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Rock Maker comes configured with all ingredients that are used in known commercial screens at the time of installation.
An ingredient definition includes the concentration, pKa or titration curve for buffers, and ingredient types (salt, precipitant, buffer, etc.).
One of Rock Maker’s powerful features is its ability to define multiple stocks of a given ingredient. A stock is an ingredient at a certain concentration; a buffer stock is an ingredient at a specific pH. Instead of adding a new ingredient in order to obtain a specific concentration or pH for use in an experiment, you simply use a different stock of the ingredient. Each stock of an ingredient has the same ingredient ID.
The Ingredients setup tab, found under the Setup node on the Explorer, is a central repository of data for the ingredients used in your experiments.
Here you’ll find all the information Rock Maker requires in order to compute the amount of each ingredient that needs to be added to a well solution, based on an experiment design.
Note: Standard ingredients can also be used in protein formulations. For more information, see Creating Protein Formulations.
| Column | Description |
|---|---|
| ID | This ID number is automatically assigned by Rock Maker and is used by the application to track information about the ingredient. This ID number is the same for all stocks of an ingredient. |
| Type | By default, Rock Maker recognizes the following eight ingredient types:
A single ingredient may have multiple types. Each type of an ingredient has its own row on the Ingredients table. When you select an ingredient to include in an experiment design, Rock Maker will ask you to specify which type you wish to use. You may add more ingredient types to this list. See Adding Ingredient Types for instructions. |
| Name | The long name of the ingredient. When displaying the name of the ingredient on a screen, Rock Maker will display the long name whenever space allows. |
| Short Name | The short name of the ingredient. If the long name is too long to display, Rock Maker will show the short name instead. |
| Default Stock Number | The default stock selected when you add the ingredient to an experiment. Ingredients may have multiple stocks, which are separate vials of the same ingredient at different stock concentrations or pHs. You may select a different stock once an ingredient is added to an experiment. |
| Conc. Units | The units used to specify the concentration values of the ingredient. You may use whichever units are most appropriate for your experiments. Typical values are M for molar and %v/v for percentage volume over volume. |
| Stock Conc. | The concentration of the stock ingredient. Based on this value, Rock Maker can obtain the correct concentration needed for an experiment. For example, if the stock concentration of an ingredient is 1 M, and you need to use a concentration of 0.1 M in an experiment, Rock Maker knows that 10 percent of the experiment solution needs to contain that ingredient. |
| Low Conc. | The default low concentration of the ingredient used when you are designing a grid experiment or random experiment. This value is taken from the default stock's low concentration value. Once you add the ingredient to an experiment, Rock Maker allows you to change this value if necessary. |
| High Conc. | The default high concentration of the ingredient used when you are designing a grid experiment or random experiment. This value is taken from the default stock's high concentration value. Once you add the ingredient to an experiment, Rock Maker allows you to change this value if necessary. |
| Liquid Class | The type of the liquid class that your liquid handling robot uses to determine how the ingredient should be dispensed. |
| Stock Min pH | The lowest stock pH available for the ingredient. This column applies only to buffers. |
| Stock Max pH | The highest stock pH available for the ingredient. Rock Maker can obtain any pH that falls between the Stock Min pH and Stock Max pH by mixing two stocks with equal concentrations. This column applies only to buffers. |
The XML format provides a hierarchical way to organize data, so that for each ingredient that is imported, it is possible to include its stocks, CAS numbers, aliases, and other information. We recommend that you import ingredients from, and export ingredients to, an XML file whenever possible.
Important: Be sure to adhere to this practice of using ingredient stocks instead of adding new ingredients to obtain varying concentrations and pHs. This ensures far more effective analysis of experiment data.
Many ingredients are known by multiple names. Rock Maker keeps track of these in the Aliases table, which appears when you are adding or editing an ingredient.
When you import an ingredient data file, Rock Maker compares the names of the imported ingredients with the names of ingredients already contained in the Rock Maker database. If you attempt to import an ingredient that is already in the database, Rock Maker will alert you. If Rock Maker knows all possible aliases used for an ingredient, there is a much greater chance that the application will be able to identify matches when importing ingredients. You should enter an ingredient's aliases whenever possible.
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| RMC-V37R116 |