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Chemicals vs Ingredients

A fundamental difference in nomenclature between the CM and RM databases is in these two terms. But for all intents and purposes, Chemical and Ingredient are the same.

Ingredient prefixes and suffixes

A number of Ingredients may have the prefix or suffix of C3 or BCC. This idiosyncrasy is due to our conversion and import of screens from CM to RM databases. C6 should remove these for the sake of comparison and form a more operational purpose for us in our laboratory.

Stocks

These are the solutions that are defined and able to be utilised for the dispensing of a crystallisation condition. An Ingredient may have multiple defined stocks of different concentrations. They are both commercially available and, in our case, internally made up in our laboratory.

Designs, recipes, and XML formats

Both CrystalTrak and RockMaker use XML formats but with their own schema.

A CrystalTrak design is the contents of a screen whereas the CrystalTrak recipe is a set of dispensing volumes of specific stocks for use with liquid handling robotics.

The RMXML schema describes the well contents and the stocks that would make it up. But RMXML does not explicitly give volumes for dispensing.

C6 utilises a set of metrics that measure the “distance” between conditions. It incorporates chemical identity, concentration, ionic type, and pH. The scores can be used across a whole screen to compare the similarity to another screen.

A value of 0 is completely identical and 1 indicates no commonality.

A primary factor is the well ingredient with the highest relative concentration in the condition. It is the highest concentration of an ingredient relative to the highest concentration used across all screens. Buffers and detergents are excluded from this designation. Primary factors are used to help form a decision about whether a screen is more salty, or more PEG-y, in the screen attributes. A screen where 60% of the wells have a salt as a primary factor, and 40% have PEG as a primary factor, would be defined under screen attributes as 60% %salt and 40% %PEG.

A buffer is a chemical that helps maintain a set pH in a condition. It is important to note that the

Internal diversity score

The distance metric can be applied to compare conditions within a screen to understand how diverse it is.

A value of 0 indicates a low diversity and 1 indicates a set of very diverse conditions in a screen.

For example, an optimisation screen is likely to have low diversity as there is a limited range of Ingredients, concentrations, and pH values whereas a sparse-matrix screen such as JCSG+ is likely to have a much higher score.

“In stock”

The BCC lab dispenses a core set of screens but may not have any of the commercial screens in stock. Ticking the “In stock” box will limit to a very small set of screens and this functionality is here more for BCC staff purposes

Find Similar Screens

Search for similar screens available based on various distance metrics. Searches use a query screen and can searches can be narrowed to specific vendors or all available screens.

Find Chemical In Screens

Search for screens containing an ingredient of interest. (see note on “Ingredient prefixes and suffixes” in above section on nomenclature)

Find Condition In Screens

Search for screens based on a specified condition in a screen as the search query.

Compare Screens

Compare two specified screens using the distance metric both overall between the screens and identifying identical conditions and common ingredients.

Compare Screen Conditions

A binary comparison of two specified well conditions

View All Screens

Display a list of all screens available in C6

Filter Screens By Folder

Filtered list of screens available by vendor

Folder Structure

A list of all folders. Includes vendors and sub-folders used to organise vendor sets of screens

Screen Attributes

A list of screens (optionally organised by folder) with attributes ranging from diversity and proportions of primary factors

Screen Stock

Screens physically present in the BCC laboratory

Ingredients

All ingredients present in the underlying RockMaker database (see note on “Ingredient prefixes and suffixes” in above section on nomenclature)

PEGs

Filtered list of ingredients for all polyethylene glycols in the underlying RockMaker database

Stocks

list of all defined stocks in the underlying RockMaker database

Ingredient Stocks

List of all stocks grouped by Ingredient name

Ingredient Aliases

All defined aliases for ingredients that may be known with multiple names based on various nomenclature conventions or abbreviations

Types

The types of ingredients that are available for tagging of ingredients

Ingredient Types

List of all ingredients and their tagged types

Ingredient Titration Curves

Titration curves and datapoints for all define Ingredients tagged as buffer type

Ingredient CAS Numbers

Chemical Abstracts Service registry number/s for every defined Ingredient.

Screen Description

An overview of the screen location in the folder structure, the date it was created, and any manual annotations if present

Export

· Csv-row: a comma separated values file with every condition on a new row

· Text: a plain text file of all conditions as a list

· XML: A CrystalTrak design XML

· Recipe (CSIRO stocks): A CrystalTrak recipe XML with stocks available in the BCC lab

· Recipe (Original stocks): A CrystalTrak recipe XML with stocks defined by the vendor

· RockMaker (CSIRO stocks): A RockMaker XML design with stocks available in the BCC lab

· RockMaker (Original stocks): A RockMaker XML design with stocks defined by the vendor

Barcodes

Barcodes defined in the underlying RockMaker database. Values starting with “Z” are physically available in the BCC lab with values in parentheses indicating its dispensed volume

Screen Structure

The definition of the screen geometry (eg 96 well format), the number of chemicals present, and the internal diversity score

A graph and accompanying table representation of the composition of the screen, using counts of Ingredients present in each well and their Ingredient Type(s) as defined in RockMaker. This provides insight into the chemical space explored in the screen beyond what is indicated by the Active Ingredient Type for each Well Ingredient. As ingredients can have up to 10 different types, the total Ingredient Type Counts in each screen will typically be larger than the number of well conditions in the screen.

Well Contents

A table of the screen contents per well. The well location, well composition, calculated pH, and a recipe for dispensing of 1 mL of the condition using BCC stocks