35th ENC, 13APR94
Section III notes: Setting up an NMR pulse
sequence/experiment database.
Chaired by Herb Schwartz. notes taken by Mike Jablonsky.
I. Opening remarks " The situation " or what are we trying
to organize?
***
OVERHEAD
The Situation:
1. Large number of NMR experiments/pulse sequences are
available.
2. New useful experiments are becoming available more
rapidly than most nmr managers can digest.
3. To perform many experiments, particularly more
sophisticated ones, requires experience and knowledge
not readily available from standard sources (vendor
info, publications, etc.).
4. The need to use "special" experiments sometimes
comes up unexpectedly or in a "time crunch" situation.
Unless one is very lucky, they might not be able to reach a
friendly applications specialist from their vendor or other
specialist via phone or e-mail within the time constraints
needed.
5. The e-mail network for AMMRL appears to be nearly
universally available
and is already a prime information source for many of us.
The availability of a data base of NMR experiments is a
natural extension of what already has been accomplished.
***
R. Shoemakers Summary of this: "Sucessfully performing many of the modern,
sophisticated experiments
often requires information/knowledge not generally reported via
conventional channels. For example, in a TOCSY experiment using "trim
pulses" before and after the spin-lock, how are the trim-pulses
optimized? (maybe one other, or better, example of "undocumented tricks" could
be inserted here). Once one of us determines a tried-and-true set of
methods/parameters for a specific experiment, there is currently no
readily available means to share that newly acquired knowledge in a manner
that will be easy for others to call upon AS NEEDED."
The general goal here seems to be how to organize the above
data into some
type of database. The questions are what database to use,
what should go in it, how should it be cross-referenced (key
words, dates, authors), can the data in it be made reliable,
and how should it be accessed (gopher, ftp).
***
Overhead
Problems:
Project will need an extensive amount of data input.
The data will have to be extremely reliable.
There will have to be a mechanism to keep the data base
up to date with new information.
An appropriate computer server architecture would have
to be chosen that would be appropriate for the structure of
the data base as well as being easily accessible to most
members of AMMRL.
***
II. Remarks by Marion Buszko U of FL, Dept. of Microbiology
and Cell Science
"nmr and the info superhighway"
again, more questions to consider:
A) what to store, what to share?
B) where will it be, how will it be done, (the big one) who
will do it?
C) accessing( Mosaic, Veronica, SWAIS, www, gopher, ftp,
listservers, usenet groups.
D) servers (gopher, ftp, E-mail).
***
OVERHEAD
(Not shown due to technical problems but was discussed)
Initial Conclusions
THIS WILL BE A MAJOR UNDERTAKING INVOLVING MANY
PEOPLE OF VARIOUS EXPERTISE. IT WILL REQUIRE A
SIGNIFICANT AMOUNT OF TIME AND PERHAPS FINANCIAL
RESOURCES ONCE COMPLETED, IT WILL REQUIRE AN ONGOING
COMMITTMENT TO MAINTAIN, IMPROVE AND UPDATE THE SYSTEM.
DO WE AS AMMRL AND AS INDIVIDUALS WANT TO PROCEED WITH
THIS PROJECT??
***
III. "Panel Discussion" [remarks are written w/o regard to
contributor].
These were the general issues raised, not necessarily in
chronological order or order of importance.
A) How can we guarantee reliable information in the data
base?
Do we need a verification system, i.e., another user actually
running the expt. using only the info provided before the
expt. is considered usable? [who has time to do this?]
B) Who will setup, update, and cross ref the database?
C) What should go into the data base? We must not have
information overload, but the database will require a minimum
"mass" in order to work.
1) general nmr data-- similar to the protein data bank
2) chemical shifts
3) pulse sequences--as in the form of the working
microprogram or as in "Journal" format. [There was
much discussion here]
4) parameters for pulse sequences, along with comments and
hints so anyone can set up the expt. in a mimimal time.
5) should the data be in a general form (see 3)), or be
machine specific?
6) specific parameters, e.g, for a given sample
concentration, how many scans are required to give a certain
S/N, and how long will this take
7) a list of vendors and users (similar to what AMMRL does
now)
D) How should the database be accessed?
Ways to divide up the data base:
1) instrument (type and vintage)
2) user
3) nucleus
4) expt type (noesy, inept, inverse, etc.)
5) key word
6) flow charts, i.e., menus
E) How should the data be verified?
1) expts. (pulse sequences) should be dated,
commented, hints given.
2) expts. must be referenced.
3) contributing author should be noted; would this imply
the
author is open to questions and help inquiries?
4) see A)
F) Should we even have a separate nmr data base, or should
we be part of another data base? (such as the U of Wisconsin
BIODATA Bank)
ELDON ULRICH INFORMED THE GROUP ABOUT THE EXPANSION OF
THE BIOLOGICAL MAGNETIC RESONACE DATA BANK (BMRB) UNDER THE
AUSPICES OF THE MADISON NMR FACILITY. (SEE ENC POSTER
ABSTRACT#WP112.) HOWEVER THIS IS CURRENTLY LIMITED TO NMR
EXPERIMENTS OF BIOLOGICAL OR BIOCHEMICAL APPLICATION.
G) How can a pulse program written in one format be used by
a different language? Should there be a "universal
translater" for Varian -> Bruker, Bruker AM -> Bruker AMX?
Again, should the expts be written general or specific?
IV. Main Points to Consider
A) We are not competing with cutting edge research groups.
We mainly want access to the information which will allow one
set up expts on their own spectrometer.
B) The data must be easy to access.
C) We must decide what database shall we use.
D) We must decide where it will be located and who will set
the system up.
E) Reliability of data (MUST BE ADDRESSED).
Summary below written by H. Schwartz.
To summarize a key point of my initial concept, avoid
the "reinventing the wheel" syndrome if all possible. By
having useful information in a data base on what to do and
what not to do in performing experiments initially, much time
will be saved by many labs. The same concept should be used
in creating the data base. Information already available
should be incorporated whenever possible. This includes the
efforts mentioned by the Madison and Florida groups, as well
as vendor supplied information. {Several vendor's contacted
after this session gave a range of responses with respect to
the availability of their pulse sequence and parameter
help files. They ranged from complete availability and
enthusiastic cooperation to cautious "lets talk about this
later".}
Below is a copy of the handout distributed at the
discussion group. It is the most important part of the
presentation because at this point the feedback of AMMRL
members is needed on whether we should take on this
project. Those at the discussion group were generally very
enthusiastic about the concept, several expressed their
willingness to participate. Please either mail or e-mail a
copy of this form to me, indicating what you like or don't
like about the categories suggested. But most important, add
to the bottom whether you are willing to spend some (?) time
on some aspect of the project, and what aspect you would
prefer (i.e. Setting up database, testing sequences and
parameters, entering data, etc.)
We will need a minimum number of people who not only like
this concept, but are willing to work on it.
Thank you all for your time and attention. Please note
my e-mail address in the ENC directory was incorrect.
vnmr1@nmribm.chem.rpi.edu Herb Schwartz,
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Name.................................................
Affiliation ......................................
Potential Data Base Categories
Yes | No | Not Sure
Name or Acronym
Full Name
Key Words
Purpose
References
Sequence
Phase Tables
Alternate Experiments
Special Hardware
Sample Consideration
Parameter Suggestions
Small Molecule
Macromolecules
General Suggestions
Processing Hints
Bruker Suggestions
Varian Suggestions
JEOL Suggestions
Chemagnetics Suggestions
Miscellaneous Hints or Suggestions
Please add your own suggestions below:
......................................................................
*******************************************************
Herb Schwartz Director: Major Instrumentation Center
Chemistry Department
vnmr1@nmribm.chem.rpi.edu Rensselaer Polytechnic Institute
(518-276-6779) Troy, N.Y. 12180