Dear Mark,
And of course this one is topical:-
http://publicationethics.org/case/lost-raw-data
Best wishes,
John
Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athe
have a look at this case, no danger of your coordinates going to anyone but
yourself if you do it this way:
http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers
On 26 Apr 2012, at 12:02, Jrh wrote:
> Dear Colleagues,
> I have followed this thread with great i
Dear Jeremy,
Thank you for the attached cartoon, most warmly welcome by all those in
need of a "displacement activity" in this gruesomely cold and rainy month of
April.
Oh those terrible French! I know them, I am one of them ;-) .
I found the Wikipedia entry on the subject qu
Dear Colleagues,
I have followed this thread with great interest. It reminds me of the Open
Commission Meeting of the Biological Macromolecules Commission in Geneva in
2002 at the IUCr Congress. Ie at which it was concluded that protein
coordinates and diffraction data would not be provided to r
On Wednesday, April 25, 2012 09:40:01 am James Holton wrote:
> If you want to make a big splash, then don't complain about
> being asked to leap from a great height.
This gets my vote as the best science-related quote of the year.
Ethan
--
Ethan A Merritt
Biomolecular Structure Cent
An effective tactic that has not been mentioned yet is simply to attach
your coordinates and map to a blanket email and send it simultaneously
to all of your competitors. The key thing here is "all". Send it to
EVERYONE who might serve as a reviewer for your structure. This may
sound like
topic: Supplying PDB file to reviewers
It seems that this discussion has somehow reached the conclusion that if
a reviewer asks for model/data, there absolutely must be an ulterior
motive to cheat you out of your high profile publication.
On the other hand, it seems like the intent of such review
I agree completely with Ed and made a similar suggestion when this
discussion came up last time i.e. the reviewer should reveal the identity
if he wants coordinates. Even data (including raw data if need be) can be
given in those cases. As reviewer has a reason to suspect and therefore
want to ins
Manoj,
while reviewer-bashing is my favorite pastime too (recent gem: "studying
transcription factors will not advance our understanding of mechanistic
enzymology"), you should remember that they are unpaid individuals who
volunteer their time to help you to improve your paper (or so the idea
goes
It seems that this discussion has somehow reached the conclusion that if
a reviewer asks for model/data, there absolutely must be an ulterior
motive to cheat you out of your high profile publication.
On the other hand, it seems like the intent of such reviewer is also
misunderstood as if the only
Just a thought:
When a reviewer asks for the model/data,
1) The reviewer should be given at most 24-48 hours of time to give
comments after receiving the data.
2) (S)he should declare to the editor that the paper is going to be
accepted if everything with the data/model is okay. The reviewer sho
When I hear of a reviewer holding up a publication and then publishing
something similar, my first reaction is fury and I feel the case should be
investigated and this immoral individual should be exposed. However I can
see that there are many shades of gray here. We're all biased in that we
tend
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
El 19/04/12 18:42, Patrick Loll escribió:
>>
>> Well, it is clear from this comment that in different fields there are
>> different rules... . In macromolecular Xtallolgraphy, where some pe
Bosch, Juergen wrote:
To pick a bit on George's point with MR & citation.
Here's how you can read it in the paper from your favourite competitor:
A homology model was generated using [fill in any program for ab initio
prediction] and subsequently used for molecular replacement with Molrep.
The
reat degree of well placed trust and see real value in pre-publication
>> review of structures, not just papers -
>> I'm sure this is true for the overwhelming majority of the
>> macromolecular world too.
>>>
>>> Colin
>>>
>>> -Origina
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This is off course a valid point. A desperate graduate student faking a
structure risks his or hers career and reputation, while an anonymous
referee, "borrowing" someone
El 19/04/12 18:42, Patrick Loll escribió:
>>
>> Well, it is clear from this comment that in different fields there are
>> different rules... . In macromolecular Xtallolgraphy, where some people deal
>> with biologists from biomedical sciences, the impact of journals is an
>> important aspect dur
> Biology is obsessed with high impact, and I argue science is ill served by
> this preoccupation.
When two equally good scientists apply for a job, which one will be selected,
the one with N-C-S publications or the one with J-B-C publications?
Alex
On Apr 19, 2012, at 9:42 AM, Patrick Loll wro
>
> Well, it is clear from this comment that in different fields there are
> different rules... . In macromolecular Xtallolgraphy, where some people deal
> with biologists from biomedical sciences, the impact of journals is an
> important aspect during evaluation and, unfortunately, pre-publica
board [mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of
herman.schreu...@sanofi.com <mailto:herman.schreu...@sanofi.com>
> Sent: 19 April 2012 13:54
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: Re: [ccp4bb
; > Colin
> >
> > -----Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> herman.schreu...@sanofi.com
> > Sent: 19 April 2012 13:54
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Off-topic: Supplying PDB
elming majority of the macromolecular
> world too.
>
> Colin
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> herman.schreu...@sanofi.com
> Sent: 19 April 2012 13:54
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Off-to
options:
>>>>
>>>> 1) submit the coordinates and structure factors to the pdb to get a
>>>> priority date as has been suggested before. Many journals require
>>>> anyways a pdb code before acceptance of the paper. One could even
>>>> publish
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: 19 April 2012 13:54
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This is off course a valid point. A desperate graduate student faking a
structu
Thanks Ian,
Of course it'd have to be "something else" :-) but the capability of
displaying models and maps via a web-browser is at least within current
capabilities.
Perhaps the "whole" model or electron density doesn't need to be presented -
perhaps just a representative chunk or chunks w
but the real figure
>>> is probably much higher, as some journals
>>> provide this facility themselves. The sense I get from the
>>> small-molecule community is that they (we) have a
>>> great degree of well placed trust and see real value in pre-publication
>&
> Crucially this does *not* allow the coordinates or maps to be downloaded, but
> visually inspected online - via some form of web-browser plugin; Aztex Viewer
> or similar.
Anthony, it would have to be something other than AstexViewer since
the distributed version at least allows you to do a "S
;> great degree of well placed trust and see real value in pre-publication
>> review of structures, not just papers -
>> I'm sure this is true for the overwhelming majority of the
>> macromolecular world too.
>>>
>>> Colin
>>>
>>> ---
gt;
>> Colin
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> herman.schreu...@sanofi.com
>> Sent: 19 April 2012 13:54
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Off-topic: Sup
; herman.schreu...@sanofi.com
> Sent: 19 April 2012 13:54
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
>
> This is off course a valid point. A desperate graduate student faking a
> structure risks his or hers career and reput
CP4BB@JISCMAIL.AC.UK] On Behalf Of
Jobichen Chacko
Sent: Thursday, April 19, 2012 2:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear All,
Here comes the problem of blind reveiw, the authors are always at the
receving end to share all there data,
Jobichen Chacko
Sent: Thursday, April 19, 2012 2:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear All,
Here comes the problem of blind reveiw, the authors are always at the
receving end to share all there data, results and now the full
cordinate
Dear Marc,
I would release the PDB coordinates at the RCSB. The release will protect
you from
use of the coordinates since you have now acquired a release date prior to
referee viewing.
Assuming that an honest referee would request the coordinates only to
verify that all is well
before fina
Dear All,
Here comes the problem of blind reveiw, the authors are always at the
receving end to share all there data, results and now the full
cordinates to an unknown person, just trusting the journal editor. Why
don't the journals think about making the name of the reviewer also
public.
Eventhou
Thanks a lot to everyone for their insightful comments I certainly had
an interesting day trying to digest all that was said! Although my initial
reaction to the request was to turn it down since I had never heard of
such a request before, I decided in the end to accede to the request,
since not
Hi,
There is the exact same problem when releasing a software,
possibly open source, before the corresponding article is accepted.
And I don't know a correct solution to this problem.
Regards,
F.
On 04/19/2012 05:34 PM, Yu Wai Chen wrote:
Dear Marc,
As a reviewer I find it difficult to “vis
-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Joel Tyndall [joel.tynd...@otago.ac.nz]
Sent: Thursday, April 19, 2012 7:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Marc,
As a reviewer I find it difficult to “visualise” a structure based on
a static 2D figure.
I echo Joel's comments. If the (unreleased) coordinates are not
supplied by the authors on request, I would simply refuse to review the
paper on that ground. I suppose one can trust a repu
Dear Marc,
The only way a reviewer can really judge the quality ofa structure and
verify the claims made in a structural biology manuscript is by having
access to the pdb files and x-ray data. I have myself as a reviewer
requested co-ordinates and data for this purpose, and the results can be
Hi,
I think this practice (requesting the data) is getting more and more
common these days with some "scientists" having published fake
structures. You are far more protected from scientific misconduct when
you provide the data to referees (this takes place through an editorial
system - you s
y thoughts
Joel
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marc
Kvansakul
Sent: Thursday, 19 April 2012 10:34 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear CCP4BBlers,
I was wondering how common it is that reviewers reque
Is your structure already searchable in the PDB ?
You might be able to send the validation report perhaps ?
How close to publication are you ?
Jürgen
On Apr 18, 2012, at 6:34 PM, Marc Kvansakul wrote:
Dear CCP4BBlers,
I was wondering how common it is that reviewers request to have a copy of the
I always request both the final model and the experimental data
(assuming that they are not yet available directly from the PDB).
Obviously, this is done with assurances of confidentiality.
I don't think it's common though, since I was never asked to provide the
same by reviewers.
What exactly is
Dear CCP4BBlers,
I was wondering how common it is that reviewers request to have a copy of the
PDB coordinate file for the review purpose. I have just been asked to supply
this by an editor after several weeks of review, after one of the reviewers
requested a copy.
Not having ever been asked t
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