Living Molecules is an app that allows capturing, archiving and creating of molecular glyphs, which function like QR codes for chemical structures, reactions and data.

Overview

Capturing glyphs

Archiving data

Creating glyphs

Importing data

Exporting data

Summary

Overview


The Living Molecules app allows you to turn chemical structures into a molecular glyph, which can be used on documents like posters, manuscripts or web pages. Anyone who has the app can use the camera to capture molecular glyphs, and bring the chemical data onto their device. A molecular glyph is the chemical equivalent of a QR code.

The molecular glyph has a distinctive style, which is recognisable for use in hardcopy documents such as posters or printed manuscripts. This is a way of providing additional supplementary information that is not contained on the printed page: any passerby who has the app can snap the glyph, view the underlying structures, reactions and data, then import it. Once imported, the data can be used in a variety of ways, such as exporting to other chemistry aware mobile apps.

Capturing glyphs


To capture a molecular glyph, you first need the glyph to be displayed on a surface. This can be a piece of paper, or computer monitor, or the screen of a mobile device. If you are trying this out for the first time, you should ideally either print out this web page, or read it on a secondary device.

This is an example of a molecular glyph (for more, see gallery).

Open the Living Molecules app on your iPhone, iPod or iPad. Select the Capture panel on the app: it will show the camera feed, with a hexagon target icon in the middle:

Now point your device camera toward the molecular glyph, which should be displayed on a computer screen, or on a piece of paper. You will need to adjust the distance and orientation of the device so that the targetting hex is a close overlap with the boundary hex of the glyph.

Note that you have some latitude with distance and rotation about the Z-axis, but you do need to hold your device parallel to the paper:

Once you have an approximate line up with the target hex, move the device around until it locks on. When that happens, you will see the matching in operation. The outline of the hexagon is used to establish the exact size and shape of the glyph, while the black dots on the inside make up the data payload.

The payload contains just enough information to establish a source and identification for the data, so that the content can be downloaded from the internet and viewed:

For most glyph types, it is necessary to have an active internet connection to capture them. Exceptions include the demo glyphs, one of which is shown above, which do not need network access because the content is stored by default within the app. Glyphs that have already been imported into the archive also do not need to be downloaded again.

Archiving data


Once a molecular glyph is captured, it can be imported. On importing, the chemical document is stored within the app, and so can be accessed by selecting the Archive panel:

Archived chemical documents are referred to as datasheets. They can consist of a single molecule, a collection of molecules, a collection of reactions, any of the above with associated scalar data (numbers, text, etc.), as well as datasheets with special properties, such as those used by the SAR Table app.

Selecting any of the entries makes it the current archive item (see below). Tapping on the caret icon to the right brings up a preview of the document:

Documents can be deleted from the archive by swiping left or right and confirming the deletion. Data can also be utilised by exporting it to other apps (see below).

Creating glyphs


The Living Molecules app can create molecular glyphs for any data that it has in the archive. Use the Archive panel to select one of the documents, then switch to the Create panel. If the document is already stored online, or is one of the demo examples that come with the app, the panel will display the glyph onscreen:

If you have two mobile devices, it is possible to test out the glyph recognition capabiity by pointing the other device at this screen. The most useful options are available from the Export button at the top right:

This allows the glyph to be exported to the photo roll, copied onto the clipboard, or sent by email.

Each of these options allow the graphical representation of the glyph to be transported to an environment where it can be consumed. For example, the bitmapped image can be saved and used in a web page, or it can be pasted into a document that is being used to create a manuscript or a poster.

Note that for some kinds of imported data, there is no known association with an online resource, e.g. molecules or datasheets that were downloaded from an arbitrary internet page or opened from other apps. In these cases, the Create panel will not show a glyph, but rather it will display a preview of the content, and a button to Upload it:

Before a glyph can be created, the data must be uploaded to a datasheet storage service that is hosted on molsync.com. This service operates anonymously, and serves up content openly. This means that as soon as you upload your data, it will become openly available on the internet. While nobody will necessarily know that you uploaded it, or any information other than what you supply in the document itself, it is public, and is not protected by any kind of security fences.

Once the data is uploaded to molsync.com, it is assigned an identity handle, because it can now be accessed online, e.g.

http://molsync.com/share?ds=1

The identity handle is used in the generation of the glyph, and its encoding allows anyone else to access the data using the Capture capabilities of the Living Molecules app.

Importing data


The Living Molecules app can import data by capturing molecular glyphs, but it can also receive chemical content from other apps (e.g. MolPrime, MMDS) and it can also be used to receive chemical data downloaded from the internet (e.g. ChemSpider molecule download).

Using the Open With feature from another chemically aware app, or the mobile web browser, select Living Molecules as the destination app. The app will be launched, and it will immediately add the new entry into the archive.

Exporting data


Creating a molecular glyph for an archived item is a form of exporting, since the data needs to be uploaded to molsync.com in order to share it. Data can also be made available to other chemistry aware apps by using the Export button from the Archive panel. Such apps include MMDS, SAR Table, MolPrime, MolSync, Reaction101 and Yield101.

Summary


The Living Molecules app creates and consumes molecular glyphs, which are chemical QR codes. The data is stored on the cloud, and can also be archived within the app. The device camera is used to capture chemical data by scanning the glyph. Glyphs can be embedded in posters or other types of printed documents in order to add an extra dimension of computer-readable supplementary data.

See Also


Mobile Molecular DataSheet (iOS), Molecular Glyphs, Products