New electronic laboratory notebook available

[lpatiny]

We just finished our new electronic laboratory notebook designed for organic chemists ... but not only! Have a look at www.c6h6.org and our small explanation video https://youtu.be/SHN07asZaGc

Hope you would be interested in using it !

[MedChemProf]

@lpatiny I have been trying it out using Chrome on Windows 7. Interface to enter reaction does not seem to work with reagents or compounds not in database. Would it be possible to record a video on how to set up a reaction with reagents and products that are not in the database? Also, how is solvent accounted for in scheme or table?

[lpatiny]

The product has to be in the database before. A product for us is called a 'sample'.

I did a video to show you how to add it. Also note that purity may be enter in %, M (molar) or L (loading)

https://youtu.be/4UBwnFCBlvU

[mattodd]

That's great, Luc. I encourage everyone to have a go and provide feedback. It's an essential next technology for OSM to be able to record lab-based research in a way that is easily automatically linked to other, relevant research that is going on. See SCINDR Related: #372 .

[mattodd]

Hi @lpatiny - further to what we discussed offline in Germany, I'm going to encourage 3 of my students to put up a sample lab notebook write-up as a real-world trial. We'll share the links for the pages here when those are in progress. Beautiful piece of work, I hope this trial goes well.

[lpatiny]

@mattodd Maybe we could organise a hangout meeting next week with the students so that I show them couple of tricks ? What time would be ok for you ?

[edwintse]

Hi @lpatiny, I'm one of the students that Mat has asked to trial your notebook and I'd like to give some feedback.

• I like the incorporation of NMR analysis tools directly into the lab notebook, along with a place to put all other characterisation data associated with the sample.

• The reagent searching feature is really useful, minimising the time needed to look up densities, etc.

• It appears that once you create a new reaction and give it a code, you can't edit the reaction code at a later date. Enabling the editable option in the module parameters allows you to edit it but the changes are never saved. Is there a way to do this?
• Similarly to before, when you create a reaction and it shows up in the reaction list, I am unable to delete a reaction. Enabling the remove row options lets you delete the reaction but when you refresh the reactions list the deleted reaction comes back. Can this be made permanent?
• Are you able to make a video on how best to use the NMR analysis features? Things like doing manual peak picking (manual threshold), coupling, shifting spectra in overlay mode, etc.
• Is it possible to incorporate a lasso tool in the structure drawing tool to allow for easier selecting/deleting of compounds? The options for deleting compounds are not very intuitive at the moment.
• Would it be possible to paste compounds into the drawing tool using SMILES strings? This would make it easier to put in compounds drawn in chemdraw.

[mbhebhe]

Hello @lpatiny .I am also one of the students that Mat asked to trial your notebook. It is very useful and handy. I also like the NMR component and the reagents table. Just one question, some of my tabs are blue and some are red? What does that mean? We thought it meant that the 'page' hadn't been saved, but some pages do not have the save button.

[lpatiny]

Hello @mbhebhe. Nice you are testing it ! The red tabs means NOT SAVED !!! Just click on save in the corresponding tab and it should become black. The data are always continuously saved locally in the mean time. Concerning NMR did you succeed to attach a jcamp ? On a bruker spectrometer the instruction tojdx allows to save 'real / imaginary' part that you can attach to your 'sample' page.

[lpatiny]

@edwintse

It appears that once you create a new reaction and give it a code, you can't edit the reaction code at a later date. Enabling the editable option in the module parameters allows you to edit it but the changes are never saved. Is there a way to do this?

Indeed the reaction code is fixed because it is also related to all the samples that will be created from this reaction so that it would be problematic to rename it.

Similarly to before, when you create a reaction and it shows up in the reaction list, I am unable to delete a reaction. Enabling the remove row options lets you delete the reaction but when you refresh the reactions list the deleted reaction comes back. Can this be made permanent?

We have a feature that allows to manage reaction and delete them. Currently it is not available to everybody because we find it very risky ... I think we need in this case also to propose the 'undelete' feature. I will speak with the team to implement this.

Are you able to make a video on how best to use the NMR analysis features? Things like doing manual peak picking (manual threshold), coupling, shifting spectra in overlay mode, etc.

The NMR analysis feature is not currently designed to replace a specialised program but I will add a video. We are working on a more advanced tool for processing NMR spectra.

Is it possible to incorporate a lasso tool in the structure drawing tool to allow for easier selecting/deleting of compounds? The options for deleting compounds are not very intuitive at the moment.

JSME (the molecule drawing editor) remembers the last molecule you were 'hover'. So if you go over the molecule you want to delete and then go to the delete icon you will see the molecule becoming red and it is that one you will delete.

Would it be possible to paste compounds into the drawing tool using SMILES strings? This would make it easier to put in compounds drawn in chemdraw.

Yes it is already possible ! Actually you should rather use molfile rather than SMILES (at least you keep the coordinates of the atoms). In ChemDraw copy as molfile Then go over the drawing applet and press CMD + V (on mac) or CTRL + V (on windows) It may be either a molfile, molfile v3000 or SMILES.

[edwintse]

@lpatiny Great!! Thanks for answering all those questions.

[mcoster]

Wow, great initiative @lpatiny! I would like to get my next round of project students to try this out. I have had a play with it - just a couple of quick questions...

• the typical synthetic organic chemist's workflow involves drawing the intended reaction into their labbook, working out stoichiometry, conducting the reaction, workup, purification and then characterisation of the products. My team would typically assign a batch code after purification based, eg. the order of elution from chromatography, eg. mjc-1-1a and mjc-1-1b would be the first and second samples to elute from a column. Can this approach to batch codes be handled by c6h6 by eg. assigning a temporary batch code when the rxn entry is generated, then revising the batch code at a later time?

• how is it best to handle byproducts and unexpected products when using c6h6 as an ELN?

[lpatiny]

@mcoster

In the database we have 2 kinds of records:

• reaction
• sample

The reaction will contain all the information about the schema, reagents, products, etc. The reaction is characterised by a code like LP1000 (initials + sequential number).

A sample contains all the physical characteristics (spectra, physical characteristics, etc.). It is characterised by a code that is expected to be the same as the reaction code and a batch.

For us a batch may be anything like F1, After 30min, before distillation, crude, ... but can not be renamed after. Keywords can however be added to a sample to specify if it is pure, etc. (still work in progress). We are also working on a one-click submission to Zenodo to get DOI for specific data set.

So practically in a reaction:

• Clicking on 'Add product' just search in the schema for a product and allow to calculate a yield. The molecular formula may be changed anytime to recalculate the yield. If you want to add some analytical results on your final product click on the little icon on the right of the product line and this will add a 'sample' in which you may change the structure and attach any spectra and analytical results

• If you just want to add a spectrum to follow a reaction or the crude product but you didn't isolate the product, clicking on 'Add sample' add an analytical results.

[lpatiny]

New from today, you can upload xray results as CIF or PDB.

When you edit a sampleyou have now a more general drag / drop box

A dialog box will appear showing the possible target for this experimental result:

If you upload an Xray from the main screen there is now:

And it allows to directly measure and display xray results:

[lpatiny]

We added the possibility to put alpha and Rf. Please tell me if it is not as you would expect and if you see some more solvents that I should put for Rf!

[lpatiny]

In the reaction page, from the box containing the shortcuts you may now also add a timestamp in the procedure. Just click on the logo representing a calendar

And the date will be inserted at the level of the cursor