The train Type controls the top speed and acceleration/deceleration performance. A type of "(Deleted train)"is interpreted as a request to delete that train from the timetable.

Headway controls how many times per hour a run is made.

NB Minutes and SB Minutes are the number of minutes (modulo the train headway) past the hour at which a train is to leave its origin station. So a headway of 15 and a NB minutes of 3 says that the train leaves from its southern origin at 3, 18, 33 and 48 minutes past the hour. Negative numbers are also allowed (-3 being equivalent to 57).

Train colour tells how to shade the time-distance lines for different trains. It is a six-character hexadecimal string in the format rrggbb. "ff0000" is saturated red, etc. If you're unfamiliar with this nonsense, web search for "rrggbb html".

Pad% is the percentage by which the inter-station trip time of a train shuold be increased to allow for recovery from minor service irregularities. The default is 10 percent, which is in line with or better than present-day Caltrain-style operations; 7 percent is typical for a functioning passenger rail network in an advanced first world industralised democracy.

The Fleet is used to compute the number of trains of different types required to operate the timeable.
Trains with the same "fleet" are assumed to use the same pool of interchangable equipment and so two trains with the same fleet that respectively arrival at and depart from the same terminal station can be operated by the same physical train (and crew) should tbe turnback dwell time between arrival and departure be great enough.

The Operates choice determines whether a given train runs in both directions, northbound only, or southbound only. (Highly asymmetrical operation being typical of old fashioned "commuter railroading".)
As a convenience when developing a timetable, a train's direction may also have placeholder value of "(Placeholder)", which suppresses any display of or computation using that train, but does not delete it from the timetable. This is useful for reducing output clutter when attempting to focus on other trains.

The user interface for specifying Stops is less than wonderful, I know. But you're all Brave Engineers, so deal with it!

• The stop format requires exactly 28 stops to be specified, starting from the north at SF Transbay and progressing to SJ Tamien.
• Each stop is separated by punctuation, typically a "." character.
• Each stop is either a number of seconds of dwell time; or an empty string which means that the train bypasses (or does not operate as far as) that station.
  A dwell of 0 seconds is another way of specifying "does not stop".
  Thus "30.0...30" represents a train stopping for 30 seconds at two stations and skipping three intermediate stops.
• Typical dwell times:
  20s is appropriate for first world train regional rail operations (level boarding; adequate door capacity, etc);
  45s is optimistic for Caltrain today given its 19th century platforms and equipment and operating practices, especially at busier stops;
  90-120s may be appropriate for "major" stops, either for inter-regional trains or for trains making connections.
• As a weird special case (sorry!), trains exiting the corridor are indicated by a "dwell" time of 1 second.
  Altamont trains to or from SF have a "dwell" of 1 at Atherton (and 0 at all points further south), and so have a stop specification that ends with ".1...........".
  Altamont trains to or from SJ "dwell" for 1 at Santa Clara and might end with ".1..900." ("900" being an arbitrary terminal turnback dwell);
  and non-stopping trains destined to happening Los Banos "dwell" for 1 at Tamien and end with ".1".
• "Short turn" trains are indicated by leading and/or trailing non-stops (ie blanks).
  So for example a train stop specification starting with ".......900" indicates termination (northbound) or origin (southbound) at Millbrae;
  and one ending with "900............" operates only north of Redwood City.
• The "dwell" time at terminal stations must thus be greater than 1 second, but it otherwise irrelevant to trip time computation.
  It is, however, used to compute the number of trains required to operate the timetable: longer turnback times (15-30 minutes = 900-1800 seconds is typical for Caltrain-style "commuter railroading") waste more trains and crews than the less slovenly 10-20 minutes = 600-1200 seconds which is unambitious for a post-1970 "S-Bahn" or "RER"

Some sample stop patterns for your cutting-and-pasting pleasure

The example terminal dwell time "900" is chosen to represent a 15 minute turnback time: that being optimistic for Caltrain/FRA freight-style operation; but unambitious elsewhere)