2123451 2009-10-31 10 1 324 1471-2105 http://www.biomedcentral.com/1471-2105/10/324/ KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database Software; Web-based applications; Metabolic pathway maps; KEGG Markup Language; Biomechanics The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes. eda2d9e9-34c5-11e1-b86c-0800200c9a66 759af938-34ae-11e1-b86c-0800200c9a66 2009-10-31T24:00:00 e601872f-4b7e-4d88-929f-7df027b226c9 40e90e2f-446d-460a-98e5-5dce57550c48 2009-10-31T24:00:00 df943548-c67e-4c96-8c4f-1c0aa144b1c0 4bdfc4ac-7c74-456d-9d3b-b1e4267b90a9 2009-10-31T24:00:00 19258084-7068-4be1-8cfd-171952060f0c 1332d166-4c65-481b-adde-aac0bdc475a3 2009-10-31T24:00:00 1123453 49815870-1cfe-11e1-8bc2-0800200c9a66 b7135ad0-1d00-11e1-8bc2-0800200c9a66 2009-10-01T00:00:00 3123451 eda28bc2-34c5-11e1-b86c-0800200c9a66 ad87a6e2-5093-4550-86da-ead48cc3f385 2009-10-31T24:00:00 8123451 eda28bc2-34c5-11e1-b86c-0800200c9a66 a7e0dc90-1be4-4fd9-9ff7-bdfb8a95a1eb 2011-05-31T24:00:00 4123452 98072417-c98b-46dc-99aa-364bb672cd63 e87469e5-d6bd-458c-b7ef-90e314749c51 2009-10-31T24:00:00 14123451 10.1186/1471-2105-10-324 2009-10-31T24:00:00 31d222b4-11e0-434b-b5ae-088119c51189 bccb3266-689d-4740-a039-c96594b4d916 5123451 eda2b2e2-34c5-11e1-b86c-0800200c9a66 5a270628-f593-4ff4-a44a-95660c76e182 5123452 eda2b2e2-34c5-11e1-b86c-0800200c9a66 5a270628-f593-4ff4-a44a-95660c76e182 14123452 10442/8849 2011-12-04T24:00:00 baaa59e1-745b-46e3-b068-aaa3dae9eef9 bccb3266-689d-4740-a039-c96594b4d916 5123453 eda2b2e2-34c5-11e1-b86c-0800200c9a66 5a270628-f593-4ff4-a44a-95660c76e182 5123454 eda2b2e2-34c5-11e1-b86c-0800200c9a66 5a270628-f593-4ff4-a44a-95660c76e182 2123452 2011-05-31 12 1 238 1471-2164 http://www.biomedcentral.com/1471-2164/12/238 Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of E. coli activates the expression of atoDAEB operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that atoSC is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the atoDAEB promoter as the single, cis-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the E. coli genome. eda2d9e9-34c5-11e1-b86c-0800200c9a66 759af938-34ae-11e1-b86c-0800200c9a66 2011-05-31T24:00:00 2038-12-31T24:00:00 e601872f-4b7e-4d88-929f-7df027b226c9 40e90e2f-446d-460a-98e5-5dce57550c48 2011-05-31T24:00:00 df943548-c67e-4c96-8c4f-1c0aa144b1c0 4bdfc4ac-7c74-456d-9d3b-b1e4267b90a9 2011-05-31T24:00:00 19258084-7068-4be1-8cfd-171952060f0c 1332d166-4c65-481b-adde-aac0bdc475a3 2011-05-31T24:00:00 2014-06-01T24:00:00 1123453 49815870-1cfe-11e1-8bc2-0800200c9a66 b7135ad0-1d00-11e1-8bc2-0800200c9a66 2011-05-31T24:00:00 2123451 eda28bc9-34c5-11e1-b86c-0800200c9a66 a7e0dc90-1be4-4fd9-9ff7-bdfb8a95a1eb 2011-05-31T24:00:00 7123451 eda28bc9-34c5-11e1-b86c-0800200c9a66 a7e0dc90-1be4-4fd9-9ff7-bdfb8a95a1eb 2010-04-01T00:00:00 4123452 98072417-c98b-46dc-99aa-364bb672cd63 e87469e5-d6bd-458c-b7ef-90e314749c51 2011-05-31T24:00:00 8123451 KEGGconverter KEGG; KGML; converter; metabolic pathways KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. 5b90f961-6489-4500-bb6a-5b60ead25a2d 759af938-34ae-11e1-b86c-0800200c9a66 2011-03-31T24:00:00 1123453 e4d7b130-1cfd-11e1-8bc2-0800200c9a66 b7135ad0-1d00-11e1-8bc2-0800200c9a66 2011-03-31T24:00:00 3123451 eda28bc2-34c5-11e1-b86c-0800200c9a66 ad87a6e2-5093-4550-86da-ead48cc3f385 2011-03-31T24:00:00 14123452 http://www.url.org/KEGGconverter/ 2011-12-04T24:00:00 baaa59e1-745b-46e3-b068-aaa3dae9eef9 bccb3266-689d-4740-a039-c96594b4d916 7123451 Alkali metal-containing, organometallic products organometallic products An alkali metal-containing, organometallic product, which is hydrocarbon-soluble, is prepared by reacting an organo-alkali metal reactant in which the alkali metal atom is bonded to a carbon atom, e.g. cyclohexyl-lithium, with a di(organooxy)-alkaline earth metal reactant, e.g. di-n-butoxy-magnesium, in an organic solvent at about -20° to +120°C. The organo-alkali metal reactant can be prepared by reacting an organo halide with an alkali metal, and this can be done in situ, i.e. in the presence of the di(organooxy)-alkaline earth metal reactant. The organometallic product has approximately the same chemical reactivity as the organo-alkali metal reactant from which it is prepared, but is more soluble in hydrocarbon solvents. 274e99d8-1e36-4b3e-a998-2a3384e79f64 759af938-34ae-11e1-b86c-0800200c9a66 2010-04-01T00:00:00 e601872f-4b7e-4d88-929f-7df027b226c9 40e90e2f-446d-460a-98e5-5dce57550c48 2010-04-01T00:00:00 1123453 e4d7b130-1cfd-11e1-8bc2-0800200c9a66 b7135ad0-1d00-11e1-8bc2-0800200c9a66 2010-04-01T00:00:00 5123451 CrossRef DOI prefix service The service of issuing DOI prefixes to publishers persistent identifier; Digital Object Identifier 5123452 BMC service The publisher service of issuing DOI suffixes to new articles persistent identifier; Digital Object Identifier 5123453 NHRF Repository The NHRF Repository produces suffixes to issue complete Handle identifiers new for new items persistent identifier; Handle 5123454 Handle System prefix service ">The service of issuing Handle system prefixes for use by third parties persistent identifier; Handle