New ELN for Pictet-Spengler Approach

25 May
Published by MatTodd

To host the raw data from the Pictet-Spengler approach to the enantioselective synthesis of PZQ Michael has started an Electronic Lab Notebook. We're using the open source Southampton Lab Blog interface for this, since we're collaborating with them on a couple of things related to this site.
Given that it's open source, the lab blog system can be changed and enhanced by anyone. This is a great chance to make the lab blog perfect for experimental organic chemistry, e.g:
1. How do we best report TLC data - at the moment we're taking photos, but this is cumbersome.
2. Wouldn't it be great if we could include machine-readable, and also editable, chemical drawings rather than pictures? How do we do this?
I hasten to add that as a trained experimental organic chemist I have no idea whatsoever how to do any of this - but I know what we need!
(I made an appeal at Google for help in this project a few months back - there's a real opportunity for the development of the killer organic chemistry ELN here based on the Soton system.)


How else would you add the TLC? Do you have anything in mind? If you're on Blog2 then I've just written a little uploader that throws files up onto a blog from a directory. It wouldn't be too hard to change it to for instance grab something from the web, e.g. Flickr. Chemical drawing is harder although I know they have done some plugins using e.g. Simile services so grabbing something like Twirlymol might be feasible.

jcbradley's picture

We've been adding your reactions to the <a href=" Attempts database</a> and these are represented in a way that machines can understand.  For example you can do substructure searches for reactants or products, reaction success, yield, etc.  The entries will always point back to your lab notebook.  We'll keep adding them periodically but let us know if your students would like to add entries more quickly.  All of the molecules are represented as ChemSpiderIDs in the database, which is nice because you can use a web service from ChemSpider to automatically render images (as we do in the book). Maybe Cameron can use a similar approach to automatically render your reactions schemes.
I noticed your spreadsheets are in image format.  Is there any way to embed the actual sheet?  You could use Google Spreadsheet perhaps. That way all the calculations will be part of the chain of provenance.  I know that miscalculations are often caught early in my group using this approach.
The last NMR I saw is also in image format - wheras previously you had uploaded JCAMP-DX.  Are you running into some problems with that format?