Hi Vedrin,

Thank you for your feedback.  I have added some 
further explanation below your comments where 
appropriate.  As you have pointed out, some of 
these issues are stylistic, and so open to 
individual preference, so a consensus would certainly be useful.

Regards,
David

At 02:21 AM 5/18/2010, Vedrin Jeliazkov wrote:
>Hi David,
>
>Please find below some further comments.
>
>On 18 May 2010 02:45, David Gallagher <gallagher.da at gmail.com> wrote:
> > Hi Vedrin,
> >
> > I ran a quick test with ToxPredict and have the following comments on the
> > user interface.  My first test involved entering my own structure to make a
> > toxicity prediction.
> >
> > First impressions: the interface seems to have progressed well since I last
> > looked and is much more robust with detailed explanations to help the first
> > time user, and with no problems or 404 errors etc. noted.  Obviously, the
> > results/reporting function still needs to be addressed, so I have ignored
> > that for now.
>
>This is work in progress.
>
> > 2.  I entered the SMILES string for my structure into the box, then clicked
> > "Next".  The screen refreshed and my entry was deleted.  I saw an error
> > message "We did not find any matching entries for the search you performed
> > in the OpenTox database. Please try again.", 
> however, I was not expecting to
> > search any database, but simply wanted 
> ToxPredict to make a prediction on my
> > structure.
>
>Well, in the contextual help on this screen it is clearly stated what
>the functionalities provided by the Search and Draw tabs are, quote:
>
>• Search: You can enter any free text, including but not limited to
>CAS registry number, EINECS number, SMILES, InChI, chemical name, or
>any other keyword; ToxPredict will automatically recognize the
>intended search type and return zero, one or more hits, depending on
>the search type, the information currently available in the OpenTox
>database and the selected preferred number of hits.
>• Draw: You can draw a chemical structure in the built-in editor and
>perform exact structure or substructure search, or structural
>similarity based search; ToxPredict will return zero, one or more
>hits, depending on the search type, the information currently
>available in the OpenTox database and the selected preferred number of
>hits.
>
>Moreover, the same help section also indicates that if you would like
>to import your own structures, you should use the Upload tab, quote:
>
>•Upload: You can upload your own dataset(s); ToxPredict accepts SDF,
>MOL, CSV and RDF input file formats, among many others.
> >  I checked but could see how to do this.  Am I missing something?
>
>Do you think that the Help text is not clear? Would you advise some
>changes in it?

(See user-interface issues, item 2 below.)  The 
text is quite clear, but there is too much 
information here, so many people will not read it 
in detail.  If you want to upload a file, you do 
not need detailed instructions on using the 
"Draw" function. So, the detailed instructions 
for using the "Draw" function could be put on the 
"Draw" tab, and would only be viewed when that 
tab was selected.  Similarly, the detailed 
instructions for using the "Upload" function 
should be put on "Upload" tab, etc.

The current text could then be replaced with:

First, enter your chemical structure using one of 
the three methods below, then click the "NEXT" button

This gives a cleaner looking page which is faster 
to comprehend, and if necessary, the user can 
explore the various tabs to find out more about the various options.

> > 3.  When I sketched a structure using the "Draw" tool, I got the same error
> > as in (2) above.
>
>This is expected behaviour (see comments in point (2) above).
>
>I would like to mention that we could easily broaden the semantics of
>Search and/or Draw tabs to include data upload, in addition to
>database search. There are various ways to do this, e.g:
>
>1) perform a database search and if no hits are returned AND the user
>has entered a valid SMILES/drawing, transparently accept the user
>supplied structure for prediction, in the same way as this would be
>achieved through the Upload tab;

Yes, this is the intuitive response.  Why is it 
necessary to do a search at this stage, if the 
user didn't ask for it?  I would have thought 
that the search would be performed (by default) 
at the same time as the Prediction, so all results could be presented together

>2) same as (1), but asking the user to confirm that he agrees to
>import this structure in the database;
>
>Please also consider that some users might not be happy to import
>their own structures in the OT database for various reasons., even if
>Authentication and Authorization was already in place. Hence, the need
>to clearly separate Search from Upload (at least in our opinion) ...

If they do not or can not use the draw or upload 
functions, then they would have to use the search 
function to see if their molecule was already 
available, and if not, they would be told to 
upload or draw the structure.  Of course, 
searching for a particular molecule by name or 
registry number involves similar confidentiality 
risks as uploading the actual structure.

> > 4.  Uploading a Mol file, this worked as expected.
> >
> > Some minor user-interface issues which could improve the look and feel of
> > ToxPredict:
> >
> > 1. "NEXT" button
> > For most users of the Roman alphabet, the eye naturally scans from top left
> > to bottom right of a page so, after entering any required data, the last
> > place one intuitively looks for the "Next" step  is usually the bottom
> > right.  With the current design, the "NEXT" button can appear at the top
> > right or sometimes the top left (depending on 
> page width).  The bottom right
> > would be a more intuitive place to place the "NEXT" button.
>
>Agreed. Suggested fix: make the Navigation bar appear both on top and
>at the bottom of the screen. Do you think this would solve the issue?

Just the bottom right should be sufficient.  This 
simplifies the top bar and prevents it wrapping when the window is narrowed.

> > 2. Instructions
> > The text instructions, although very helpful, are unnecessarily long.  Some
> > of the text is in triplicate.  I would suggest only succinct explicit
> > instructions to be displayed, with a "more info" link if necessary.
>
>Well, obviously in addition to being long, the text is not clear
>enough, considering the above mentioned problems you've encountered
>with the Search and Draw tabs. Could you suggest better (shorter and
>more concise) contextual help texts for each of the screens? In
>addition, we could hide the Help text in a +Help menu item, which
>would be expanded only if the user clicks on it -- would this be more
>convenient in your opinion?

See above (move the detailed instructions to the relevant tabs)

> > 3. LOGOs
> > The OpenTox and Ambit logos are too large and 
> draw the user's attention away
> > from the functionality.  They would be better placed in the centre at the
> > bottom of the page, and made smaller.
>
>Please specify the dimensions of the logos that you deem acceptable
>and we would try to apply them.

The current OpenTox logo (18-05-2010) seems about 
the right size, so perhaps the ambit logo could 
be made a similar size, then these items could be 
centered at the bottom of the page.  Also, just 
one single font style for the accompanying notes might look better.

> > 4.  Display results
> > The "Display results' seems to be an unnecessary manual step, the results
> > should be displayed automatically after the calculations are completed.
>
>Disagree. At the Estimate page, the users should be able to check
>which calculations have been completed successfully before going to
>the Results page. In case that there are some errors, the users should
>be able to check the error details at the Estimate page as well,
>instead of being automatically transferred to the Results page.
>Depending on the errors, they might prefer to run the prediction again
>or select different models,etc ..., instead of going to the results

If there are errors this makes sense, but why 
would you not go straight to the results page if 
there are no errors?  Or even show any errors 
along with the successful results?

>page.
>
> > 5.  Data entry
> > Ideally, the data entry (i.e. Search, Draw, 
> or Upload) should be independent
> > of the subsequent Database Search and Predict functions.  Currently, only
> > "Uploaded" structures can be used for predictions, and not "Drawn"
> > structures.
>
>The statement in your last sentence is wrong. Any structure (or even
>set of structures), that have been found in the OpenTox database to
>satisfy the search criteria that the user has defined either in the
>Search or Draw tabs can be used for predictions. The OT database
>contains a superset of the full list of REACH-relevant substances
>(currently 150369 chemicals). Of course, substances that are not
>included in the OT database could also be submitted for predictions
>through the Upload tab. As discussed already above, please specify
>whether you think that the semantics of Search/Draw should be enriched
>to include Upload as well, in addition to this same functionality,
>provided by the Upload tab.

I think this is already addressed above, for 
consistency, it should be possible to perform a 
prediction and/or search (for tox info) on any 
compound, regardless of the method that was used 
to enter it (i.e. Upload, Draw, or Search)

There may be some confusion here in that "Search" 
can mean to search for a chemical structure in 
the data base at the data entry point, or to 
search for recorded toxicity data and relevant 
publications relating to a structure at the prediction point.

>The structure you've uploaded doesn't happen to exist in OT database
>for some reason. A closer look reveals quite a few similar structures
>though:
>
>http://apps.ideaconsult.net:8080/ambit2/query/similarity?type=url&search=http%3A%2F%2Fapps.ideaconsult.net%3A8080%2Fambit2%2Fcompound%2F150368%2Fconformer%2F435224&threshold=0.65&max=100
>
>Yours is the last one in the list. If you had selected a similarity
>(or substructure) search in the Draw tab (instead of exact structure
>match you've obviously performed, which is the default), then your
>query would have returned some of these chemicals, depending on the
>selected Tanimoto coefficient and desired number of hits. Again, any
>suggestions for better wording of the Help text, explaining these
>functionalities would be most welcome.
>
> > This section seems to function inconsistently at present.
>
>Well, it depends on what you perceive as consistent. Obviously our
>perception is different from yours, but we would be happy to implement
>yours, provided that you specify it in more details ;-)
>
> > 6.  Standardisation on terminology
> > For consistency, it may be better the change "Step 4, Estimate" to "Step 4,
> > Predict", as this would then match the title "ToxPredict".  Otherwise, the
> > question arises, what is the difference between Estimate and Predict?
>
>Agreed.
>
> > 7.  Tag line
> > A tag line such as "Toxicity predictions, just enter your structure..."
> > under the title would succinctly explain the 
> function of the page.  "OpenTox
> > Demo application" could be repositioned at the bottom of the page.
>
>Agreed.
>
> > 8.  Disclamier
> > There should be a disclaimer at the bottom of the page (in small print)
> > explaining that computational chemistry predictions should not be relied
> > upon alone, but used as part of a weight of evidence, etc., etc......
>
>Agreed. Could you suggest the text for this Disclaimer?

Good point, we need some legally acceptable text 
here that will protect our users and ourselves, 
(which I am not qualified to provide), so lets chat to Barry about this issue.

> > Please let me know if you need any further explanation on any of the points
> > I have mentioned.
> >
> > All in all, ToxPredict seems to be progressing well, good work!
> >
> > Regards,
> > David
>
>Last, but not least -- it would be also nice to hear some other
>opinions on the controversial topics -- anyone?
>
>Kind regards,
>Vedrin