nmrshiftdb-users — For users of the nmrshiftdb database

[Nmrshiftdb-users] Consider contributing

[Christoph S. <c.s...@un...>]

Dear Colleagues,

quite some time has passed since my last email to this nmrshiftdb-users=20
mailing list.
Meanwhile, we have both released version 1.0 of NMRShiftDB as well as=20
published a technical article on the database [1]. The number of=20
registered users has grown considerably and is still growing at a rate=20
of about one per day. This is a lot, if you take into account that we=20
are not yet advertising the database on a large scale.
You will also have noticed that we have passed the 6000 structures=20
boundary. The database software has stabilized considerably and is now=20
running for weeks without reboot :-)

Now I'm taking the chance to point your attention to a few important issu=
es.

1. CONSIDER CONTRIBUTING

One of the more interesting feature of NMRShiftDB, which makes it=20
different from existing databases in the field, is the option for the=20
user to contribute datasets. Only by this mechanism, NMRShiftDB will get=20
bigger and better. Please consider contributing to NMRShiftDB by=20
entering datasets (a structure, a spectrum, an assignment and some=20
additional data) which are interesting for you. This could be either=20
from your own work or from the current or past literature.
If there are electronic collections of such data in your institution,=20
consider donating them to NMRShiftDB. We will be happy to write a parser=20
for this data.
Just think about one dataset per week (~15 min, depending of the dataset=20
size). With 200 users, this makes 1000 datasets per year, which would be=20
a nice start. We are also looking for people to act as reviewers of datas=
et.

2. POST QUESTIONS, HINTS, ETC., TO THIS LIST

This email list is supposed to be forum of information exchange between=20
NMRShiftDB users. If there are any questions, hints, comments, etc.,=20
consider sending your email to this list. This will make the discussion=20
more efficient and transparent, compared to an email exchange between=20
just the administrators and you. We would love to get some feedback from=20
your side. Further, consider reporting bugs and filing requests for=20
enhancements (RFE) via http://www.sourceforge.net/projects/nmrshiftdb

3. UPDATE

We are currently working on a stand-alone client of NMRShiftDB, which=20
will allow you to maintain offline versions of NMRShiftDB, to enter and=20
maintain your own data offline, and to synchronize selected datasets=20
with the online version of NMRShiftDB. An alpha version should be=20
available soon.


With best regards,

Christoph Steinbeck and Stefan Kuhn


[1] Steinbeck, C.; Kuhn, S.; Krause, S. NMRShiftDB - Constructing a=20
Chemical Information System with Open Source Components. Journal of=20
Chemical Information & Computer Sciences 2003, 43, 1733 - 1739.
http://dx.doi.org/10.1021/ci0341363

--=20
Dr. rer. nat. habil. Christoph Steinbeck (c.s...@un...)
Groupleader Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

Re: [Nmrshiftdb-users] Bugfix release 1.0.1

[Egon W. <eg...@sc...>]

On Monday 01 December 2003 10:51, Stefan Kuhn wrote:
> > I can only find a 1.0 release on SourceForge...
>
> I did not yet find time to put things on the upload page. I will do this
> today.

Would be better to put things first online for download, and then send out the 
announcements...

> > > There are also some new features, most
> > > notably the rating system, which enables users to vote on the quality
> > > of entries (for detailed information, see
> > > http://www.nmrshiftdb.org/portal/pane0/Help?URL=using.html#rating).
> >
> > Is this a good idea? In my opiniion a record is correct or not, i.e.:
> > - the assignment is correct or not
> > - the Mhz of the apparatus determines some quality parameters
> >    on the position, but that's just experimental details...
> >
> > But why add a voting system? Why would a vote be better than the original
> > entry? Can anyone vote? Even people with less experience than the
> > submitter? I'm not confinced that this is a good idea... (please convince
> > me)...
>
> Obviously you are right with this. Data is either wrong or right, but the
> question is how to determine this? Also the reviewers are not able to see
> errors. So our idea was to enable the accumlation of opinions. 

I can agree with this view.

> For example,
> a user recently suggested that something must be wrong with the assignments
> of Strychnine. 

Then he should file a bug report... an extensive one, not just a voting 
system... it's to limited... if he thinks its wrong, then he should give his 
arguments why the entry is wrong... and these arguments can be reviewed, and 
if considered valid, the entry should be revised, *and* keep the original 
'bad' entry for archieval purposes... in other words, add a new spectrum to 
the database with the corrected assignments, and *keep* the original, but 
deprecate it so that it no longer shows on the website...

> Now he could give this opinion in a more formal way. Note
> that spectra never get deleteted because of a rating, 

I think a spectrum should *never* be deleted what soever, just deprecated into 
a archival database... it's important to track down the complete history of a 
structure...

> they only are no
> longer used for predictions if the mark falls below 5 (this can never
> happen due to a single vote). Christoph and me get noticed if this happens,
> so we can have a look at it. We will see if the rating system is used. If
> it is not accepted, it's OK for me as well.

We'll see what happens...

> Thanks for comments.

Thanks for taking them seriously.

Egon

Re: [Nmrshiftdb-users] Bugfix release 1.0.1

[Stefan K. <ste...@un...>]

Wellcome to our first discussion on the nmrshiftdb-users maiing list ...

Am Saturday 29 November 2003 12:04 schrieb E.L. Willighagen:
> On Friday 28 November 2003 16:04, Stefan Kuhn wrote:
> > Dear NMRShiftDB users,
> > on Wednesday version 1.0.1 of the NMRShiftDB software was deployed to=
 the
> > servers. This is mainly a bugfix release, fixing problems with displa=
y of
> > explicit Hs and some other problems.
>
> I can only find a 1.0 release on SourceForge...

I did not yet find time to put things on the upload page. I will do this=20
today.

>
> > There are also some new features, most
> > notably the rating system, which enables users to vote on the quality=
 of
> > entries (for detailed information, see
> > http://www.nmrshiftdb.org/portal/pane0/Help?URL=3Dusing.html#rating).
>
> Is this a good idea? In my opiniion a record is correct or not, i.e.:
> - the assignment is correct or not
> - the Mhz of the apparatus determines some quality parameters
>    on the position, but that's just experimental details...
>
> But why add a voting system? Why would a vote be better than the origin=
al
> entry? Can anyone vote? Even people with less experience than the
> submitter? I'm not confinced that this is a good idea... (please convin=
ce
> me)...

Obviously you are right with this. Data is either wrong or right, but the=
=20
question is how to determine this? Also the reviewers are not able to see=
=20
errors. So our idea was to enable the accumlation of opinions. For exampl=
e, a=20
user recently suggested that something must be wrong with the assignments=
 of=20
Strychnine. Now he could give this opinion in a more formal way. Note tha=
t=20
spectra never get deleteted because of a rating, they only are no longer =
used=20
for predictions if the mark falls below 5 (this can never happen due to a=
=20
single vote). Christoph and me get noticed if this happens, so we can hav=
e a=20
look at it. We will see if the rating system is used. If it is not accept=
ed,=20
it's OK for me as well.
Thanks for comments.
Stefan

>
> > The
> > changelog can be found at http://nmrshiftdb.sourceforge.net/CHANGELOG.
>
> Egon

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

Re: [Nmrshiftdb-users] Bugfix release 1.0.1

[E.L. W. <eg...@sc...>]

On Friday 28 November 2003 16:04, Stefan Kuhn wrote:
> Dear NMRShiftDB users,
> on Wednesday version 1.0.1 of the NMRShiftDB software was deployed to the
> servers. This is mainly a bugfix release, fixing problems with display of
> explicit Hs and some other problems. 

I can only find a 1.0 release on SourceForge...

> There are also some new features, most
> notably the rating system, which enables users to vote on the quality of
> entries (for detailed information, see
> http://www.nmrshiftdb.org/portal/pane0/Help?URL=using.html#rating). 

Is this a good idea? In my opiniion a record is correct or not, i.e.:
- the assignment is correct or not
- the Mhz of the apparatus determines some quality parameters
   on the position, but that's just experimental details...

But why add a voting system? Why would a vote be better than the original 
entry? Can anyone vote? Even people with less experience than the submitter?
I'm not confinced that this is a good idea... (please convince me)...

> The
> changelog can be found at http://nmrshiftdb.sourceforge.net/CHANGELOG.

Egon

-- 
eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

[Nmrshiftdb-users] Bugfix release 1.0.1

[Stefan K. <ste...@un...>]

Dear NMRShiftDB users,
on Wednesday version 1.0.1 of the NMRShiftDB software was deployed to the=
=20
servers. This is mainly a bugfix release, fixing problems with display of=
=20
explicit Hs and some other problems. There are also some new features, mo=
st=20
notably the rating system, which enables users to vote on the quality of=20
entries (for detailed information, see=20
http://www.nmrshiftdb.org/portal/pane0/Help?URL=3Dusing.html#rating). The=
=20
changelog can be found at http://nmrshiftdb.sourceforge.net/CHANGELOG.
Yours,
Stefan Kuhn

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] NMRShiftDB release

[Stefan K. <ste...@un...>]

Dear NMRShiftDB users,
We proudly announce the release 1.0 of the NMRShiftDB software, which has=
 been=20
running on our servers for the last few days. We found the software to be=
=20
stable and the set of features to be complete enough to justify this step=
. We=20
are well aware that this release is not perfect, but development will=20
continue and you are welcome to suggest bugs and enhancements. Detailed=20
information about the release can be found in=20
http://nmrshiftdb.sf.net/CHANGELOG and=20
http://nmrshiftdb.sf.net/RELNOTES. On http://www.sf.net/project/nmrshiftd=
b you=20
will find a binary and a source version of the software and a database=20
snapshot (not containing personal data).
Our thanks go to all who made this possible, especially to our users who =
were=20
patient enought to use and test the software.
Currently most development efforts go into our standalone client which wi=
ll=20
offer the possibility to build local databases and to synchronize them wi=
th=20
the nmrshiftdb servers after data have been collected as well as a much m=
ore=20
convenient input interface.

With best regards,

Stefan Kuhn and Christoph Steinbeck

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] Re: NMRShiftDB network is growing

[Christoph S. <c.s...@un...>]

Dear NMRShiftDB users,

a new server has been added to the NMRShiftDB network, named
cubic.nmrshiftdb.org and hosted at the Cologne University Bioinformatics
Centre (CUBIC). Due to load balancing at work you can still use
http://www.nmrshiftdb.org as a gateway and will be redirected to one of=20
the three servers.

Further, we are glad to announce that the German Research Counsil
(Deutsche Forschungsgemeinschaft, DFG) has made setting up of this=20
server possible and is sponsoring further development of NMRShiftDB.

Last not least, we have almost reached our goals for the NMRShiftDB 1.0
release. After a few more weeks of testing, version 1.0 will be=20
available on all servers.

NMRShiftDB is a database made *by* users *for* users. Please consider
contributing data to this repository to make it a success. The steep
growth of the database in the last month has been due to generous
contributions from various inhouse database, but ultimately, day by
day contributions from users like you will be the most important source
of data.

Greetings,

Stefan Kuhn and Christoph Steinbeck

--=20
Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

[Nmrshiftdb-users] Latest NMRShiftDB feature

[Stefan K. <ste...@un...>]

Dear NMRShiftDB users,
probably the last feature before our upcoming release: On your personal p=
age=20
(link on top of page) you now find an overview of your unreviewed=20
contributions and, in case you are a reviewer, of spectra assigned to you=
 and=20
not yet reviewed. Here you can go directly to the review page. This shoul=
d=20
make life easier for our reviewers (who still get the emails).
Greetings,
Stefan Kuhn
--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] NMRShiftDB news

[Stefan K. <ste...@un...>]

Dear users,
we installed a new version of the Marvin applets, which are signed. This =
makes=20
it possible to directly load and save files. You need to declare these=20
applets as trusted once in order to use this. Although the applets are no=
t=20
our own ones, we believe them not to be malicious, as does the CA, Thawte.
We also can announce that we have now reached the full set of features fo=
r the=20
1.0 realease.
Regards,
Stefan Kuhn

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] News from NMRShiftDB

[Stefan K. <ste...@un...>]

Dear NMRShiftDB users,
we have received a batch of new data, so the database has grown significa=
ntly.=20
Thanks to Mr. Kolshorn from the University of Mainz for that!
We also added a search for conditions feature, which makes it possible to=
=20
search for e. g. the assignement method. The predicition portlet now show=
s a=20
real histogram of the found values.
Regards,
Stefan Kuhn

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] New nmrshiftdb features

[Stefan K. <ste...@un...>]

Dear users,
there are some new features in nmrshiftdb:
Firstly the keyword search is more flexible. See the Help for a descripti=
on.
Secondly you may submit atom identifiers with a molecule. They do not=20
influence the atom numbering, but may be usefull if the literature uses=20
labels like 1', 2'', 3'''... or greek letters.
Thirdly on sourceforge there is now a separate tracker for errors in the =
data=20
(as opposed to errors in the program aka bugs) which can be found at=20
http://sourceforge.net/tracker/?atid=3D560728&group_id=3D20485&func=3Dbro=
wse. We=20
also put a link to this tracker on the details portlet.
Regards,
Stefan Kuhn

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] New nrmshiftdb feature

[Stefan K. <ste...@un...>]

Dear nmrshiftdb users,
we decided to have the assignment method as a further measurement conditi=
on.=20
From now on you will be able to specify this.
Regards,
Stefan Kuhn
--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] New features

[Stefan K. <ste...@un...>]

Dear NmrshiftDB users,
from tomorow there will be new features available on nmrshiftdb.org:
Firstly it is now posssible to add new keywords/names to molecules if you=
 add=20
a spectrum to an existing molecule.
Secondly a search for multiplicities is possible. The search is done via =
the=20
"Search by molecule/spectrum properties"-form. The syntax is similar to t=
he=20
molecular formula search, but with S,D,T or Q instead of element symbols.=
 See=20
the help for details.
Stefan Kuhn
--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] New literature managment system

[Stefan K. <ste...@un...>]

Dear users,
from tomorrow a new literature reference management system will be online=
 on=20
NMRShiftDB. It has the advantage of giving better control of format of=20
references and will also enable more specific search capabilities (curren=
tly=20
only author and title search are implemented). If anything is unclear, do=
 not=20
hesitate to ask ! The help will be updated soon.
The old entries will keep their old references and these will be displaye=
d in=20
details. If you edit a spectrum and add a new style reference, the old=20
reference will be deleted, else it will be kept.
Enjoy!
Stefan

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] Feature freeze

[Stefan K. <ste...@un...>]

Dear friends of NMRShiftDB,
we are planning to move towards a stable realease soon. In order to do so=
=20
there will be a feature freeze for NMRShiftDB. This does not mean that=20
development will stop, but it means that there will be a break in adding =
new=20
features. If you think there are features needed which should be in the f=
irst=20
stable realease you are encouraged to suggest this either on this list or=
 on=20
https://sourceforge.net/tracker/?group_id=3D20485&atid=3D370485.
Stefan

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-5092
My public PGP key is available at http://pgp.mit.edu

[Nmrshiftdb-users] NMRShiftDB status report

[Christoph S. <c.s...@un...>]

***
PRE-SCRIPTUM A: Please consider making feature requests and bug reports=20
using the feature and bug trackers on SourceForge=20
http://sourceforge.net/projects/nmrshiftdb

PRE-SCRIPTUM B: Consider posting to this mailing list. The list is open=20
for any discussion regarding NMRShiftDB.
***

Dear NMRShiftDB User,

status reports like this one are preceded by a news update, followed by=20
a general section, which will be updated and reposted on a regular=20
basis, as soon as this is justified by a certain number of new=20
registrants or an important update of NMRShiftDB.

CURRENT UPDATE

NMRShiftDB does now have about 75 registered users with 5 to 7 users=20
constantly connected.
Meanwhile, NMRShiftDB has been moved to a new 2-node failsafe cluster=20
with a greatly improved performance. This cluster is kindly hosted and=20
supported by the Max-Planck-Institute of Chemical Ecology in Jena,=20
Germany (http://www.ice.mpg.de).
The group that develops NMRShiftDB has moved to the Cologne University=20
Bioinfomatics Center (CUBIC, http://www.cubic.uni-koeln.de/steinbeck),=20
where we will soon install our first external mirror.


GENERAL REMARKS, CAVEATS, HINTS

- NMRShiftDB is an open-source, open-content database for organic=20
molecule and their NMR data. Currently we support proton and carbon 1D=20
NMR spectra. Support for proton spectra is incomplete, however, due to=20
missing possibility for entering multiplicities and coupling constants.

- Up to date, NMRShiftDB is not complete, not comprehensive and not=20
stable. Please consider making detailed bug reports using the bug and=20
feature trackers at http://sourceforge.net/projects/nmrshiftdb

- We feel dedicated to the ideas of the open-source movement and we thus=20
need your support but even more we need your patience with the initial=20
imperfections of NMRShiftDB.

- NMRShiftDB will only grow through contributions by the community. If=20
you are interested in contributing spectral assignments, either from=20
your own work or from the literature, please contact me or the=20
NMRShiftDB administrator to organize the reviewing process.
We urge you to consider contributing. One structure + spectrum +=20
assignment per month is better than nothing, one per week is better than=20
one per month, etc. :-)


USAGE

General usage of NMRShiftDB should be straightforward for everyone=20
familiar with other spectral databases.

Two important points should be stressed here:

- Please send comments, bug reports, feature requests or just a "hello"=20
to the nmr...@li... mailing list  (The lists=20
homepage with archive is=20
http://lists.sourceforge.net/lists/listinfo/nmrshiftdb-users).

- Please consider using the bug tracker and feature tracker at=20
http://sourceforge.net/projects/nmrshiftdb to file feature requests and=20
bug reports.


CONTRIBUTIONS

Please email to c.s...@un... if you want to discuss=20
potential contributions.

With a growing number of people willing to contribute structures and=20
spectra, we need a better organization of the reviewing process.
NMRShiftDB's architecture provides support for so called "review=20
groups". Theses groups are to organize contributors in small clusters,=20
whose members review each other's contributions.

If a workgroup in an academic or industrial environment decides to=20
contribute to NMRShiftDB, the members of this group could, after=20
registration on NMRShiftDB, form a review group to facilitate the=20
exchange of data neccessary for reviewing.

Please be aware of the fact that anonymous peer review is no issue in=20
NMRShiftDB - instead, reviewer and submitter need to work closely=20
together in order to ensure data quality.
This can, for example, be done by faxing or e-mailing each other the=20
original data (for example copies of the paper from which the data was=20
taken).
The reviewing will become even easier if you augment your source with=20
handwritten notes, marks, etc., that highlight the data which have been=20
entered. Often, measurement conditions, solvents, and other interesting=20
data are nastily hidden within the text. :-)
So, as soon as you contribute your first few data sets, you will be=20
assigned to a review group. If you want to form a review group with=20
colleagues from your laboratory, in order to facilitate the exchange of=20
the underlying material, that's fine. Just send us an email=20
(c.s...@un...).


SPONSORING

Last but not least we would like to point your attention to the=20
possibility of sponsoring NMRShiftDB by either

* providing money for people entering data from the literature in order=20
to keep NMRShiftDB growing - any amount is welcome -

or

* providing money for new hardware, which will be used for installing=20
NMRShiftDB mirrors. These mirrors will be installed in institutions,=20
which are willing to collaborate with us and which should be=20
geographically and network-topologically distinct from our institut in=20
order to provide the highest possible availability of NMRShiftDB.

or

* installing an NMRShiftDB mirror on your site, which will be available=20
under whatevernameyouchoose.nmrshift.org. This comes down to buying a=20
reasonably well equipped standard PC, hooking it up to the internet and=20
installing Linux and the NMRShiftDB software. Of course you will get all=20
the help you need from our side.

If you consider sponsoring the project please contact us=20
(c.s...@un...).

Best regards,

Christoph Steinbeck


--=20
Dr. Christoph Steinbeck (e-mail: c.s...@un...)
Groupleader Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-5092

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

[Nmrshiftdb-users] Regular Status Update for NMRShiftDB

[Christoph S. <ste...@ic...>]

Dear NMRShiftDB Registrant,

with a slowly growing community of registered users, while still being 
in beta status, we are going to post status updates for NMRShiftDB a 
little more frequently than it will be happening in the future when 
NMRShiftDB is stable.

These postings, like this one, are preceded by a news update, followed 
by a general section, which will be updated and reposted on a regular 
basis, as soon as this is justified by a certain number of new 
registrants or an important update of NMRShiftDB.

CURRENT UPDATE

This week we will be receiving the new hardware for NMRShiftDB.
As soon as the move has been performed, NMRShiftDB will be running on a 
high-availability cluster of initially two servers which can be easily 
extended later. We should see a significant performance boost once this 
has been completed.


GENERAL REMARKS, CAVEATS, HINTS

- NMRShiftDB is an open-source, open-content database for organic 
molecule and their NMR data. Currently we support proton and carbon 1D 
NMR spectra. Support for proton spectra is incomplete, however, due to 
missing possibility for entering multiplicities and coupling constants.

- Up to date, NMRShiftDB is not complete, not comprehensive and not 
stable. Within the next weeks the system will be moved to a reasonable 
hardware platform and stress-testing can begin. We hope that the system 
will be reasonably stable within the next half year.

- We feel dedicated to the ideas of the open-source movement and we thus 
need your support but even more we need your patience with the initial 
imperfections of NMRShiftDB.

- NMRShiftDB will only grow through contributions by the community. If 
you are interested in contributing spectral assignments, either from 
your own work or from the literature, please contact me or the 
NMRShiftDB administrator to organize the reviewing process.
We urge you to consider contributing. One structure + spectrum + 
assignment per month is better than nothing, one per week is better than 
one per month, etc. :-)


USAGE

General usage of NMRShiftDB should be straight forward for everyone 
familiar with other spectral databases.

Two important points should be stressed here:

- Please send comments, bug reports, feature requests or just a "hello" 
to the nmr...@li... mailing list  (The lists 
homepage with archive is 
http://lists.sourceforge.net/lists/listinfo/nmrshiftdb-users).

- Please consider using the bug tracker and feature tracker at 
http://sourceforge.net/projects/nmrshiftdb to file feature requests and 
bug reports.


CONTRIBUTIONS

With a growing number of people willing to contribute structures and 
spectra, we need a better organization of the reviewing process.
NMRShiftDB's architecture provides support for so called "review 
groups". Theses groups are to organize contributors in small clusters, 
whose member review each other's contributions.

If a workgroup in an academic or industrial environment decides to 
contribute to NMRShiftDB, the members of this group could, after 
registration on NMRShiftDB, form a review group to facilitate the 
exchange of data neccessary for reviewing.

Please be aware of the fact that anonymous peer review is no issue in 
NMRShiftDB - instead, reviewer and submitter need to work closely 
together in order to ensure data quality.
This can, for example, be done by faxing or e-mailing each other the 
original data (for example copies of the paper from which the data was 
taken).
The reviewing will become even easier if you augment your source with 
handwritten notes, marks, etc., that highlight the data which have been 
entered. Often, measurement conditions, solvents, and other interesting 
data are nastily hidden within the text. :-)
So, as soon as you contribute your first few data sets, you will be 
assigned to a review group. If you want to form a review group with 
colleagues from your laboratory, in order to facilitate the exchange of 
the underlying material, that's fine. Just send us an email.


SPONSORING

Last but not least we would like to point your attention to the 
possibility of sponsoring NMRShiftDB by either

* providing money for people entering data from the literature in order 
to keep NMRShiftDB growing - any amount is welcome -

or

* providing money for new hardware, which will be used for installing 
NMRShiftDB mirrors. These mirrors will be installed in institutions, 
which are willing to collaborate with us and which should be 
geographically and network-topologically distinct from our institut in 
order to provide the highest possible availability of NMRShiftDB.

If you consider sponsoring the project please contact us.

Best regards,

Christoph Steinbeck

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

[Nmrshiftdb-users] Problems with chemical shifts

[Christoph S. <ste...@ic...>]

Anh Tho Nguyen wrote:
> hello,
> 
> I am very happy to be a member of nmrshiftdb-users but I sometimes get problem in introducing NMR chemical shifts. Could you please give me some advices.
> 
> Yours sincerely,
> Nguyen Anh Tho

Would you be able to specify the problem in greater detail?
Do you mean that there are problems with searching for similar spectra 
using a list of chemical shifts?

There was a known bug in the spectrum search:
If you have inserted two or more empty lines at the end of you shift 
list, which easily happens without you even noticing it, you would get 
an error message regarding wrong characters.
This bug has been fixed yesterday.

If there are any other problems, please file a bug on the NMRShiftDB bug 
tracker http://sourceforge.net/tracker/?group_id=20485&atid=120485 
(preferred) or report the bug to the list.

Cheers,

Chris

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

[Nmrshiftdb-users] (no subject)

[Anh T. N. <ann...@ul...>]

hello,

I am very happy to be a member of nmrshiftdb-users but I sometimes get problem in introducing NMR chemical shifts. Could you please give me some advices.

Yours sincerely,
Nguyen Anh Tho

[Nmrshiftdb-users] Status Update for NMRShiftDB

[Christoph S. <ste...@ic...>]

Dear NMRShiftDB Registrant,

with a slowly growing community of registered users while still being in 
beta status, we are going post status updates for NMRShiftDB a little 
more frequently than it will be happening in the future when NMRShiftDB 
is stable.

These postings, like this one, will be preceded by a news update, 
followed by a general section, which will be reposted on a regular 
basis, as soon as this is justified by a certain number of new 
registrants or an important update of NMRShiftDB.

CURRENT UPDATE

With a growing number of people willing to contribute structures and 
spectra, we need a better organization of the reviewing process.
NMRShiftDB's architecture provides support for so called "review 
groups". Theses groups are to organize contributors in small clusters, 
whose member review each other's contributions. Please be aware of the 
fact that anonymous peer review is no issue in NMRShiftDB - instead, 
Reviewer and Submitter need to work closely together in order to 
facilitate the reviewing process and to ensure data qualtiy.
This can, for example, be done by faxing or e-mailing each other the 
original data (for example copies of the paper from which the data was 
taken).
The reviewing will become even easier if you augment your source with 
handwritten notes, marks, etc., that highlight the data which have been 
entered. Often, measurement conditions, solvents, and other interesting 
data are nastily hidden within the text. :-)
So, as soon as you contribute your first few data sets, you will be 
assigned to a review group. If you want to form a review group with 
colleagues from your laboratory, in order to facilitate the exchange of 
the underlying material, that's fine. Just send us an email.

GENERAL REMARKS, CAVEATS, HINTS

- NMRShiftDB is an open-source, open-content database for organic 
molecule and their NMR data. Currently we support proton and carbon 1D 
NMR spectra.

- We need your help in order to make NMRShiftDB stable and comprehensive 
and thus a success.

- Up to date, NMRShiftDB is not complete, not comprehensive and not 
stable. Within the next week the system will be moved to a reasonable 
hardware platform and stress-testing can begin. We hope that the system 
will be reasonably stable within the next half year.

- We feel dedicated to the ideas of the open-source movement and we thus 
need your support but even more we need your patience with the initial 
imperfections of NMRShiftDB.

- NMRShiftDB will only grow through contributions by the community. If 
you are interested in contributing spectral assignments, either from 
your own work or from the literature, please contact me or the 
NMRShiftDB administrator to organize the reviewing process.
We urge you to consider contributing. One structure + spectrum + 
assignment per month is better than nothing, one per week is better than 
one per month, etc. :-)

- Please send comments, bug reports, feature requests or just a "hello" 
to the nmr...@li... mailing list  (The lists 
homepage with archive is 
http://lists.sourceforge.net/lists/listinfo/nmrshiftdb-users).

- Please consider using the bug tracker and feature tracker at 
http://sourceforge.net/projects/nmrshiftdb to file feature requests and 
bug reports.

Best regards,

Christoph Steinbeck

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

[Nmrshiftdb-users] (no subject)

[Anh T. N. <ann...@ul...>]

NGUYEN ANH THO

[Nmrshiftdb-users] Current Status of NMRShiftDB database

[Christoph S. <ste...@ic...>]

Dear NMRShiftDB Registrant,

thanks very much for becoming a member of the NMRShiftDB constributors 
community.

Please be informed of the following:

- NMRShiftDB is an open-source, open-content database for organic 
molecule and their NMR data. Currently we support proton and carbon 1D 
NMR spectra.

- We need you help in order to make NMRShiftDB stable and comprehensive 
and thus a success.

- Up to date NMRShiftDB is not complete, not comprehensive and not 
stable. Within the next two weeks the system will be moved to a 
reasonable hardware platform and stress-testing can begin. We hope that 
the system will be reasonably stable within the next half year.

- We feel dedicated to the ideas of the open-source movement and we thus 
need your support but even more we need your patience with the initial 
imperfections of NMRShiftDB.

- NMRShiftDB will only grow through contributions by the community. If 
you are interested in contributing spectral assignments, either from 
your own work or from the literature, please contact me or the 
NMRShiftDB administrator to organize the reviewing process.
We urge you to consider contributing. One structure + spectrum + 
assignment per month is better than nothing, one per week is better than 
one per month, etc. :-)

- Please send comments, bug reports, feature requests or just a "hello" 
to the nmr...@li... mailing list  (The lists 
homepage with archive is 
http://lists.sourceforge.net/lists/listinfo/nmrshiftdb-users).

- Please consider using the bug tracker and feature tracker at 
http://sourceforge.net/projects/nmrshiftdb to file feature requests and 
bug reports.

Best regards,

Christoph Steinbeck

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..