Software and Databases Guide

The EnzymeML Software and Database Guide provides a summary of all EnzymeML-compatible software systems and databases currently available.

COPASI

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI is a versatile with powerful features for representing enzyme models, simulation, and data analysis, visulaization and output.

Reference

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. (2006) COPASI–a COmplex PAthway SImulator. Bioinformatics 22, 3067-74. DOI: 10.1093/bioinformatics/btl485

STRENDA-DB

STRENDA DB is a storage and search platform supported by the Beilstein-Institut that incorporates the STRENDA Guidelines in a user-friendly, web-based system. If you are an author who is preparing a manuscript containing functional enzymology data, STRENDA DB provides you the means to ensure that your data sets are complete and valid before you submit them as part of a publication to a journal. Data entered in the STRENDA DB submission form are automatically checked for compliance with the STRENDA Guidelines; users receive warnings informing them when necessary information is missing.

A successful formal compliance is confirmed by the awarding of a STRENDA Registry Number (SRN) and documented in a fact sheet (PDF) containing all input data that can be submitted with the manuscript to the journal. In addition, each dataset is assigned a DOI that allows reference and tracking of the data. The data become publicly available in the database only after the corresponding article has been peer-reviewed and published in a journal.

Reference

Swainston N, Baici A, Bakker BM, Cornish-Bowden A, Fitzpatrick PF, Halling P, Leyh TS, O’Donovan C, Raushel FM, Reschel U, Rohwer JM, Schnell S, Schomburg D, Tipton KF, Tsai MD, Westerhoff HV, Wittig U, Wohlgemuth R, Kettner C. (2018) STRENDA DB: enabling the validation and sharing of enzyme kinetics data. FEBS J. 285, 2193-2204. DOI: 10.1111/febs.14427

SABIO-RK

SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. It describes participants and modifiers of the reactions, as well as measured kinetic data (including kinetic rate equations) embedded in their experimental and environmental context. The system offers standardized data for metabolic and newly also signaling reactions by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. It enables the access to kinetic data for experimentalists and modellers. Thereby, SABIO-RK facilitates the exchange of the data between experimentalists and modellers, supporting the setup of quantitative computer models.

The data in SABIO-RK is either manually extracted from published literature or directly submitted by experimenters. It is curated by experts and supplemented with additional information from other databases and biological ontologies.

Reference

Wittig U, Rey M, Weidemann A, Kania R, Müller W. (2018) SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. Nucleic Acids Res. 46, D656-D660. DOI: 10.1093/nar/gkx1065