The Living Molecules app has recently been released on the
and it's free.
The app can recognise molecular glyphs, which are equivalent to chemical QR codes. The device camera can be
used to collect and import data by aiming it at a printed glyph. The app can
also be used to import data from other sources, upload it to public storage, then create a new glyph, which can be
used to share the data on posters, manuscripts or websites. For more information, see Living Molecules.
Mobile apps, web interfaces, cloud computing, software as a service: collectively these make up the platform of the future.
Chemistry software is making the transition, and Molecular Materials Informatics is at the forefront, with a catalogue of
apps for sophisticated workflows, education and reference material. Backed up by best of breed cheminformatics algorithms running
on cloud-hosted webservers, these tools can be used to accomplish complex tasks that were previously the exclusive
domain of desktop computing.
Modern computing platforms provide numerous benefits over legacy desktop applications: low cost, ultimate ease of
deployment, no system administration, and elegant user interfaces with low barriers to learning. Most scientific
software in use today is based on software design principles that were appropriate for workstations of the 1980s. Three decades
later, consumer internet software provides the reference point for what is now referred to as the user experience. At
Molecular Materials Informatics, we believe we can provide that level of quality, and solve hard scientific problems
at the same time.
Creating new content on a mobile device is tricky for chemistry because so many tasks require a good way to draw chemical
structure diagrams. Small touchscreens are not well suited for the legacy user interface design, so the concepts of
drawing chemical diagrams have been redesigned to match the capabilities and limitations of the mobile touchscreen. The
gesture-based sketcher can be seen in MolPrime,
and can be used to quickly draw perfect publication quality diagrams on a screen as small as that of an iPhone.
With the diagram drawing problem solved, the Mobile Molecular DataSheet (MMDS)
app can be used to create reaction schemes and manage datasheets, which are collections of structures, reactions,
scalar data and text annotations. The SAR Table app can be used to decompose structures
into scaffolds and substituents, and analyse the relationships between structure fragments and activity.
Handling data on modern platforms involves a lot of sharing: with the previous generation of software, a document would be
normally edited with one
monolithic desktop application. Nowadays a document typically needs to be passed between mobile apps, webservices,
computation clusters and desktop applications to complete a workflow. More often than not data needs to be shared
between multiple collaborators, who may be using a heterogeneous mix of software and platforms, then eventually published.
In this data rich age, publishing means not only creating perfect quality graphics for viewing, but also preserving the
raw data in a fully interpretable form.
All of the mobile apps produced by Molecular Materials Informatics make extensive use of
interprocess communication. Molecules, reactions and collections can be sent out
as email attachments, or unpacked from incoming email or downloaded from the internet.
Chemical data can be rendered using many different graphics formats, such as bitmapped images, vector graphics
(SVG and EPS) and even Microsoft Word or Excel documents, in which embedded structures and reactions are drawn
as vector graphics objects that look equally great on screen or as part of a printed manuscript.
Using the MolSync app, documents can be shared collaboratively
via Dropbox. Data can be uploaded to molsync.com and made available to the world as data
or rendered content (e.g. example content), or
tweeted directly from within a mobile app. Publicly shared data can be referenced by a
molecular glyph, which can be captured using the Living Molecules
app, which acts like a QR code reader & creator for chemistry data. Public content can be recognised
by the Open Drug Discovery Teams (ODDT) app, which is a magazine-like
reader for drug related content, which also happens to be chemically aware.
One of the compelling use cases for mobile apps is providing a specialised client to lookup online databases. Pairing the
structure-drawing technology from Molecular Materials Informatics with chemical databases is a perfect match: it
is possible to search repositories such as ChemSpider, PubChem, ChEBI, eMolecules,
SPRESI and Mobile Reagents using advanced structure searching techniques. Searching of online databases
is built into the workflow capabilities of MMDS,
SAR Table and
MolPrime+, while specialised apps have been created
for searching ChemSpider, SPRESImobile
and Mobile Reagents.
While some of the mobile apps created by Molecular Materials Informatics are designed with education in mind, all of
them are relevant to chemists at any point in their career, from high school onward. Working with chemical data
is a task that is relevant to experts and beginners alike: all chemists need to know how to draw structures correctly,
lookup content online, access property calculations, and present the results. Consumer versions of the tools produced by
Molecular Materials Informatics are either free or affordable to almost any demographic.
The MolPrime+ app has a number of calculation features based
on individual structures, such as valence checking, molecular weight/formula calculation, mass spectroscopy distributions,
calculation of physical properties, enumeration of tautomers, and stereochemistry (R/S, E/Z).
Some of these calculations are carried out within the app, while others harness webservices to perform the underlying calculations.
The Reaction101 app was created as a collaboration with
Eidogen-Sertanty, and allows drawing of reactions, and
provides tools to help balance them. Yield101 goes on to add basic
laboratory functionality, by interconverting quantities such as grams and moles using all available information,
thereby removing tedious calculation steps.
The original technology developed by Molecular Materials Informatics consists of two parts: a core library
for mobile apps, called MMDSLib, which is the basis for chemistry apps created for native iOS, Android
and BlackBerry products. The core library provides functionality such as the gesture-based chemical diagram
sketcher, and some moderately sophisticated cheminformatics capabilities that run on the mobile device.
Serverside technology is based on Java-based projects: com.mmi for core cheminformatics functionality, and
com.molsync for the J2EE components that expose functionality to the web. The serverside functionality includes the following:
- property calculation
- tautomer enumeration
- stereochemistry assignment (CIP rules)
- model building for structure-activity relationships
- manuscript quality structure rendering
- cheminformatics format interconversion
graphics file creation, including clean room implementation of DocX and XlsX formats
(Microsoft Office, with embedded vector drawings)
- substructure searching
- scaffold analysis and R-group decomposition
- molecule and datasheet storage for public sharing
- web interface for viewing chemical content and interconverting formats
- meta-layer for searching chemical databases (ChemSpider, PubChem, ChEBI)
document collection system (Twitter, RSS) for the Open Drug Discovery Teams project
All of this support functionality is hosted on the server http://molsync.com, which is publicly accessible
and is used by a variety of apps and other tools. For non-public use, the software can be licensed for internal deployment.
To see all news items, click here.