recent published metabolic modeling results. The effort to update transcription factor binding sites with more accurate positions and lengths continues, along with the usual range of updates to transcriptional regulation, including the allosteric regulation of RNA polymerase.
  • In Humancyc [release notes] 31 new pathways were added, most of them were updated from Metacyc. These include S-reticuline biosynthesis II, methyl-5'-thioadenosine degradation, adenine and adenosine salvage, aspartate biosynthesis, calcium transport, fatty acid beta oxidation III, glutamine degradation, glycine biosynthesis, guanine and guanosine salvage, histidine degradation, methylglyoxal degradation, morphine biosynthesis, NADH repair, oxidized GTP and dGTP detoxification, phenylethylamine degradation, phosphatidylethanolamine biosynthesis III, proline biosynthesis, purine ribonucleosides degradation to ribose-1-phosphate, putrescine biosynthesis , superpathway of inositol phosphate compounds, tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate, thiamin salvage III, tRNA splicing, acetyl-D-galactosamine biosynthesis I and II and dTMP de novo biosynthesis.
Oct. 21  BioCyc.org 15.5 Website
BioCyc.org 15.5 contains 1,692 Pathway/Genome Databases, including 414 complete bacterial genomes from the Human Microbiome Project.
  • In MetaCyc [release notes] we curated new microbial biosynthetic pathways for ethylene, dTDP-D-forosamine, ornithine lipids, pyrrolnitrin, spermidine, phosphatidylcholine, and 2-aminoethylphosphonate. We also updated our coverage of molybdenum cofactor biosynthesis. We curated new microbial degradation pathways for rutin and 2-aminoethylphosphonate, as well as pathways for degradation of the polymers agarose, ι-carrageenan, κ-carrageenan, λ-carrageenan, porphyran, gellan, and chitin. Bioenergy-related microbial pathways were added for the degradation of xyloglucan and glucuronoarabinoxylan, and a pathway for xyloglucan biosynthesis was revised. In animal metabolism we curated pathways describing the metabolism of retinoid compounds and the biosynthesis of senecionine-N-oxide. In plant metabolism we curated pathways for the biosynthesis of nitric oxide, homophytochelatin, homoglutathione, 6-gingerol, justicidin B, diphyllin, neoxanthin, and santalene. We also added a plant degradation route for fatty acids with cis-double bonds on odd-number carbons, steps in the degradation of insect chitin by carnivorous plants, and a pathway for glutathione-mediated detoxification. This is also the first release of MetaCyc that incorporates metabolically engineered pathways. The engineered pathways describe the production of hydrogen and hexanol, and the synthesis of long chain fatty acid esters. The engineered pathways in MetaCyc have been clearly marked as such, to distinguish them from natural pathways.
  • EcoCyc [release notes] updates include new functions for membrane and periplasmic proteins, the addition of nearly one hundred new citations for inner membrane proteins, and the addition of several mechanisms by which RNA polymerase is regulated.
June. 8  BioCyc.org 15.1 Website
BioCyc.org 15.1 includes 1129 databases.
  • In MetaCyc [release notes] we curated new microbial biosynthetic pathways for antibiotics, a C30 carotenoid, a betaine lipid, CMP-legionaminate and demethylmenaquinol-8. New microbial degradation pathways focused on polymers that make up plant biomass. Others included degradation of L-rhamnose, sulfoacetaldehyde, S-methyl-5-thioadenosine and chlorogenic acid. We added seven new pathways for hydrogen production in different organisms. New archaeal pathways included the methylaspartate cycle, biosynthesis of archaeosine and 6-hydroxymethyl-dihydropterin diphosphate, and degradation of starch and xylose. We also added four vertebrate hormone biosynthetic pathways from HumanCyc. In plant secondary metabolite biosynthesis, pathways included scopoletin, sporopollenin, salidroside, sulfur volatiles, methylhalides, salicin and salicortin, salicylate glucosides, specific volatile esters, o-diquinones, and flavonoids. We also added pathways for oxidative cleavage of carotenoids, and cyanide detoxification. In plant primary metabolism new pathways included several for fatty acid biosynthesis, as well as pinitol, adenosine 5-phosphoramidate, laminaribiose, and callose. We added new chloroplast pathways for the early stages of starch granule degradation and two enzymatic mechanisms for detoxifying reactive carbonyl compounds. We also updated 12 microbial and plant pathways with new information.
  • EcoCyc [release notes] has been extensively updated, with the addition of three new metabolic pathways, new functions for several membrane and periplasmic proteins, and corrections to many transcription factors and their binding sites.
  • In HumanCyc [release notes] we have completed our flux balance analysis model building project, which has resulted in a more complete metabolic network. We have filled gaps in pathways by adding reactions from the MetaCyc database, better defined directionality for some reactions, balanced reactions and instantiated compound classes. From a basal nutrient set the network is able to produce a complex biomass including many membrane lipids and steroid hormones. We have also added 16 human pathways from MetaCyc.
Mar. 18  BioCyc.org 15.0 Website
BioCyc.org 15.0 includes 1129 databases.
  • EcoCyc [release notes] updates include several key targets for β-lactam antibiotics among the peptidoglycan synthesizing enzymes, a pathway to degrade cinnamate and 3-hydroxycinnamate, and the addition of new consensus sequences for 45 transcription factors.
  • In MetaCyc [release notes] we curated new microbial pathways for inorganic sulfur and iron metabolism, oxalate degradation and degradation of several plant secondary metabolites. We also curated biosynthetic pathways for bacterial organic solutes, bacterial signaling compounds, microbial secondary metabolites and two pathways involving tRNA modification that are found in many organisms. A new animal pathway for thyronamine metabolism was also added and a dozen other pathways were updated. In plant metabolism we added new biosynthetic pathways for caffeoylglucarate, plaunotol, δ-guaiene, pterostilbene, and tartrate. New plant defense-related pathways included the breakdown of glucosinolates and the formation of the volatile (C16)-homoterpene TMTT. Updated plant pathways included biosynthesis of the (C11)-homoterpene DMNT and plant sterols.
  • With this release of HumanCyc, [release notes] we have begun work on the development of a flux balance analysis model. This has involved systematic reaction balancing, reaction direction resolution and compound instantiation. Preliminary FBA modeling has identified candidate reactions and pathways for propagation from MetaCyc to fill gaps in the HumanCyc metabolic network.
  • This release of BsubCyc [release notes] contains a number of updates to gene functions. In addition, the accidental deletion of a number of Gene Ontology terms has been corrected.


Dec. 3  BioCyc.org 14.6 Website
BioCyc.org 14.6 includes 1004 databases.
  • EcoCyc [release notes] has two new pathways, sedoheptulose biphosphate bypass and aerotactic two-component signal transduction. All the existing two-component pathways have been updated as well, along with the addition of a number of new structures for key transport proteins and the updating of curation for many transcription factors.
  • MetaCyc [release notes] 14.6 includes 55 new pathways, 13 newly revised pathways, and 9 new superpathways. Our additions to microbial metabolism include a reorganization and update of purine metabolic pathways (which are also found in higher organisms) and pathways for the synthesis and degradation of fluorinated organic compounds, fermentation in Clostridium acetobutylicum, manganese oxidation, and degradation of sulfonates and salicylates. We also added another pathway for the synthesis of coenzyme M, as well as biosynthetic pathways for alkanes by cyanobacteria, exopolysaccharides, salinosporamide A, spirilloxanthin, CDP-2-glycerol, rhamnolipids, polyhydroxydecanoate, and fungal fusicoccins. A new animal pathway was added for juvenile hormone III biosynthesis in insects. New plant pathways cover the biosynthesis of secondary metabolites including methylketones, labdane-type diterpenes, C-glycosylflavones, and O-methylation of tricetin. We also added three new salicylate glucosides biosynthesis pathways and two new biosynthetic pathways for the unusual fatty acids dicranin and sciadonate. In addition, we also updated the reactions in MetaCyc with the latest information from the NC-IUBMB, curated additional database links to KEGG reactions and compounds, and imported additional compound database links from PubChem.
  • With this release of HumanCyc, [release notes] we have added 107 new transport reactions and newly assigned more than 300 proteins to these transport activities. We have added literature citations, evidence codes and comments to many of these transport activities.
  • BsubCyc [release notes] now contains Gene Ontology term assignments imported from UniProt. We added more than 29,000 GO annotations, which are largely based on computational evidence.


Oct. 1  BioCyc.org 14.5 Website
BioCyc.org 14.5 includes 1004 databases.
  • EcoCyc [release notes] changes include an extensive updating of two-component pathways, with the majority now showing correct localization of components and an intuitive depiction of their phosphotransfer reactions. RNases have been similarly updated to have significantly more accurate and comprehensible reactions, along with the addition of a new pathway covering tRNA processing.
  • MetaCyc [release notes] 14.5 includes 56 new pathways, 8 newly revised pathways, and 4 new superpathways. Additions to microbial metabolism include pathways from a wide variety of fields. Some highlights include oxygen producing pathways, biotin, spermidine, norspermidine and chromobactin biosynthesis, and diphenylamine, aniline, phenylethylamine, carbazole and caffeine degradation. Similarly, new plant pathways cover many different fields. Some of these describe lychnose biosynthesis and degradation, plastidial p-aminobenzoate biosynthesis, petivericin, phloridzin, juvenile hormone III and glutamine biosynthesis, brassinosteroid hormones inactivation, caffeine degradation, and recycling of the prenyl tag from farnesylated proteins. In animal metabolism we added several pathways that describe the biosynthesis and degradation of the important glycosaminoglycans dermatan sulfate, chondroitin sulfate, and heparan sulfate.
  • HumanCyc [release notes] automated and manual updates are continuing; the database now includes all genes and proteins from the Uniprot Complete Proteome for H. Sapiens . We have updated Uniprot and EntrezGene links and have created and curated lipid and proteoglycan metabolic pathways.
  • BsubCyc [release notes] now contains links to GenoList and the STRING protein interaction network database. The representation of riboswitches has been improved.


June. 16  BioCyc.org 14.1 Website
BioCyc.org 14.1 includes 673 databases.
  • EcoCyc [release notes] EcoCyc updates include two new signal-transduction pathways and three new catabolic pathways.
  • MetaCyc [release notes] In this release of MetaCyc we added 67 new pathways and significantly revised 37 pathways, for a total of 104 new and updated pathways. In microbial metabolism we added numerous pathways describing the biosynthesis or degradation of a large variety of compounds. One of the main topics in microbial metabolism during this release was peptidoglycan biosynthesis. We now cover more details of this important process, such as amidation of L-glutamate residues in the pentapeptide component, formation of cross-bridges, and trans-peptidation. We added new variants that describe peptidoglycan biosynthesis in important pathogens among the staphylococci, mycobacteria and enterococci, as well as new pathways that explain the nature of resistance to antibiotics that interfere with peptidoglycan synthesis such as vancomycin and teicoplanin. New plant pathways cover the metabolism of plant defense compounds, signaling compounds, polyamines, fatty acids and sphingolipids. Of note are six monoterpene biosynthesis pathways whose products are used in cosmetic fragrances and as food additives. Last, but not least, are a few animal pathways, including the degradation of hemoglobin by the malaria parasite Plasmodium, the biosynthesis of diphthamide, and the biosynthesis of certain melanin pigments.
  • HumanCyc [release notes] curation continues in conjunction with the Pharmacometabolomics Research Network (PMRN). This is a multi-year collaboration to develop tools and provide resources for the metabolomics community; to this end we have focused on curation of information from the scientific literature concerning chemical compoundsand enzymes of interest to the PMRN and the larger field of metabolomics. For this release, we have curated metabolic pathways for vitamins, ingested nutrients and energy regulation.
  • BsubCyc [release notes] now includes data on transcriptional regulation that was imported from DBTBS. Orthologs for B.subtilis genes have been included in this release, enabling use of all comparative analysis tools.


Mar. 18  BioCyc.org 14.0 Website
BioCyc.org 14.0 includes 505 databases.
  • EcoCyc [release notes] EcoCyc updates include one new metabolic pathway and a new signaling pathway, as well as updates to a selection of transport proteins and cytochrome c biogenesis proteins, and coverage of the transcription initiation literature through the end of 2009.
  • MetaCyc [release notes] includes 41 new pathways, 12 newly revised pathways, and 3 new superpathways. Areas that received special attention in microbial metabolism include biosynthesis of bacterial siderophores, acetoin and butanediol metabolism and biosynthesis of the mycobacterial cell wall. New plant pathways focused on secondary metabolism and include biosynthesis of 4-hydroxycoumarin and degradation of ginsenosides. Additions in mammalian metabolism include pathways for ascorbate biosynthesis and the degradation of tocopherol and melatonin.


Nov. 21  BioCyc.org 13.6 Website
BioCyc.org 13.6 includes 506 databases [list of new DBs].
  • EcoCyc [release notes] continues to update entries for transcription factors, metabolic enzymes, and membrane proteins to include new data and new functions.
  • In MetaCyc, [release notes] we added 43 new pathways and significantly revised 8 pathways, for a total of 51 new and updated pathways. A few highlights of the additions include the following: In eukaryotic metabolism, several pathways for the metabolism of inositol phosphates and phosphatidyl-inositol phosphates. In plant metabolism, pathways for the biosynthesis of echinatin, coumestrol, flavonol glucosides, dehydroscoulerine, camptothecin,and phaselic acid. In prokaryotic metabolism, pathways for the degradation of several lignin-derived compounds, including syringate, ferulate, vanillin, vanillate, 5,5'-dehydrodivanillate and guaiacylglycerol-β-guaiacyl ether; pathways for biosynthesis of the indolocarbazole alkaloids rebeccamycin, K-252 and staurosporine, and pathways for the biosynthesis of archaebacterial phospholipid building blocks.


Oct. 08  BioCyc.org 13.5 Website
BioCyc.org 13.5 includes 505 databases [list of new DBs].
  • In EcoCyc [release notes] we added two new metabolic pathways and the DpiAB two-component signal transduction pathway. New functions for a number of protein complexes were discovered, including two new ATP binding cassette (ABC) transporters for phospholipids and lipopolysaccharides, a membrane-bound selenate reductase and a periplasmic aldehyde ferredoxin oxidoreductase.
  • In MetaCyc, [release notes] 72 pathways were added or updated for a total of 1,400 pathways.


Oct. 13  Version 13.5 of Pathway Tools
We announce the release of Version 13.5 of Pathway Tools software.

Significant developments:

  • New Omics data analysis and graphing capabilities in desktop Pathway Tools
  • Regulatory Overview now available in Web mode
  • Quick search enhancements in Web mode
  • New toolbar commands to find current object in other databases in Web mode
  • Uniprot protein feature import tool in desktop Pathway Tools

Version 13.5 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

June. 22  BioCyc.org 13.1 Website
BioCyc.org 13.1 includes 507 databases [list of new DBs].
  • EcoCyc [release notes] has been updated with 4 new metabolic pathways, a number of membrane and transporter updates, and 18 newly identified small proteins. Summaries have been completed for all transcription factors that have at least one experimentally characterized site or interaction, and evidence codes and references have been added to all 210 manually curated promoters.
  • In MetaCyc, we added 56 new pathways [release notes] and revised 10 more, for a total of 66 new and updated pathways.In prokaryotic metabolism we added many new archaeal pathways. We also added several pathways for biosynthesis of bacterial auto-inducer compounds and significantly expanded our coverage of degradation of chloro-substituted aromatic compounds. In animal metabolism, we added new biosynthetic pathways, including pathways for dolichol and dolichyl-phosphate, creatine-phosphate, histamine and CMP-sialic acid derivatives. In plant metabolism we curated pathways for biosynthesis of the plant hormones indole-3-acetyl amino acids, jasmonyl amino acids and hydroxyjasmonate sulfate, as well as the flavonoids quercetinsulphates, chrysoeriol and luteolin glycosides. In addition, we added pathways for thiamine (vitamin B1) biosynthesis, serine racemization and calamenene terpenoid biosynthesis.


Mar. 9  BioCyc.org 13.0 Website
BioCyc.org 13.0 includes 409 databases [list of new DBs].
  • EcoCyc [release notes] now allows full-text searching of 24,000 articles and 6,000 abstracts via the Textpresso search tool. Other curation is ongoing, with recent additions including proteins that were recently identified as playing major roles in maintaining cell shape and composition.
  • This update of MetaCyc [release notes] introduces 92 new pathways, covering diverse metabolic fields. Of note are the much expanded coverage of chloro-aromatic compound degradation, and a new pathway for mycolic acid biosynthesis in the human pathogen Mycobacterium tuberculosis H37Rv. We have also revised 17 existing pathways by adding commentary and updated enzyme and gene information, for a total of 109 new and updated pathways.


Mar. 11  Version 13.0 of Pathway Tools
We announce the release of Version 13.0 of Pathway Tools software.

Significant developments:

  • The Web interface of Pathway Tools has undergone a major upgrade.
  • Pathway Tools is now able to import and export data using the BioPAX Level 3.0 standard.
  • Pathway Tools now includes a tool that performs reachability analysis of the metabolic network within a PGDB.

Version 13.0 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

2008

Oct. 16  Version 12.5 of Pathway Tools
We announce the release of Version 12.5 of Pathway Tools software.

Significant developments:

  • Tips system.
  • New tools for propagating MetaCyc updates to other PGDBs.
  • Ability to customize pathway diagrams for PowerPoint or publications.
  • Enhancements to Structured Advanced Query Form and Regulatory Overview.
  • Graph tracks for ChIP-chip data.

Version 12.5 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

Oct 15   BioCyc.org 12.5 Website
BioCyc.org 12.5 includes 376 databases [list of new DBs]. EcoCyc release [release notes] EcoCyc has undergone a significant revision that lets us display electron transfer pathways including correct localization of reactions and proton transport across the membrane. 11 new electron transfer pathways show off these new features, along with the usual crop of updated gene functions, other new metabolic pathways, enhanced curation of cell surface components, and other updates. In MetaCyc [release notes] In MetaCyc we added 72 new pathways and significantly revised 7 pathways for a total of 79 pathways. Of the new pathways, 12 were contributed by curators at http://plantcyc.org and 2 were contributed by Cynthia Krieger at http://pathway.yeastgenome.org/biocyc/. New microbial pathways added include more detailed coverage of fatty acid biosynthesis and new pathways for the biosynthesis of trehalose, acetoin, L-asparagine, butanediol, CDP-diacylglycerol, glycine betaine, molybdopterin guanine dinucleotide, aflatoxins, geosmin, rifamycin B and gramicidin S. We also added pathways for nitrate assimilation in cyanobacteria and the degradation of sulfoacetaldehyde. In plant metabolism we continued to enhance our coverage of secondary metabolites, including the biosynthesis of thalianal, marneral, baruol, arabidiol, apigenin, sorgoleone, furaneol, cinnamate esters and acridone alkaloids. We also added pathways for the degradation of lotasutraline, amygdalin, prunasin, and dhurrin. Plant pathways of primary metabolism added include the biosynthesis of xylogalacturonan, crepenynic acid, vernolic acid, nicotianamine and lupinate. We also added a plant wound healing and defense pathway, and transport pathways for nicotianamine, and ammonia.

June 27   BioCyc.org 12.1 Website
BioCyc.org 12.1 includes 371 databases [list of new DBs]. EcoCyc release [release notes] includes the usual wide range of updates covering topics as diverse as peptidoglycan metabolism and DNA repair, as well as a new collection of 259 experimentally verified novel transcription start sites. In MetaCyc [release notes] we added 101 new pathways and significantly revised 13 pathways for a total of 114 new and revised pathways. Highlights among the new microbial pathways added include enhanced coverage of the biosynthesis of quinones, CDP-3,6-dideoxyhexoses and secondary metabolites. In plant metabolism we continued to expand coverage of the biosynthesis of secondary metabolites that have applications in medicine and industry. Plant pathways of primary metabolism added include the biosynthesis of cell wall polysaccharides, wax esters, hypusine and homospermidine. We also added pathways of auxin metabolism, phytosiderophore production and iron chelation and transport.

Apr 1   BioCyc.org 12.0 Website
BioCyc.org 12.0 includes 371 databases [list of new DBs]. In EcoCyc [release notes], we added more than 1000 GO term assignments with experimental evidence codes and approximately 30,000 GO term assignments with computational evidence codes from UniProt, now covering more than 80% of the gene products of E. coli. Updates were made to approximately 40 membrane, transporter, and membrane structure-related proteins . In MetaCyc [release notes] we added 51 new pathways and significantly revised 15 pathways for a total of 66 new and revised pathways. Highlights among the new microbial pathways added include a newly discovered autotrophic CO_2 fixation pathway and pathways in the areas of xenobiotic degradation and antibiotic biosynthesis. New plant pathways include the Rubisco shunt and biosynthesis of a variety of secondary metabolites, many of which have potential applications in medicine and agriculture. We also updated the reactions in MetaCyc by incorporating supplement 13 from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology.

Apr. 1  Version 12.0 of Pathway Tools
We announce the release of Version 12.0 of Pathway Tools software.

Significant developments:

  • Macintosh Port.
  • New multi-platform installer.
  • New tracks mechanism for ChIP-chip data.
  • NCBI Taxonomy integrated into Pathway Tools.
  • Wed accounts system.
  • Incorporation of genome annotation updates.

Version 12.0 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

Dec. 06  BioCyc.org 11.6 Website
BioCyc.org 11.6 includes 371 databases [list of new DBs]. In EcoCyc [release notes], the EC-to-GO mapping has been used to assign GO terms to all enzymes with EC numbers. In addition, transcriptional initiation is now up-to-date across the entire database, and a number of transporters and metabolic pathways have been updated. In MetaCyc [release notes] we added 79 new pathways and significantly revised 30 additional pathways since the last release. Major additions include a much better coverage for the microbial degradation of nitroaromatic compounds, the metabolism of urate and allantoin, and acetate fermentations. We also added pathways for the biosynthesis of bacteriochlorophyll a, several GDP-sugars, the compatible solutes glucosyl- and mannosyl-glycerate, the enzyme cofactor tetrahydrobiopterin, and several naturally occurring β-lactam antibiotics, among others. In plant metabolism, we curated six new secondary metabolic pathways, covering the biosynthesis of linalool, vanilla, steroidal glycoalkaloid, taxol and ginsenoside, and the degradation of cysteine sulfoxides.

Aug. 15  BioCyc.org 11.5 Website
BioCyc.org 11.5 includes 371 databases [list of new DBs]. Changes in EcoCyc [release notes] include the addition of newly predicted genes, one new metabolic pathway, several updated "classic" pathways, and updates to the representation of the ArcA response regulator and its binding sites. In MetaCyc [release notes] we added 10 new pathways since the last release, and significantly revised 5 existing pathways, for a total of 15 new and updated pathways. We updated our coverage of the biosynthesis of adenosylcobalamin (vitamin B12), one of the most structurally complex small molecules made in nature. We added pathways for biosynthesis of the important vitamin L-ascorbate (vitamin C) in bacteria and in mammals, a pathway for the biosynthesis of the amino sugar donor UDP-N-acetyl-D-galactosamine, pathways for degradation of the pentose sugars arabinose and xylose, and a pathway for degradation of the sugar acid glucuronate.

May. 25  BioCyc.org 11.1 Website
BioCyc.org 11.1 includes 261 databases [list of new DBs]. Updates continue in EcoCyc [release notes], including the addition of 6 new metabolic pathways, updates of many classic biosynthetic pathways, updates to 43 membrane and transport-related proteins, and the addition of GO and MultiFun terms to all transcription factors. In MetaCyc [release notes], we added 39 new pathways since the last release, and significantly revised 31 existing pathways. We also created 1 new superpathway, for a total of 71 new and updated pathways. New microbial pathways cover many different fermentations, the metabolism of the amino acids glutamate, glutamine, aspartate and asparagine, the degradation of the pesticide parathion and related compounds, the metabolism of the vitamins B6 and B12 and many additional topics. New plant pathways focused on the biosynthesis of alkaloids, hydroxycinnamic acid amides, and phenylpropenoids.

Mar. 22  BioCyc.org 11.0 Website
BioCyc.org 11.0 includes 260 databases [list of new DBs]. EcoCyc [release notes] updates include revisions and enhancement of major pathways such as glycolysis, curation of transcriptional regulatory genes involved in nitrogen metabolism, and updating of a number of protein functions based on a complete genome reannotation performed by the Paulsen group at TIGR. In MetaCyc [release notes], we have added 47 new pathways since the last release, and significantly revised 26 existing pathways. We also created 12 new superpathways, for a total of 85 new and updated pathways. New microbial pathways include the degradation of methylglyoxal, acetone, benzene, catechol, xylene, naphthalene, phenol and threonine, and the biosynthesis of aminopropanol and aminopropanoil phosphate. New plant pathways include the metabolism of betalains, a reconstruction of the lipoxygenase (LOX) pathway, biosynthesis of oleoresin compounds, and a number of new pathways concerning various compound classes, such as terpenoids.

Mar. 23  Version 11.0 of Pathway Tools
We announce the release of Version 11.0 of Pathway Tools software.

Significant developments:

  • New Genome Overview.
  • New Regulatory Overview.
  • Catalytic domain protein feature.
  • Automatic patch loading.
  • Metabolite tracing.
  • New BioVelo Query Language (Web mode only).

Version 11.0 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

Jan. 10  BioCyc.org 10.6 Website
BioCyc.org 10.6 includes 261 databases [list of new DBs]. EcoCyc [release notes] changes include updated evidence codes for a large number of proteins, updated curation for flagellar proteins, transporters and membrane proteins, prediction of transcription units for genes that were not part of existing transcription units, and extended notes for a number of regulatory proteins. In MetaCyc [release notes], we have added 93 new pathways since the last release, and significantly revised 32 existing pathways, for a total of 125 updated pathways. New microbial pathways include homocysteine and siroheme amide biosynthesis, nitroethane degradation, and variants of carbon disulfide oxidation, carbon tetrachloride degradation, hydrogen oxidation, lysine and sucrose degradation, and the reductive TCA cycle.

2006

Sept. 18  BioCyc.org 10.5 Website
BioCyc.org 10.5 is now available. EcoCyc [release notes] has reached a major curation milestone of having manual curation for all gene products. This release also adds two new metabolic pathways and 364 new single-gene transcription units. In MetaCyc [release notes],we added 44 new pathways since the last release, and significantly revised 24 existing pathways, for a total of 68 updated pathways. New Microbial pathways include the biosynthesis of cell components such as tetrapyrroles, lipids and peptidoglycan, and the degradation of several aromatic compounds. In addition, we significantly expanded our coverage of methanogenesis. New plant pathways include acetyl-CoA biosynthesis, mitochondrial membrane lipid cardiolipin biosynthesis, activation of the secondary metabolite glucosinolate, biosynthesis of the alkaloid morphine, the anthocyanin salvianin, the phenylpropenoids ferulate, sinapate and coumarin, and the terpenoids artemisinin and saponin.

Sept. 12  Version 10.5 of Pathway Tools
We announce the release of Version 10.5 of Pathway Tools software.

Significant developments:

  • Ability to generate metabolic map poster.
  • Ability to generate genome poster.
  • Ontology upgrade for signaling interactions.
  • New reaction editor.
  • Consistency checker.
  • Sequence retrieval tools.

Version 10.5 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

May. 19  BioCyc.org 10.1 Website
BioCyc.org 10.1 is now available. EcoCyc [release notes] highlights include new links to protein information at MODBASE and Swiss-Model, updated Uniprot links, extensive curation additions, including all 82 tRNAs, many other proteins and several updated or new pathways, and continued curation of the pathogenic E.coli O157:H7. In MetaCyc [release notes], 47 new pathways were added since the last release, and 21 pathways have been significantly revised, for a total of 68 updated pathways. Additions in microbial metabolism include variants of the tricarboxylic acid (TCA) cycle, glycolysis, pyruvate fermentation, new amino-acid biosynthesis and degradation pathways, 2-oxobutanoate degradation, and 2-methylbutyrate biosynthesis. Additions in plant metabolism include new pathways for the biosynthesis of geranyl diphosphate, geranylgeranyl diphosphate and trans, trans-farnesyl diphosphate, ascorbate, aurone, coenzyme A, isoflavonoid, wighteone and luteone, and several anthocyanins, as well as new pathways for the degradation of chlorophyll and triacylglycerol, NAD/NADH phosphorylation and dephosphorylation, and sulfate assimilation. In addition, the reactions in MetaCyc were updated with the latest information (as of February 2006) from NC_IUBMB, by incorporating supplement 11.

Mar. 13  BioCyc.org 10.0 Website
BioCyc.org 10.0 is now available. EcoCyc [release notes] highlights include updates to genes and gene boundaries to match the most recent revised E. coli annotation, addition of Gene Ontology terms in EcoCyc gene pages, additional links to databases such as EchoBASE and PDB, extensive curation of the the pathogenic O157:H7 strain PGDB, and continued curation of functional areas such as transcriptional regulation, and DNA replication and repair. In MetaCyc [release notes], 47 new pathways were added since the last release, and 15 pathways have been significantly revised, for a total of 62 updated pathways. Curated areas for microbial pathways include mostly the degradation of various amino acids and of nicotinate. New plant pathways cover many topics, including biosynthetic pathways of both primary and secondary metabolism.

Mar. 16  Version 10.0 of Pathway Tools and the BioCyc Database Collection
We announce the release of Version 10.0 of the BioCyc databases and Pathway Tools software.

Significant developments:

  • Pathway Tools now provides display,editing, and schema support for Gene Ontology.
  • New author crediting system.
  • Improvements to relational database support.
  • New Auto-checkpointing of PGDB updates.

Version 10.0 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

In addition to EcoCyc [release notes] and MetaCyc [release notes] updates, the Pathway Tools software has been enhanced.

2005

Dec. 15  BioCyc.org 9.6 Website
BioCyc.org 9.6 is now available. EcoCyc [release notes] highlights include the addition of two new pathways, Gene Ontology (GO) classifications to gene pages, many updated and expanded annotations, curation of genes for RNA degradation, processing, DNA replication, and many curation updates to polypeptides. In MetaCyc [release notes], a total of 117 pathways have been curated. Curated areas include nitrogen, thiol, amino acid metabolism, arsenic detoxification, degradation of natural and xenobiotic compounds. In plant metabolism, 52 pathways are new, and 3 pathways were updated.

Dec. 1  BioCyc.org 9.5 Website
BioCyc.org 9.5 is finally available. Highlights: The BioCyc Database Collection now contains a database for each of 204 organisms, up from 162 organisms six months ago and 17 organisms twelve months ago. Pathway holes have been filled and operons have been predicted in most of these pathway/genome databases. MetaCyc [release notes] contains updated EC reactions, a new cellular location ontology, and 30 more pathways and 724 more chemical structures than in the May 2005 release. New features in the Pathway Tools software which runs the BioCyc web site are listed in the following news item.

Sep. 30  Version 9.5 of Pathway Tools and the BioCyc Database Collection
We announce the release of Version 9.5 of the BioCyc databases and Pathway Tools software.

Significant developments:

  • User-created pathway/genome databases can now be stored in a MySQL 4 database.
  • PathoLogic and the Editors are now included on Windows 2000 and Windows XP.
  • New comparative analysis capabilities, including a comparative genome browser, and summary tables that compare various attributes across a set of selected organisms.
  • The Web versions of the Cellular Overview Diagram and the Omics Viewer have been enhanced to include magnified individual pathway images and navigation menus.
  • PathoLogic now infers transport reactions from text description in the genome annotation.

Note that neither these new software features nor any data updates appear on the BioCyc.org website yet. Unveiling of the updated website, including data updates, will be delayed for another week or two.

Version 9.5 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

In addition to EcoCyc [release notes] and MetaCyc [release notes] updates, the Pathway Tools software has been enhanced.

May 23  BioCyc.org 9.1 Website
BioCyc.org 9.1 is now available. Highlights: EcoCyc [release notes] has reached a milestone: it now contains citations to over 10,000 peer-reviewed publications. MetaCyc [release notes] contains 62 more pathways than in the previous release 3 months ago. The 22-step cholesterol biosynthesis pathway, supported by over 40 literature citations, has been added to HumanCyc [release notes] .

Feb. 28  Version 9.0 of Pathway Tools and the BioCyc Database Collection
We announce the release of Version 9.0 of the BioCyc databases and Pathway Tools software.

Significant developments:

  • The BioCyc database collection at BioCyc.org includes 142 new databases, bringing the collection to 162 total databases

  • A new horizontal genome browser is available for use with all organism databases

  • Operon depiction in gene pages has been improved

  • Our pathway layout algorithms have been improved to produce more compact pathway displays

The big news in this release is that 142 new databases have been added to the Web version of the BioCyc collection as a result of a collaboration between the Karp group at SRI International and the Ouzounis group at the European Bioinformatics Institute. The new databases include most sequenced prokaryotic and eukaryotic genomes, and include predicted metabolic pathways and operons (for bacteria). For more details click here. However, note that the new databases are currently available only through the BioCyc.org Web site, and are not yet available for local download either as data files, or in conjunction with Pathway Tools. We are seeking funding to remedy this situation.

Version 9.0 is a major release, meaning this version includes a new version of the downloadable software/database bundle that couples Pathway Tools with the BioCyc collection.

In addition to EcoCyc [release notes] and MetaCyc [release notes] updates, the Pathway Tools software has been enhanced.

Feb. 28  142 New BioCyc PGDBs
A joint effort by the groups of Peter Karp at SRI International and Christos Ouzounis of the European Bioinformatics Institute has expanded the BioCyc database collection to 162 members, including most fully sequenced prokaryotic and eukaryotic genomes.

The new databases were generated by the PathoLogic program, which predicted their metabolic pathways and their operons (bacteria only). [list of new PGDBs]

The new databases are available for adoption [more] for curation and updating by interested scientists. No one group can curate all the world's genomes. Our goal is to see experts in different organisms work together to update the description of each organism's genome and biochemical network to produce an up-to-date information repository about each organism.

Feb. 28  Release of BioCyc Open Chemical Database
The BioCyc Open Chemical Database (BOCD) is a collection of chemical compound data from the BioCyc databases. Most of the compounds act as substrates in enzyme-catalyzed metabolic reactions, but some compounds serve as enzyme activators, inhibitors, or cofactors. Chemical structures are provided for the majority of compounds. The compounds include extensive lists of synonyms, and have undergone several types of quality control, including validation by a reaction-balance checker applied to the BioCyc databases.



2004

Nov. 9  BioCyc.org 8.6 Website
BioCyc.org 8.6 is now available. EcoCyc [release notes] and MetaCyc [release notes] have been updated. EcoCyc now contains an updated genome sequence, as described in the release notes.

Sep. 17 BioCyc 8.5 and Pathway Tools 8.5 Released
BioCyc 8.5 and Pathway Tools 8.5 have been released to licensees and updated on the BioCyc.org web site. A Bacillus anthracis database has been created for the BioCyc collection. In addition to EcoCyc (E. coli database) and MetaCyc (metabolism database) updates, enhancements have been made in the Cellular Overview, the Omics Viewer, the Pathway Hole Filler, the handling of chemical structure diagrams, and several other areas of Pathway Tools.

Sep. 17 Pathway Tools and BioCyc Online Licensing Pathway Tools and BioCyc licensing, which formerly required a paper license agreement, are now processed entirely online at http://BioCyc.org/download.shtml

Jul. 13 Green and Karp paper on Pathway Hole Filling algorithm available
A recent paper in BMC Bioinformatics describes an algorithm first present in version 8.0 (Mar 2004) of Pathway Tools for finding candidate genes that code for unidentified enzymes in metabolic pathways in Pathway/Genome Databases. See http://www.biomedcentral.com/1471-2105/5/76 .

Jul. 13 New MetaCyc Web Site
The web site describing the MetaCyc database of metabolic pathways and enzymes has been expanded and redesigned to provide extensive information about MetaCyc, such as about its curation procedures and usage. The expanded Web site is available at URL http://MetaCyc.org/ .

Jul. 1  BioCyc.org 8.1 Website
BioCyc.org 8.1 is now available. EcoCyc [release notes] and MetaCyc [release notes] have been updated.

May  18  EcoCyc is now an open database.
  1. The EcoCyc database is now freely available to all users in all institutions, commercial and non-commercial.
  2. The EcoCyc database may be redistributed in whole or in part, with or without applied modifications.

Note that the EcoCyc database is still made available under an SRI license agreement that is similar to an open-source license agreement. Please see the terms of that agreement.

To download the EcoCyc database, please see URL http://biocyc.org/download.shtml and click-through the open-access license agreement to obtain the database.

Apr. 13  PlasmoCyc has Moved
The home page and a few other pages of the Plasmodium falciparum database PlasmoCyc are still hosted by Stanford, but the database itself is now part of the BioCyc Database Collection. The search page is here.

Apr. 13  PseudoCyc has Moved
PseudoCyc has moved out of the BioCyc Database Collection and into the Pseudomonas Genome Project.

Mar. 31  BioCyc 8.0 and Pathway Tools 8.0 Released
BioCyc 8.0 and Pathway Tools 8.0 have been released to licensees. Databases for Human, E. coli O157:H7, and Shigella flexneri are now part of the locally installable version of BioCyc. In addition to EcoCyc (E. coli database), MetaCyc (metabolism database), and HumanCyc updates, new features include (1) a pathway-hole filler that has been added to the PathoLogic pathway-prediction component of Pathway Tools and (2) built-in database-sharing capability.

2003

Nov. 7  E. coli O157:H7 and Shigella flexneri Databases
EcoO157Cyc and ShigellaCyc are the newest databases in the BioCyc collection, bringing the number of E. coli databases in the collection to three. Ongoing work will compare strains K12, O157:H7, and Shigella. Currently available only on the biocyc.org website or as a set of flat files, the two new databases will be available as part of the BioCyc software/database bundle in February.

Nov. 4  BioCyc.org 7.6 Website
BioCyc.org 7.6 is now available. It includes two new E. coli databases: EcoO157Cyc and ShigellaCyc. In addition, EcoCyc, MetaCyc, CauloCyc, VchoCyc, MtbRvCyc, MtbCdcCyc, and HumanCyc have been updated. (Note: Local installations of HumanCyc are currently available only through purchased subscriptions.)

Aug. 29  BioCyc 7.5 Released
BioCyc 7.5 and Pathway Tools 7.5 have been released to licensees. In addition to EcoCyc (E. coli database) updates and MetaCyc (metabolism database) updates, new features include references, which link to abstracts, at the bottom of each page, an improved pathway class hierarchy, and a new evidence classification system. The Carnegie Institution has released a Java API to Pathway Tools.

May 27  HumanCyc, Encyclopedia of Human Genes and Metabolism
HumanCyc is now browsable at http://HumanCyc.org. Local installations of HumanCyc are currently available only through purchased subscriptions. Contact for more information.

May 27  BioCyc.org 7.1 Website
BioCyc.org 7.1 is now available. EcoCyc, MetaCyc, CauloCyc, VchoCyc, and MtbRvCyc have been updated, and HumanCyc is being introduced. (Note: Local installations of HumanCyc are currently available only through purchased subscriptions.)

Mar. 5  BioCyc 7.0 Released
BioCyc 7.0 and Pathway Tools 7.0 have been released to licensees. The offerings that had been available for Sun Solaris are now available for Linux too (except for the Oracle option). In addition to EcoCyc (E. coli database) updates and MetaCyc (metabolism database) updates, new features include support for alternative splice forms, the option to display external gene web pages instead of BioCyc gene web pages, and Significance Analysis of Microarrays (SAM).

Feb. 10  SRI International Announces HumanCyc, a Genome-Derived Database of Human Metabolism
Click here to see the full announcement.

2002

Nov. 12  Click-Through Licensing of BioCyc Flat File Databases
SRI now offers a faster way to obtain a license for the BioCyc flat file databases. In some cases, a license agreement can be obtained and approved online in a matter of minutes. See the Flat File section of the Download page for more information.

Sep. 27  Pathway Tools Grant Awarded
SRI's Bioinformatics Research Group (BRG) has received a grant from the NIH National Human Genome Research Institute to support further development of the Pathway Tools software that underlies the BioCyc databases. The grant will also allow the BRG to provide support services to Pathway Tools users outside SRI to assist them in developing new pathway/genome databases for other organisms.

Aug. 30  BioCyc 6.5 Released
BioCyc 6.5 and Pathway Tools 6.5 have been released to licensees. In addition to EcoCyc (E. coli database) updates and MetaCyc (metabolism database) updates, new features include a Perl-based query API, expression time series animation on metabolic charts, and importing Stanford Microarray Database (SMD) expression data onto metabolic charts.

Aug. 30  New M. tuberculosis CDC1551 Database
A new database for the CDC1551 strain of Mycobacterium tuberculosis, made available today, now complements the M. tuberculosis H37Rv database, which has been available since April. An ongoing task is to determine which differences between the two databases indicate actual differences between the two strains. Both databases are joint work with Dr. Gary Schoolnik of Stanford University.

May. 28  BioCyc story in Wired News
Wired News ran a story today on BioCyc (a.k.a. EcoCyc) and Pathway Tools.

Apr. 23  New BioCyc Website
The BioCyc website replaces what was formerly called the EcoCyc/MetaCyc website. The new BioCyc site includes the EcoCyc and MetaCyc databases. The design of BioCyc emphasizes BioCyc as a growing collection of many Pathway/Genome Databases.

Apr. 23  BLAST Search
BLAST searches can now be performed from the BioCyc query page. A user can submit a sequence for searching against any of the genomes in BioCyc.

Apr. 23  New Improved M. tuberculosis Database
BioCyc contains a new pathway/genome database for the H37Rv strain of Mycobacterium tuberculosis. This new database contains 144 pathways, a significant improvement over the previous M. tuberculosis database for the same strain, which had 105 pathways. This database is joint work with Dr. Gary Schoolnik of Stanford University.

Apr. 23  All-new V. cholerae Database
A new pathway-genome database for Vibrio cholerae is now available through BioCyc. This database is joint work with Drs. Gary Schoolnik and Alfred Spormann of Stanford University.

Apr. 20  Outdated EcoCyc URLs
With the closure of DoubleTwist Corporation, domain names (listed below) that used to provide access to EcoCyc are no longer functional. If you maintain a website that contains hyperlinks to EcoCyc, please update them to point to EcoCyc.org.
  • Outdated: EcoCyc.DoubleTwist.com
  • Outdated: EcoCyc.PangeaSystems.com
  • Outdated: EcoCyc.PanBio.com

  • Apr. 1  MetaCyc Grant Awarded to SRI and Carnegie Institution
    SRI's Bioinformatics Research Group has received a grant from the NIH National Institute of General Medical Sciences to continue developing the MetaCyc metabolic pathway database. The grant is joint work between SRI and the Department of Plant Biology at the Carnegie Institution of Washington. A group at Carnegie will be adding plant metabolic pathways to MetaCyc.