STEP 1 Login / Register Each model is associated with a particular user. Only the user who creates the model record can edit the model and reaction information associated with that record. In addition, the user can designate the model "Public" or "Semiprivate" or "Private", the latter two meaning only the user can view all of the the record information (such as would be appropriate for a model under development). If you don't register (and login), you can view all (public) records. If you register (and login), you can upload model records to the database. To register as a user, click on the Login / Register link in the upper right above and fill in the "New User Registration" form. To login as a user, click on the Login / Register link in the upper right above and enter your username and password.

	STEP 2 Create/Use Bibliographic Record Each model must be associated with a particular bibliographic record. First, one must create a bibliographic record, or use an existing one. To use an existing bibliographic record, go to the Bibliography section and search for it by author, title, year, or any other information. To create a new bibliographic record, go to the Bibliography section and enter a new record. STEP 3 Create New Model Record The model record is created from the Bibliographic Display form. Click on the button in the bibliographic record display.

	STEP 4 Enter Model Information Model information is inputted in the "Edit Model Record" form. There are several sections where model information should be entered. Identifiers Descriptions Conditions Reaction Set Related Models Files Notes More detailed information and instructions for each section can be found in the "Edit Model Record" form. STEP 5 Save New Record Click on the button in the "Edit Model Record" form. This will create a new Model Record with the information supplied. One can always save at any time, and later go back and edit record, to complete input of model record information.

	pre STEP 6 Assemble Reaction Set The reaction set text file must contain BOTH species thermo and reaction rate information in the file in Chemkin-like block format. ELEMENTS .... END SPECIES .... END THERMO .... END REACTIONS .... END STOICH .... END (added feature, but NOT implemented yet) REFERENCES .... END (added feature) A short example mechanism/reaction set file is provided here formatted as HTML and TEXT.. STEP 6 Upload Reaction Set A Reaction Set for the model/mechanism is uploaded AFTER the new record is created. First, click on in the "Models Display" form. Then, click on and select a file from your computer. Then, click on . This uploads the text file to the database.

	STEP 7 Parse Reaction Set The Model Reaction Set "text file" is uploaded to the database. But, now it must be parsed. Click on . This parses the reaction set, checking for errors and the like. Note: For a small reaction set (100-200 reactions), this might take <1 seconds. For a large reaction set (1000-2000 reactions), this might take 5 seconds. STEP 8 Identify Species Symbols The database program now looks up all the species symbols in the reaction set to see if they are already found in the database. It also prepares the database for import of the information. At this step, any symbols not identified should be identified if possible. For each species Symbol NOT identified, one has two fundamental choices. Use the symbol as a new "species" in the database Or, identify it as a new "symbol" to be associated with a species already in the database Use this symbol and add it to database Existing Species 1 in database with same molecular formula Existing Species 2 in database with same molecular formula etc Note: Although it is preferred to identify the symbols at time of import, one can always go back and identify/reassign them later using Species Edit. STEP 9 Import Data The text file has already been uploaded, parsed, species symbols identified, and information prepared for import. One needs to actually import the data into the database. Click on Note: For a small reaction set (100-200 reactions), this might take 5 seconds. For a large reaction set (1000-2000 reactions), this might take 10-20 seconds. STEP 10 Finish Import The reaction set has now been imported into the database. Click on and return to Model Display.

	and beyond Other Stuff One can now view, edit, browse, etc to model information and data. In "Model Display" form Click on to see the original reaction set text file. Click on to see the parsed reaction set in a text file format. Click on to view all the species in the model. One can view/edit species information, get thermo about the species, etc. Click on to view all the reactions in the model. One can view/edit reaction information, find similar reactions, browse, sort, etc.

Overview | Models | Reactions | Species | Bibliography | Help