As mentioned in a recent post, the molecular glyph recognition algorithm used by the Living Molecules app is going to have a few more iterations before it’s in peak condition. The current public version (1.0.1) does not behave too well in low lighting conditions, which is not so bad for using with an iPhone, because it comes with its own flashlight, but that’s not the case for iPads. The last couple of days has been spent pulling everything apart and putting it all back together again, because it turns out that distinguishing between white and black is slightly more complicated than one might think. Continue reading
Month: May 2013
Reaction mapping in MMDS
Further to the previous post that mentioned a new atom-mapping interface for the Mobile Molecular DataSheet (MMDS) app, the next step is an atom-to-atom pairing interface for reactions. A very short 30 second YouTube clip will show you how this works. Continue reading
Atom mapping in MMDS
The next version of the Mobile Molecular DataSheet is going to add a couple of user interface segments for viewing and editing the atom mapping number property. Shown on the right is the menu bank for providing mapping numbers for an individual molecule. Perhaps not so very interesting in and of itself, but the next step is to construct a slightly more intricate user interface for providing atom-to-atom mapping pairs for reactions.
In case you’re wondering, the answer is yes: this is going somewhere specific. Atom-to-atom mapping is a core prerequisite for getting into the world of reaction transforms.
Living Molecules, now with its own illumination
Last week, the Living Molecules app was released on the iTunes AppStore, in its “minimum viable product” form, to use the parlance of our times. To no great surprise, the recognition sequence for taking camera images and applying an algorithmic transform to decode the binary payload was less than perfect in version 1.0, though due to a couple of rookie mistakes on my part, the nature of those imperfections taught me a couple of things that I should have already known. Continue reading
Making posters with Living Molecules
Since the Living Molecules app is now live on the iTunes AppStore, it’s time to say a little more about what its intended purpose is. While the potential uses of a “molecular QR code” system probably include a whole lot of things that I haven’t thought of, the original concept was inspired by the idea of adding supplementary information to posters.
The example poster on the right (click for the PDF version) takes the concept of “supplementary” to an absurdity, but that’s OK, because it’s a demo poster made to prove a point: each of the 17 molecular glyphs corresponds to a portion of the molecule collection that makes up the raw data for the Approved Drugs app. The data is hosted on molsync.com, where it has been residing for some time (note that it can also be found in the Drug Repurposing topic for Open Drug Discovery Teams).
If you were to print out this Letter-sized poster and stick it up on a wall, anyone who walks up and takes a look at it will either: (1) recognise the molecular glyphs for what they are, whip out their iThing and open up their already installed copy of Living Molecules; or (2) read the explanatory text to find out what it’s all about, snap the regular QR code at the top to get to the iTunes AppStore to download the free app, then proceed as for (1); or (3) send me an angry email demanding that an Android version be made available immediately.
For a more realistic poster, which is describing actual science rather than a techno-utility, >95% of the surface area of the poster would be taken up with the usual things: title, attribution, feature pictures, captions, text, graphics, etc. A modestly sized molecular glyph might be found in a corner, with a little note mentioning something like “The actual data used to produce the structure-activity plots shown above is available by capturing this glyph“.
Sharing structures with SketchEl and molsync.com
The latest version of SketchEl (1.60) has added a new feature: sharing of content via molsync.com. From either the molecule editor or the datasheet editor, the underlying content can be directly uploaded, making it openly accessible to the greater internet.
While SketchEl is not technically a product of Molecular Materials Informatics, the copyright is held by me, it’s made available via the Gnu Public License, and it gets a bit of maintenance from time to time. It is a conventional and fairly capable 2D structure drawing program that is written in pure Java, and runs on all the major platforms. It can even be used as an applet, though that doesn’t matter as much as it used to. It also allows editing of molecular spreadsheets (“datasheets”) that contain molecules and various scalar data. Over the years (since 2005) it has served as a test bed for a few ideas, like the SketchEl molecule file format, and I still use it regularly for editing structures and collections.
The newly added sharing feature offers to upload the current molecule or datasheet. Once the upload is complete, the result is available in the form of a URL, which can be opened in the browser, e.g. http://molsync.com/share?mol=3161:
This is the same workflow that is available via several mobile apps, like MMDS and MolPrime+, either for sharing directly as a web page, or as a prelude to tweeting out the data. Once you have the data uploaded to the site, the content is served up in viewable form, and can be downloaded in various cheminformatics and graphics formats. It can be shared by any sort of internet distribution means, and there are lots of clickable icons for bouncing it out via Twitter, Facebook, LinkedIn, Google+, etc.
Notice also that the page includes the molecular recognition glyph – that’s the black hexagon with the square dot pattern in the middle. The timing is no coincidence, because it means that as soon as the Living Molecules app gets through the appstore review process, the following workflow will be possible:
- Draw molecules and/or assemble them into a datasheet with textual content, properties, etc., using any desktop platform (Linux, Windows, Mac, whatever)
- Share the content on molsync.com
- Export the molecular glyph and include the graphic on a poster
- Put up the poster at a conference, and anyone with an iThing can snap the glyph and access the underlying data
Of course, using many of the content creation apps the data can be created on a mobile device as well, but adding the feature to SketchEl now makes that a choice: create content on mobile or desktop, whichever is most convenient at the time. And it’s not just for making posters either, but that is one of the original use case proposals.
Molecular glyphs on MolSync.com
The molsync.com sharing page has a new feature, as shown on the screenshot to the right (click on it to see the live version): there’s now a black hexagon with a grid pattern in the middle, which is a molecular recognition glyph designed to work with the Living Molecules app. The simplest way to describe it is that it’s a molecular QR code, suitable for inclusion on posters or various other documents. The content can be accessed by using the Living Molecules app to “snap” the glyph, after which it continues on to download the data and make it available for viewing, storing and exporting.
The app has been submitted to the iTunes AppStore, so with any luck, it will be available for download (free) in a week or so!
Cheminformatics 2.0 