Philosophical Goals
Smartnotebook is less about solving the nmr assignment problem, it is more about creating a basic environment which best allows the assignment process to occur. Smartnotebook is more art than science, it is all about the user interface. It is about showing the relevant information or providing the means by which the user attains the relevant information.
Smartnotebook is about bookkeeping in the assignment process and calling
other software. The project wants to be as interesting to software developers
as it is to users. It wants to showcase software written by developers.
The most un-interesting and time consuming part of a developers job is
documentation and user-interface design and bug fixing. The most frustrating
part to the user is having to learn wacky interfaces which may or may not
work correctly or be documented. It is the hope that
smartnotebook can be trusted to look
after the basic user interface while the developer concentrates on providing relevant
assignment information. Smartnotebook is far from a perfect user interface,
but it can evolve to wherever the nmr community decides to take it.
Smartnotebook does not actually compute potential
sequential connectivities, it farms that task out to a
relational database
and reads back the answers. Smartnotebook knows
how to read the connectivity patterns file because the relevant fields are
defined in the configuration files.
This separation is a good thing, a user could
potentially add/correct the connectivities before smartnotebook sees them,
and secondly, the software which computes connectivities
could develop separately
or be completely replaced by something better in the future.
Note that the creation of any spectral display involves calling
several nmrview routines in the correct manner.
Because the drawing routines are basic in nmrview, and because there
is no other snb dependency to nmrview, it is with a fair amount of confidence
that smartnotebook claims compatibility with any version of nmrview
or any user-modified version of nmrview. This is very important because nmrview easily
lends itself to hybridized versions. NmrviewJ is quite different though and it may
take some time for snb to claim compatibility with this software.
You do not have to know nmrview to use smartnotebook.
Nevertheless, if you are familiar with nmrview you will have all of the
powerful tools within nmrview available.
Although it appears advantageous that snb allow the user to indicate
peaks which are missing or mis-interpretted, implementation would be
awkward. The spectral display graphics belong to nmrview, thus a mouse
click on a displayed peak only has meaning within nmrview. For those people
who realize they can modify nmrview tcl scripts in order to communicate
the information back to snb, I suggest that the time and convenience saved
in peakpicking will be more than offset by errors and compatibility issues
of marrying snb to nmrview.
Many users have indicated that the ability to manually create connections
within snb would essentially circumvent the above issues. Therefore starting
with version 4.0 and higher we have added this ability.
If you are changing the software in smartnotebook, all I ask is that you
let me know via email. I will release several minor revisions of 5.x
and at least one more major revision. If there is a chance to encorporate
your nice changes, then I would do so.
This file last updated:
Questions to:
bionmrwebmaster@biochem.ualberta.ca
Experimental Independence
Smartnotebook is not restricted to certain types of nmr data one must collect.
The software achieves experimental independence through the use of
interchangeable configuration files. These
are highly documented, simplistic tcl scripts which
define what the spectra are and how they can be displayed in
order to provide the user with the best visual perspective for evaluating
connectivity patterns.
As new experiments emerge or new ways of analyzing current nmr data emerge, the
ability to design and share these configuration files is certainly
an appealing aspect. Note that the configuration files are currently
written to provide the information necessary for calling nmrview.
The relationship between smartnotebook and nmrview
It is important to realize that smartnotebook does not draw any spectra.
The routines
which handle the spectral display aspects are found entirely within Bruce Johnson's
nmrview software. Bruce had the foresight to make these routines accessible to
users, they are easy to use and understand.
The relationship between snb and peakpicking
Smartnotebook prefers to have nothing to do with modifying the
user's input peakpick files, it is the user's responsibility to
validate the peakpick information . The
user can modify peakpick files via nmrview or through the use of another
program. Smartnotebook provides the means to re-read peaklists and re-calculate
connectivities based on changed peaklists.
Smartnotebook as a learning tool
Why bother with smartnotebook
Let me quickly summarize the advantages of using smartnotebook.
If you are not sure about reviewing this software then consider
the following:
The software is surprisingly fun to use even
for the person with limited nmr experience. Smartnotebook is built on top
of nmrview and other tools, but knowledge of these other tools is optional.
The software is open source because we believe smartnotebook offers a basic
bookkeeping/assignment environment that developers may want to exploit.
We are serious about support and future software development. We
try hard to keep good documentation, examples, release notes, and the
update of web pages. We release bug fixes, we reply to email.
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