Dear All,
I agree with Craig (and others).
Please put me down as one who thinks only numbering a computer file is just not a good way to store information, for any subject.
While it is possible to write a script (or scripts for multiple programs) that would systematically dig through folders and subfolders scanning files for particular strings, it must not be unreasonable to request that a “save as” feature could be added to the software generating the data? Are there underlying software issues that would prevent this ability/feature?
For our case with hundreds of users, and many research groups we needed an efficient and robust method of searching, and importantly confirming contents in our archives.
We use an in-house scripted automatic file saving format -> date.instrument_samplename_experiment
e.g.
2015.10.28.m400_thrombin_1H-1D
and this file is put in a directory named after the user and their supervisor.
Any of these pieces of information are available within the saved data in some form or another, but we’ve found it’s very quick and easy for uses of all experience levels to find their information with the format we’re using.
Best wishes,
Ryan
-----------------------------------------------------------------------------------
Ryan T. McKay, Ph.D.
NMR Laboratory Supervisor
Room E3-17A Email: ryan.mckay_at_ualberta.ca <mailto:ryan_at_nanuc.ca>
Department of Chemistry Phone: (780) 492-9950
University of Alberta Fax: (780) 492-8231
Edmonton, Alberta Cell: (780) 920-8871
Canada T6G 2G2
http://www.chemistry.ualberta.ca
> On Oct 28, 2015, at 2:09 AM, Craig Butts <Craig.Butts_at_bristol.ac.uk> wrote:
>
> Hi all,
>
> I stand corrected and must apologise to Clemens for my comment about Icon above. Icon does enable you to change the filename for every spectrum within a given sample in a flexible fashion. I've just succesfully run a sample through IconNMR which created sub-folders 'Craig_Proton', 'Craig_Carbon', 'Craig_HSQC' by using the 'Disk' and 'Name' entries (and it gracefully dealt with the Composite HSQC experiment wanting to refer back to the 'Craig_Proton' data in a different folder). It's clunky, as it requires user-intervention for a trivial task, but not difficult and it gets the desired result.
>
> In a wider perspective, this isn't really a TS-MNova issue - it's a general concern that the default file/folder naming system at the moment is not overly helpful to the casual (non-TS) reader (and don't get me started on the fact that 'zg30' is apparently an informative identifier....). We can't expect MNova, ACD, iNMR, Microsoft Windows, Android, LINUX etc, etc to all modify their software to look inside folders for a parameter name to identify a dataset, when instead a simple fix is to generate meaningful names in the first place.
>
> It seems to me that this would be a really simple flag to add into Icon Manager i.e. "append human-readable spectrum identifier into Name" (perhaps not the best name for the flag...). But then I don't have to write the software to do this.
>
> [Rich - I'll raise you 250 UK chemists, in 30-odd research groups, of whom a fair number complain regularly about the numbered folders as a proxy for experiment names that they get for free on our other systems. Maybe your folks are more scared of you than they are of me *grin*.
> For those who want to play the now defunct V vs B game - JEOL file nomenclature also lets you put the experiment name into the filename as a default (or you can disable as you wish).]
>
> Craig
>
>
> On 28 October 2015 at 03:21, Ian Luck <ian.luck_at_sydney.edu.au <mailto:ian.luck_at_sydney.edu.au>> wrote:
> An interesting conversation, to which there may be a number of solutions. One avenue that has not come up is to focus on the processing software being used, rather than the acquisition software. Perhaps this is a feature request you should be taking up with the Mestrelab hotline rather than Bruker’s. I don’t quite follow that a product vendor should be implementing feature requests that make it easier for a customer not to use their product….
>
>
>
> Bruker acquisition parameters contain two useful parameters for determining the type of experiment performed, and these are stored in the file “acqus”. The parameters PULPROG (to an experienced eye) and EXP (to a less experienced user) can be used to determine the experiment type. All of our standard parameter sets that are used on all of our instruments have the EXP field filled in with the experiment type performed. In ICONNMR, it is also filled in automatically.
>
>
>
> The MNova Suite proclaims that you can “do virtually what you want” with MNova scripts. Have you explored the possibility of filtering experiment types using scripting within MNova? Other third party software could likewise search for this information in archived data using script methods.
>
> Additionally, if you know you will be processing data in MNova alone, and not taking it back into Topspin, you could run a batch script to rename all of your EXPNO folders based on either the PULPROG or EXP, after you have finished acquisition.
>
> The following small batch script, for instance will rename all of your EXPNO folders within an EXPERIMENT_NAME based on what your EXP parameter is. Similarly, you could rename using PULPROG instead.
>
>
>
> for /D %%i in (*) do (
>
> for /f "tokens=2 delims=<>" %%j in ('findstr /B /I "##$EXP=" "%%i\acqus"') do (
>
> ren "%%i" "%%j-%%i"
>
> )
>
> )
>
>
>
>
>
> Cheers,
>
> Ian
>
> Dr IAN LUCK
> NMR Facility | School of Chemistry
>
> THE UNIVERSITY OF SYDNEY
> Rm 150A, Chemistry F11 | The University of Sydney | NSW | 2006
> T +61 2 9351 2851 <tel:%2B61%202%209351%C2%A02851> | F +61 2 9351 3329 <tel:%2B61%202%209351%C2%A03329> | M +61 415 798 953 <tel:%2B61%20415%20798%20953>
> E ian.luck_at_sydney.edu.au <mailto:ian.luck_at_sydney.edu.au> | W http://nmrfacility.chem.usyd.edu.au/ <http://nmrfacility.chem.usyd.edu.au/>
>
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>
>
>
>
>
> From: Craig Butts [mailto:Craig.Butts_at_bristol.ac.uk <mailto:Craig.Butts_at_bristol.ac.uk>]
> Sent: Tuesday, 27 October 2015 6:06 AM
> To: Kenneth Knott
> Cc: ammrl_at_ammrl.org <mailto:ammrl_at_ammrl.org>
> Subject: Re: AMMRL: Bruker folders
>
>
>
> Hear hear Ken. I'd add to the list with:
>
> Non-NMR software has no hope of looking inside the data for information to help the searcher. For example, if we archive the data after publication the numeric file system is simply obstructive for searching without TS.
>
> And ICON gives no capability to enact Clemens' workaround.... This is especially annoying as ICON is becoming increasingly applicable and flexible for day-to-day operation (and non-routine e.g. INSIGHT-MR?). We do nearly everything through it...
>
> Craig
>
> On 26 Oct 2015 6:23 pm, "Kenneth Knott" <kknott_at_vt.edu <mailto:kknott_at_vt.edu>> wrote:
>
> Thanks everyone for the suggestions and input.. But I think I've found a correlation. The people who aren't too bothered by the Bruker data system are those using Topspin and it's included browser to process their data.
>
>
>
> Unfortunately, many of us process our data off the instrument using alternative means. We, here at Virginia Tech, use Mnova to process our data for a number of reason. The first being we find it to be superior to all others in processing. But also for a number of other reasons.
>
>
>
> 1) Users our trained on one processing software package in a multiplatform environment (Mix of Burker and Agilent/Varian sytems)
>
> 2) NUS processing is included (for free) and far superior (much faster) to Topsim
>
>
>
> In any case, when processing outside of Topshim you rely on the file. system to describe your data sets. Here is where Topshim fails miserably...
>
>
>
> 1) Exp numbers for folders is wholly undescriptive...
>
> 2) Even inside the folder, one cannot tell at a glance what the experiment is outside of 1D or 2D
>
>
>
> Sure there are ways around this once the data is loaded into Mnova using titles, but Bruker Topspin falls far short in this regard and I'm astonished that you cannot give the experiment folders any kind of descriptor.
>
>
>
> Thanks again for the help.
>
>
>
>
>
>
>
> On Fri, Oct 23, 2015 at 3:38 PM, Kenneth Knott <kknott_at_vt.edu <mailto:kknott_at_vt.edu>> wrote:
>
> So one thing that has always frustrated me about Topspin is that is saves all folders simply by the experimetn number. This gets very difficult to keep track of when I've got a suite of experiments or add to them over time.
>
>
>
> It seems to me that there must be a way to alter this to save perhaps by experiment number AND parameter set.. for example 10-C13CPD or 20-PROTONRO, etc...
>
>
>
> Can this be done? If not, how do you get around this issue?
>
>
>
> I have found the bruker 'hotline' to be less than helpful with issues such as this...
>
>
>
> Thanks!
>
>
>
> --
>
> Ken Knott
>
> Department of Chemistry
>
> Analytical Services
>
> Virginia Tech
>
>
>
> (540)267-6502 <tel:%28540%29267-6502> (Cell)
>
> (540)231-0885 <tel:%28540%29231-0885> (Office)
>
>
>
>
>
>
> --
>
> Ken Knott
>
> Department of Chemistry
>
> Analytical Services
>
> Virginia Tech
>
>
>
> (540)267-6502 <tel:%28540%29267-6502> (Cell)
>
> (540)231-0885 <tel:%28540%29231-0885> (Office)
>
>
>
>
> --
> Dr Craig Butts
> Reader in Structural and Mechanistic Chemistry
> Director of Chemical NMR Facilities
> Room S103b
> School of Chemistry
> Bristol University
> Cantocks Close BS8 1TS
> Tel: +44 (0)117 9288115
> http://www.chm.bris.ac.uk/staff/cbutts.htm <http://www.chm.bris.ac.uk/staff/cbutts.htm>
>
Received on Wed Oct 28 2015 - 10:18:07 MST