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20th January 2014 @ 11:23

There are excellent how-to guides for using the lab notebook and Github.

There are a few extra general guidelines common to both that need to be borne in mind. These are summarized below, and were originally described here and here. Some points are also mentioned in this guide to making the perfect chemistry ELN entry.

1) Context. A lab book post or a GitHub Issue must have some context, to be clear to an outsider or someone who arrives at the project at that point. For an experiment there should be a reason given for the experiment somewhere near the start, ideally with a link to another experiment or to the literature. For a good example see here. For a Github Issue there needs to be some link out to the reason for a particular issue having arisen and why it needs to be solved. For a good example see here.

2) Completion. If an experiment has been completed, a sentence to this effect (along with the conclusion derived from the experiment) needs to be placed near the beginning of the entry. For Github issues, Issues should be closed, ideally with a comment as to why the Issue is being closed, or perhaps with a link to a more recent Issue that was opened that supersedes the existing issue and makes it redundant.

3) All data. Remember that an ELN entry needs to include all data relevant to an experiment. Raw and processed data. Everything should be present that allows us to write up the compound's synthesis for publication.

4) Citations. ELN entries are the bedrock of the project. If something is being discussed on Github, or elsewhere, about some aspect of the lab work, include links to the ELN to justify statements. e.g. rather than saying "Reaction X appears to be working" instead say "Reaction X appears to be working based on the NMR spectrum [here]" Also within Github, if there are Issues relevant to other issues, simply pasting in the URL for one issue will create a link between them automatically, which can be very useful.

5) Schemes - all ELN entries should have schemes. Github entries mentioning molecules should have pictures - very easy to drag and drop.

6) Strings - Inchis need to be added to ELN entries for molecules that have been synthesized, whether they are the product of a reaction or they have been employed as reagents. Smiles appear to be less effective.

7) Tags in Github. To allow OSM to maintain active collections of activity (e.g. all molecules being made, or all activity on a particular series) we must used Github tags. When creating or commenting on an issue, please consider whether the right tags are being used.

8) When making a molecule. Create a Github Issue for the molecule. Tag it with "Being Synthesised". Provide an approximate timeline for completion of the synthesis, either using Github itself or by writing in a deadline to the Issue. Close the Issue when the molecule has been made.


Though these are more things to remember, they will make the ELN and Github much better resources for the project.

This post authored by Mat Todd