Green Lab Notebook app now available on iTunes

gln_rxneditAfter somewhat more delay than I would have liked, the Green Lab Notebook (GLN) app is now live and available on the iTunes AppStore. The feature set that made its way into version 1.0 was crafted to ensure that editing of multistep reaction experiments and automatic calculation of green chemistry metrics are fully functional, and that importing and exporting features are complete enough to be effective.

As described in previous blog posts (see here, here and here), the Green Lab Notebook app is primarily designed to capture a complete description of a chemical reaction, which is structure-centric, and as comprehensible to software algorithms in its raw form as is the graphically rendered form to a scientist. This is in contrast to the overwhelming majority of software tools designed for drawing chemical reactions, which are essentially just artwork tools, with little or no utility for machine understanding.

The fact that the app operates on a highly meaningful datastructure allows it to perform a great many value added services, as well as being reliably recorded for posterity. For example, since each of the reaction components are clearly delineated and represented by a structure in a format that can correctly infer molecular formula, it is possible to include stoichiometry as an additional field, and determine whether the reaction is balanced. Further to this, the additional annotation of the components with quantities (e.g. mass, volume, yield, etc.) allows dependent quantities to be cross-pollinated by mapping the molarities between the individual components (previously demonstrated with the Yield101 app).

Since the quantities are well described, it is also quite straightforward to calculate green chemistry metrics like atom economy, process mass intensity and E-factor. These properties are always calculated when there is enough information to do so, which is an important consideration for green chemistry as a whole, since encouraging scientists to pay attention to such metrics is much easier when it does not require additional effort to calculate them.

While many chemical reactions can be adequately described with a single step, there are many schemes where the logical description involves a series of transformations, whether the subsequent reactions were done in the same pot or by isolating an intermediate. Expressing a multistep reaction in an informatically sensible way is somewhat tricky, as is coming up with an interface that shows the arrangement on a screen of limited size. Working out the finer details of the algorithms and user interface functionality to make this effective, easy and productive consumed a large portion of the effort that went into the minimum viable product release of the app.

Besides editing of chemical experiments, there are a number of supporting features already baked into the app. For example, the solvent folder contains the Green Solvents collection, and shows the relevant environmental properties. Features from the Mobile Molecular DataSheet (MMDS) have been brought over: as well as the sophisticated touchscreen gesture-based sketcher, the scratch sheet (for temporarily stashing structures) and custom templates (for faster sketching of common fragments) are available and editable.

Data in various forms can be imported, and molecules and experiments can be exported to a number of different destinations, based on the capabilities of iOS (i.e. written to a file, sent by email, opened with a generic app, opened with a specific app, shared via MolSync, etc.). A data creation tool is, afterall, only as good as its ability to get that data to the places where it is needed.

As mentioned in various blog posts and presentations over the last year or so, there are a lot more features planned for the Green Lab Notebook app, and version 1.0 implements just enough of the full scope to make the tool useful. Besides some second order user interface additions (e.g. being able to move rows or datasheets up or down in the hierarchy), one of the major focuses for the next few releases will be to ensure that the graphical/document exporting features are maximised.

The thought here is that one of the major use cases for a lab notebook is preparing content for insertion into a report or manuscript (e.g. MS Word document). Right now the layout algorithm for showing multistep reactions is only implemented within the app itself, and in order to create content in many embeddable formats, this has to be reflected in the web services (com.mmi) software stack that powers, and is charged with the duty of creating numerous alternative graphics representations.

In its early incarnation, the Green Lab Notebook makes its claim to being associated with green chemistry due to its inclusion of  green chemistry metrics that are easy to calculate (if you have the necessary information on hand) and common solvents with environmental ratings conveniently on hand. This may be enough to justify the title of the app, but one of the next major projects is to begin collecting up well understood chemical reactions with favourable “greenness” and describing them as transforms (i.e. a reaction experiment where the structures are drawn with R-group placeholders to indicate their generic nature). With this set of transforms conveniently available, users will be able to query reactants and/or products in search of possible chemistry options of the green variety. This involves both curation and algorithm design efforts, so it won’t be happening immediately, but fun with reaction transforms is a major objective, and will be making appearances both within the mobile app, and in other parts of the Molecular Materials Informatics technology stack.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s