Hi all,
This is the first email following up on our meeting at ENC 2008 in
Asilomar. We covered five topics, each of which will be the subject
if a separate email. We'll start by discussing the outcome of the
working group on pulse sequence implementation, led by Eldon Ulrich
of the BioMagResBank. Eldon's powerpoint presentation will be posted
on the AMMRL website shortly.
Before describing the details of the session, I'll alert you to a
call for action recommended by this working group. Specifically, I'd
like you to REPLY TO THIS EMAIL to show your support for a letter
Tara Sprules and I have written, which requests that journal editors
require authors of new pulse sequences to include their pulse
sequence codes and related text files as supplementary material. All
those who reply will be listed as supporters at the end of the letter.
The full text of the letter appears below and the formatted pdf is
posted at:
http://homepage.mac.com/jkurutz/FileSharing24.html
*****
Eldon Ulrich's summary of the working group discussion
(a transcript of transparencies presented at the conclusion of the
ENC AMMRL meeting):
"Publishing Pulse Program Details"
1) Require submission as supplemental material with manuscript
2) Journals: JBNMR, JMR, JACS, MR in Chemistry
3) Requirements:
Requirements:
- pulse program
- phase table
- parameter file
Desirable:
- pulsed field gradient file
- wave form files
4) AMMRL draft letter
Signatories - AMMRl members, ENC, Euromar, ICMRDS, ACS
5) Lay ground work
- talk to editors & influentials at the meeting
6) Other items
- Encourage manufacturers to put manuals online
- encourage authors to submit pulse sequences to manufacturer
- encourage those who translate pulse programs to submit them to
public sites (e.g. www.bmrb.wisc.edu, nmrwiki.org)
****TEXT OF THE LETTER:
Editors of Journal of Magnetic Resonance, Journal of Biomolecular
NMR,Journal of the American Chemical Society, Magnetic Resonance in
Chemistry
Dear Editors,
We, the undersigned members of the Association of Managers of
Magnetic Resonance Laboratories (AMMRL), are writing to request that
you adopt a policy requiring papers that introduce new NMR pulse
sequences include the original working pulse sequence codes as
supplementary material. This will enable researchers with similarly
configured instruments to use and evaluate new sequences immediately,
and it will greatly facilitate the programming of other systems to
make use of them.
This request was formulated at the most recent AMMRL meeting, held at
the 2008 ENC. As you may be aware, AMMRL provides a valuable forum
within the MR community for the exchange of information and
experience pertinent to the management of MR facilities. At our
meeting, we discussed how best to implement new pulse sequences, and
we determined that making codes available at the journal level would
have the greatest benefit.
Finding and writing pulse sequence codes can be problematic, and this
makes it difficult to adopt new methods. Though sequence libraries
are maintained by spectrometer manufacturers, they generally rely on
voluntary contribution by authors, and are not necessarily up to
date. Most authors are willing to provide code when contacted,
however, the authors or codes can sometimes be difficult to locate,
due to job changes, system upgrades, etc. Typical pulse sequence
diagrams and associated figure legends are descriptive, but usually
do not provide all the details required to implement the experiment.
The complexity of modern pulse sequences, with many dimensions,
specific shaped pulses, and complicated timing events, simply
requires more detail than can be represented in print.
AMMRL feels that it would be extremely beneficial to the MR community
if authors publishing a pulse sequence were obliged to provide, as
supplementary material, all the files required to record data. This
includes the pulse sequence code, parameter set, and other associated
files, such as tables of gradient or pulse shapes. These are all
small (kB) text files, and should pose no technical difficulty to
provide.
To help ensure availability of pulse sequences for different
platforms, AMMRL has resolved to maintain a database of working pulse
sequences. Thus, once one person has taken the time to translate a
pulse sequence from its original form and implement it on a different
system, the information will be posted for all others to use.
We thank you for your attention to this matter, and hope that this
can become common practice.
Sincerely,
AMMRL
****
Thanks for your attention.
- Josh
Josh Kurutz, Ph.D.
Technical Director, Biomolecular NMR Facility
University of Chicago
Gordon Center for Integrative Science, room W123C
929 E. 57th St.
Chicago, IL 60637
Office: (773) 834-9805
Spectrometer Room: (773) 702-4052
Cell: (773) 315-5732
Fax: (208) 978-2599
nmr.bsd.uchicago.edu
homepage.mac.com/jkurutz
Received on Tue Apr 15 2008 - 23:41:01 MST