University of Leeds Department of Chemistry

1. University of Leeds Department of Chemistry The New MCM Website Stephen Pascoe, Louise Whitehouse and Andrew Rickard

2. Overview • Using the new MCMv3.1website Andrew • Features (Mark List, Browse, Search, Extract) • Other updates (Feedback) • Extraction into different formats Louise • FORTRAN and XML • Under the hood: Technical detail Stephen • IT perspective • Design decisions • MCM development platform (access/accord database - MySQL database) • Contextual information - reaction categories

3. The New MCM Website: Improvements • Updated to McMv3.1 (including Box and PTM models) • Improve User Experience: • Better navigation • Search/Extract tools • Simplify update and maintenance: • More integrated data representation • Facilitate inclusion of contextual information: • Protocol methodology • Reaction source • Rate uncertainty • Provide base for future development

4. www.chem.leeds.ac.uk/Atmospheric/MCM/mcmproj www.mcm.leeds.ac.uk/MCM

5. Navigational Features: Homepage

6. Navigational Features: Browse

7. Navigational Features: Search

8. Navigational Features: Search Results

9. Navigational Features: Reaction Listing

10. Navigational Features: Source information

11. Reaction categories

12. Future and Ongoing WorkKinetic Database • In the future it is hoped that the MCM can also be used as comprehensive up-to-date kinetic database. • Ideally, this large database will include literature citations for all rate constants and branching ratios for ALLreactions in MCMv3.1. • An estimation of a degree of uncertainty associated with the quoted rate parameters will also be evaluated. • This facility will provide an extremely useful reference tool for the user and subject the MCM to a broader audience. • This fits in well with the PrIMe initiative currently being put together in the US.

13. Process InforMatics Model (PrIMe) • The PrIMe initiative is a community based effort to generate data libraries, analysis software and supporting IT infrastructure that will enable a collaborative approach to the development of predictive models. • New site at NIST, Washington (http://www.me.berkeley.edu/prime/) to coordinate the development of kinetic and thermodynamic databases for combustion. • Has potential applications for atmospheric chemistry. • MJP is involved and will investigate potential for wider dissemination of the MCM and development of methods to enhance the reaction database. • DIAC will provide some funding, to augment that from DEFRA, to support the maintenance of the database associated with the MCM.

14. Navigational Features: Extract

15. Navigational Features: Extract Listing

16. Feedback: Mailing List • Keep up-to-date with updates and improvements to the MCM and website • Provides a forum for suggestions and error reporting

17. Alternative formats for subset data (1) • Numerical Fortran compatible format. • Species number allocation • Reactions represented in numerical format • FORTRAN subroutine detailing rate coefficients • Routine includes all expressions for the calculation of the complex rate coefficients and photolysis rates. • FORTRAN subroutine for calculation of rate equations. • Reactions represented in this form can easily be input into numerical integrators. • A converter which will allow users to convert their own mechanisms from a standard FACSIMILE format to FORTRAN format is in the final developmental stages and will shortly be available on the website. • This will allow the user to generate all the data files described above for any existing FACSIMILE file. • This code only extracts the reaction structure from the file, it is then up to the user to adapt the output files to allow simulation of the required conditions.

18. Fortran format

19. Alternative formats for subset data (2) XML • XML stands for Extensible Markup Language. • XML is similar to HTML but all tags are user defined. • XML is based around the concept that every piece of information is tagged. • This allows easier and more flexible storage, retrieval, and exchange of data. • A tree structure is designed for easy representation of the subset in a set of tables. • This is called a schema and defines the way in which data is represented and applies constraints to data in certain fields. • e.g. A species appearing in a reaction must be present in the species table.

20. XML Format

21. species definitions reaction definitions species species number species name RO2 species species name reaction reaction number rate reaction number rate name reactants reaction number species name products reaction number species name XML Schema Design • There are 2 sets of nested tables one representing species and the other the reactions contained in the subset. • The underlined coloured entries are table keys. • Other table entries represented in this colour must hold a value of an entry in the corresponding key column.

22. Continuing work on subset formats • Numerical Fortran compatible format. • Feed back on style of Fortran output with relevance to its practicality for users. • Finalisation of Fortran converter which can be downloaded to convert existing Facsimile subsets to the numerical Fortran style. • XML • Continuing development of XML schema design. • Comparison with existing XML designs used within chemistry. • Aim to achieve a flexible and robust format for data storage, display and use.