mbhebhe
commented
6 years ago I have updated the google doc. It now has the structures instead of the schemes. Since some molecules were made by different people and multiple times by each individual, I have linked in one of each person's attempt.
Comparing my experimental to that of the one in the word doc (Series 3 characterization 070214). They are pretty similar, we can use the experimental that gives the higher yield and then just use my characterizations. So to answer your question about having an exemplar write up and then linking out other procedures, I reckon that would be good. I have started doing that on the google doc.
In my ELN I have folders for the synthesis of each molecule and pages for each attempt (that are in that folder). Then I also have a page in that folder, with the processed spectroscopic data attached (the PDFs and files). So we can link in the processed data onto the google doc.
With the stings for each molecule I'm thinking of just adding the InChl only, as with SMILES strings change when you draw the molecule slightly differently (eg, the sulfonamide, if you change the positions of the oxygens and amine you get a different string, whereas it stays the same for the InChl string)
drc007
mattodd
The composite Google Doc of supporting info-style write-up of the Series 3 organic chemistry is coming together. We need to consolidate all reports of syntheses, or at least keep all reports of synthesis of a certain molecule together. We will need a simple version of this for submission of a paper.
I've added a folder to the Series 3 repo under "Reports and Theses" called Supporting Info Style Docs which contains that Word Doc with the composite characterization data and procedures in it dating back from when Series 3 was first examined. @mbhebhe can you please look at the first synthetic report contained in there (as a tester) and think about whether we need it? How does it relate to your write-up for MNB1? Do we need both? I don't have an answer here, but I want to know how we keep track of all these write-ups. Do we have one "exemplar" write-up, and simply link out to all the others?
Can you also please think about how we keep track of the spectroscopic data? The write-up for the paper will need the traditional style write-up of NMR, MS etc (as we have it). But should we not also be linking to raw data that are housed somewhere? Is it enough that we link to the ELN page containing the data? That way we can generate the image versions of the spectra later when we submit?
I think the Google Doc needs the strings for each molecule added (SMILES, InChI and INCHIKEY? Unless you think these are not needed for some reason?
Once we have an agreed strategy in place we can add that strategy to OSM somewhere - we are facing many of the same issues over on the Series 4 paper 1 repo. But let's start with MNB1