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Special Instructions 2005B

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Instructions for Completion of Phase II/OT Science Programs: Semester 2005B

This page provides instructions for completing Phase II Science Programs  for all Gemini North and Gemini South instruments. It includes submission details and procedural changes. Please read this page carefully!

Note: As in the previous semester the Phase II deadlines are hard deadlines for queue programs (see details below). Programs that have not completed their Phase II definitions by the deadlines will be dropped from the queue.

Distribution of Phase II Skeletons

All observations must be defined using the Observing Tool (OT) software. Gemini staff have translated approved Phase I proposals into the Phase II format for loading into the OT. In this process, the observations and other details entered in Phase I are used to construct a ("skeleton") framework of your Science Program.

Instructions on skeleton retrieval were sent to PIs on June 16. As in previous semesters, the Phase II skeletons are downloaded/uploaded directly from/to the Gemini telescope databases to enable more efficient and rapid processing. See more information on using the Observing Database.

A new release of the OT ("palote") is available to support Semester 2005B Phase II preparation (as well as on-going 2004B and 2005A programs); do not use the previous "grillo" public release. There are OT installation instructions available. If you are unfamiliar with the OT, there is an OT tutorial that provides a useful introduction. In addition, each instrument also has several web pages that provide guidance on observing strategies and how to describe these in the OT.

Relaxation of Observing Condition Constraints and Other Observation Changes

For semester 2005B the queue was constructed by filling the expected observing conditions (and overfilling the poorer than average conditions) but limited to the total available queue time (i.e. the total science time less scheduled classical nights and estimated Band 1 rollover programs). Band 3 programs, which now occupy the lowest half of the queue, are unlikely to be executed, and very unlikely to be completed, if they request conditions that are better than average (especially in cloud cover and image quality).

As in the previous semester we encourage PIs of Band 3 programs, in particular, to think carefully about relaxing the observation constraints within the context of their overall time allocation and approved science goals (e.g. by observing fewer targets). One useful analogy is to consider "how would I attempt this program if it were classically scheduled and the conditions were sub-optimal?".

If during detailed definition you find that the approved observations need to be modified, please follow the change request procedure.

User Support

The National Gemini Offices are responsible for Phase II support for the "established" facility and visiting instruments as mandated by the Gemini Board. Phase II support for the other instruments remains with the Gemini Observatory staff. In outline, the Phase II process for the established instruments is as follows:

  • PIs interact with NGO support staff to complete Phase II using the OT for all observations with NIRI, including Altair, Phoenix, both GMOSs (including MOS mask design), T-ReCS, GNIRS and Michelle.
  • All Phase II Science Programs are checked by NGO staff prior to being forwarded to the Gemini Contact Scientist. (Note that Gemini CSs will return any Phase II programs that are received directly from PIs, with instructions to contact their NGO).
  • Gemini Contact Scientist checks Phase II Science Programs; if there is any problem the Science Program will be returned to the NGO support staff. The NGO staff will then iterate further with the PI.
  • Only when the Gemini Contact Scientist agrees that the Science Program is ready will it be activated in the queue for execution. The PI will be notified that their program is in the active queue and that the Gemini CS is now the primary contact point.

You can help us and speed this process by checking the program yourself (see the OT/Phase II checklist and instrument-specific checklists on the OT instrument component pages). 

If you wish to change the primary contact for this program, e.g. to a co-I, please e-mail both Sybil Adams (sadamsgemini.edu) and Simon Chan (schangemini.edu) with a copy to both Gemini Heads of Science Operations (ijorgensengemini.edu, ppuxleygemini.edu) and a copy to your National Gemini office.

To help us in tracking and resolving user problems, questions and suggestions, and thereby improving the software and web pages, please use the Gemini HelpDesk. This allows us to ensure that no queries are missed and help us improve the software and documentation. A streamlined interface is available for Phase II queries, keyed to your Gemini Program ID (e.g. GS-2005B-Q-12). As with the regular HelpDesk interface, your query will be directed to the specific NGO or Gemini support staff. Support assignments do change occasionally and you can verify the contact names from the "interactive snapshot" of the Observing Database, accessed from the contents list on the schedules web page. (The NGO and Gemini support staff email addresses are listed on the support staff web page).

Deadlines and Mechanism for Return of Completed Science Programs

The mechanism for submitting your completed Phase II Science Program is similar to skeleton retrieval (see the Observing Database information for more details) and is the same for all instruments (although submission of MOS mask definition files, and finding charts, is currently handled separately, outside of the Observing Tool, via direct email to your Gemini Contact Scientist). 

Dates for submission of completed Phase II information are (all 6pm local time):

Phase II deadlines for all instruments
Deadline Notes
12 July Early submission, recommended for any programs and especially advantageous for observations that can be executed early in the semester
12 August Mandatory deadline for all queue programs
various Deadlines for GMOS mask design and MOS updates (several dates, synchronized with lunar phase)

These deadlines apply to all queue programs including templates for Quick Response / ToO observations. (In addition there are periodic deadlines during the semester for GMOS mask design and corresponding MOS observation updates only). 

PIs of all classical programs must also submit Phase II observation definitions. The deadline for these is three weeks prior to the first scheduled night. (See the 2005B classical schedule and 2005B instrument schedule).

Programs that have not completed their Phase II definitions by the deadlines noted above will be dropped from the queue or schedule. In exceptional cases an exemption may be requested by emailing both Heads of Science Operations (ijorgensengemini.edu and ppuxleygemini.edu)

In some cases GMOS PIs may be contacted directly and asked to submit their Phase II early to provide sufficient observations for pre-imaging and MOS spectroscopy at the very start of the semester. All MOS pre-imaging observation descriptions must be submitted by the regular deadlines (see table above).

OT and Other Late-Breaking Changes for 2005B

The principal changes to the OT software are listed on the OT Hot News page. There are also several new policy changes. Here we summarise how they affect Phase II observation definition and point the user to further details.


No policy or procedural changes for 2005B. 

GMOS North and South

PIs must now define and include in their Phase II programs all spectroscopic (telluric and flux) standard star observations. 

See the GMOS baseline calibrations and Observing Tool Tips and Tricks for the full list and details of calibrations required for different types of programs.


Several new narrow-band filters are available for target acquisition. 

PIs must define and include in their Phase II programs all baseline calibrations (flats, arcs, telluric standards) and acquisition observations. The list of baseline calibrations is available and examples are given on the GNIRS OT help page. An example acquisition observation is given on the same page. 

Note also the updated offset acquisition (including "blind acquisition") procedure described below.


Imaging and spectroscopic programs must include two spectroscopic standard stars, one for before and one for after the observation (see Michelle baseline calibrations for more details). 


No policy or procedural changes for 2005B. 


No policy or procedural changes for 2005B. 


Imaging and spectroscopic programs must include two spectroscopic standard stars, one for before and one for after the observation (see updated T-ReCS baseline calibrations for more details). 

A new detector readout mode has been added for faint-source spectroscopy. The default mode assumes normal imaging or 'bright-object' spectroscopy.

Observe Class and Time Accounting

The new OT contains major infrastructure and user interface changes to enable automated time accounting, more accurate and quicker feedback to PIs of time usage and execution status, and optimised schedule planning. In the OT, each Observe type (normal science Observes and bias, dark, flat/arc Observes) now has an Observe Class associated with it. The class determines time charging, observation planning and data distribution. The Observe classes and associated charging are:

Observe Class                  Charge to
Science                        Program
Nighttime Program Calibration  Program
Nighttime Partner Calibration  Partner
Acquisition                    Program
Acquisition Calibration        Partner
Daytime Calibration            No Charge

For schedule planning purposes only, the entire observation is given an Observe class based upon the classes of the Observes it contains. The actual Observe class determines the time charging.

To make observation definition quicker, the classes default to specific values depending on the Observe type that is added to an observation:

Observe    Default Observe Class (and Charge)
Arc        Nighttime Program Calibration (Program)
Bias       Daytime Calibration (No Charge)
Dark       Daytime Calibration (No Charge)
Flat       Nighttime Partner Calibration (Partner) 
Observe    Science (Program)

These defaults are reasonable in most circumstances but will need to be changed manually by the PI in certain cases. The two most common general cases are: (a) standard star observations should have their Observe Class changed from Science to Nighttime Partner Calibration if they are a baseline calibration or to Nighttime Program Calibration if they are a special calibration, (b) acquisition observations should have their Observe Classes set to Acquisition or Acquisition Cal. as appropriate and (c) any arcs that are not mixed with science observations and can therefore be taken during the day should be changed to Daytime Calibration.

The total planned time, the time charged to the program as execution proceeds, to the partner and "not charged", and the elapsed time (normally the sum of the charged times) are now shown for each observation and for the program. The planned time excludes any acquisitions.

Quality assessment of the data by Observatory staff also affects how the data are charged. Data that passes the QA checks is charged as described above, data that does not pass but is deemed to be usable and any data that fail are "not charged" (and are tracked to improve our observing processes). 

Offset Acquisitions (Including "Blind Acquisition")

Acquisitions can be specified in two ways. The first involves an offset from another target specified by the PI as (delta RA, delta dec) in arcsec in a text note. This is not the preferred technique, however, because the offsets must be entered manually by the observer, and is therefore subject to human error.  Alternatively the reference target position may be defined as a User Target in the OT target component, giving the full (RA, dec) coordinates. This technique applies the offsets automatically, but relies on an accurate and common J2000 coordinate system for the two positions. See the updated telescope acquisition procedures for more details.

Non-sidereal objects

No significant changes for 2005B.

Calibration Time Accounting

The calibration checkbox has been removed and replaced with the Observe classes described above. 

GCAL facility calibration unit  

The Krypton arc lamp has been replaced with Xenon to provide a higher density of lines, especially for the GNIRS R=18000 mode. Moreover it is now possible to select multiple arc lamps at the same time.

Notification of Data Taken and Electronic Distribution

The "Notify PI" checkbox in the OT observation component is not yet active. 

Nevertheless, PIs will be notified by email once their data are ingested into the Gemini Science Archive and available for retrieval from GSA

Status of Submitted Programs and Observations

The 2005B queue summary and "interactive database snapshot" pages show the current execution status of all queue programs and indicates when data have been taken. (For the next level of detail, click on the "execution status" link under each program to see the status of each observation or on the execution log links in the contents list to see which observations were executed each night).

Last update June 9, 2005; Phil Puxley

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