FlowJo's Plate Editor makes setting up an experiment easier and faster, and saves time on experiments that must be repeated.
For high throughput studies, it is important to be able to annotate samples based on
The syntax of a protocol
A protocol may contain other protocols, keywords and constraints.
A protocol has attributes for name, version, creator, creation date, modification date.
A keyword has an attribute and a value.
A constraint has an attribute and a value. In numeric constraints, minValue and maxValue can be used to specify ranges>
In XML implementations this can be expressed by the following Data Type Description:
<!ELEMENT Protocol ((Protocol | Keyword | Constraint )*) >
<!ATTLIST Protocol name CDATA >
<!ATTLIST Protocol version CDATA >
<!ATTLIST Protocol creator CDATA >
<!ATTLIST Protocol modificationDate CDATA >
<!ELEMENT Keyword EMPTY>
<!ATTLIST Keyword attribute CDATA #REQUIRED >
<!ATTLIST Keyword value CDATA #REQUIRED >
<!ELEMENT Constraint EMPTY>
<!ATTLIST Constraint attribute CDATA #REQUIRED >
<!ATTLIST Constraint value CDATA # IMPLIED >
<!ATTLIST Constraint minValue CDATA # IMPLIED >
<!ATTLIST Constraint maxValue CDATA # IMPLIED >
*Please note that unlike naming schemes and file paths within operating systems, for programmatic reasons the following characters are not allowed in file or gate names and will likely cause errors within FlowJo: "/" forward slash, "\" back slash, and "&" ampersand. All other characters should work without issue.
The semantics of a protocol
When a protocol is applied to a data file, all constraints in the protocol are tested against the data file. If the file contains the keywords to satisfy all constraints, then all keywords are assigned to the file, and then all protocols are applied (using their own nested constraints and keywords).
Example:
This example will show a protocol that labels all samples with Experiment = Exp2 and Investigator = adam.
Well A1 will be labeled as a quality control, and if the file contains less than 1000 events, it will be classified as small.
<Protocol name=”stemcells”>
<Keyword attribute=”Experiment” value = “Exp2” />
<Keyword attribute=”Investigator” value = “adam” />
<Constraint attribute=”well” value=”A1” />
<Protocol name=”unstained”>
<Keyword attribute=”size” value = “small” />
<Constraint attribute=”$TOT” maxValue=”1000” />
</Protocol> </Protocol>
