Pulse sequence database documentation

From NMR Wiki

This is documents describes technical details of the pulse sequence database.

If you would like to contribute, but are not ready to get into the technicalities, please take a look at:

• Brief overview of the Pulse Sequence Database
• How to add files to the Pulse Sequence Database
• How to edit Pulse Sequence Database records

NMR experiment records

NMR experiment records are wiki pages that describe essence of the experiment regardless of implementation details on any specific hardware.

All of those documents fall into category "NMR experiment" and have automatically generated links to the relevant pulse sequence record pages.

Pulse sequence records

These are also regular pages - but in this case - one for each hardware-specific pulse sequence implementation.

Pulse sequence records can have the following (again, all of these are optional):

• listing and description of all pulse sequence parameters (see note below)
• a structured record about the pulse sequence
• link to downloadable pulse sequence source code and components
• link to the corresponding NMR experiment pages
• links to downloadable sample data

Note: internal pulse sequence parameters that are not exposed to the user should not be documented - because it is intended to be user documentation.

Pulse sequence file repository

The active file repository is actually a simple directory on the server.

This directory "revision controlled" with a mirror at the public github service.

You can contribute source code files either via github or by email at inbox@nmrwiki.org.

Described below are three things that can be done when editing pulse sequence records.

Adding/editing general information

Find a page you want to edit, click "edit" tab and put your text anywhere after the closing braces }} - if that is present on the page.

What to write

The most important part of the record is the listing of pulse sequence parameters.

Please look at the source code of the pulse sequence and write out only those parameters that are independent and must be set by the user.

The purpose of this is to simplify documentation as much as possible.

Example

{{rutgers-pulse-sequence
 |name=hetzyT1_ch3
 |synopsis={{15N}}-HSQC with T1 measurement
 |author=C.B. Rios, G.T. Montelione
 |console=Unity
 |field=500
 |observe=H
 |nuclei=HN
 |dim=2
 }}
Add your text here
[[Category:HSQC]]
 [[Category:T1]]

Adjusting template values

These (template records) compose the core of the pulse sequence record.

Template entry starts with a double opening brace and template name, e.g. {{pulse-sequence .... In this case name of template is "pulse-sequence" and the corresponding template page has title "Template:Pulse-sequence". The record ends with a double closing brace }}

Everything inside the template record is composed of name=value pairs (i.e. "parameter name" and "parameter value"). You can change those values if they are incorrect or add missing parameters.

Adding/removing tags

Tags allow retreiving records via the search interface, so they are very important.

Some tags are created by the template - to adjust those you will need to change fields in the template record.

Others will be added explicitly by the user. For example for pulse sequences containing HSQC element tag [[Category:HSQC]] will be appropriate. Just type it in in the end of the page (this is a convention for placing category links).

If some category does not exist just type in the tag the way you want to see it. Category will be automatically created.

Also as you see pulse sequence database tags are regular wiki category links.