The OS X Molecular DataSheet (XMDS) is a desktop app for Mac computers that provides a chemically aware spreadsheet editor. It is designed primarily for data entry of structure/activity data. It is currently available on the Mac AppStore, as well as the beta testing programme.

Overview

Aspects

Status

XMDS has been renamed to Molecular Notebook and has its own site, to which you should be redirected shortly.

Overview


OS X Molecular DataSheet (XMDS) is a desktop app that has been designed from the ground up to run on the Mac OS X operating system. Its primary functionality is to provide a chemically aware spreadsheet editor: it operates on a grid of editable cells, made up of typed columns, that can be molecules, numbers or plain text.

The XMDS app is for cheminformatics, meaning that it is totally dedicated to creating structure-activity data that can be viewed by people (as shown on the right), and understood equally well by computer software. This has many advantages over using a mixed software approach, such as a spreadsheet with a chemical software plugin, because XMDS understands molecular structures at all levels. The data entry process is being continually refined in order to provide the best possible native user experience, and make it as easy as possible to create data that really is as valid as it looks.

An integral part of the product is a chemical structure sketcher, which is both extremely easy to get started with, and also very sophisticated for power users who need to get a lot of work done. The default editing toolbar is very similar to what is considered normal for desktop-based structure drawing tools (such as SketchEl), and has essentially zero learning curve.

For anyone who digs a little deeper, all of the optimisations that were designed for the Mobile Molecular DataSheet (MMDS) app for use with severely limited input capabilities (i.e. no mouse or keyboard), have been ported to XMDS and meshed together with the greater range of options that is available on a desktop platform. It is possible to draw structures using the conventional toolbar, as well as action buttons, template placement fusion, keyboard shortcuts, and of course the full screen menu bar. It is even effective to draw tricky structures very rapidly using only the keyboard. To any users of mobile apps from Molecular Materials Informatics, these editing tools will be familiar.

As well as a data entry workflow that is carefully designed to be ergonomic and effective for creating large quantities of structure activity information as quickly as possible, the minimum viable product has several other key capabilities, one of which is creation of graphics: bitmaps (PNG) and vector graphics (PDF) can be created from molecular diagrams, and dragged into presentation tools, or saved as files. In this way, XMDS can be used to support communication, without sacrificing the core data, which is machine readable.


Aspects


The core data model is based on the datasheet, which is a tabular layout of rows and columns. In order to edit more complex chemical concepts, the aspect mechanism can be used to add additional meta organisation to the underlying content, and inform the editor that it should be specialised viewing and editing functionality.

Editing of chemical reactions using the Experiment plugin is a major feature. The data pulls in multiple columns, and sometimes multiple rows, to express the components of a reaction, starting with the components: reactants, reagents and products. These components are represented by structures and/or names, and are can be accompanied by quantity, stoichiometry and atom mapping information. They can also be multistep. The datastructure is rich and rigorous, and the app has a finely crafted interface for creating new reaction schemes as efficiently as possible. The concepts are related to the Green Lab Notebook mobile app, except optimised for the desktop.


Often a series of compounds is based on a common set of scaffolds and R-group substituents, and can be encapsulated by varying the pieces. The SAR Table plugin is used to break out each row into scaffolds and substituents, as well as a molecule column that automatically updates itself based on the components. This is an effective way of preparing content for publications, or curating tables of fragments from previously published content. It can also be used to interact with software that performs scaffold analysis functions on chemical datasets. The concepts are closely related to the SAR Table mobile app.


Other aspects are less overt. The Assay Provenance aspect, for example, retains key header information about a particular assay, against which the molecules are presumed to have a measurement. In addition to some of the biological metadata, it also holds information about the allowed units, and their format definitions. The actual recorded value for each molecule is kept in a rigorously maintained format where [relation, value, units, error] are abstracted in a strictly machine readable form, thus avoiding the common problem with ad hoc definitions where numeric values are required.


Status


The XMDS app is currently in its minimum viable product stage, and delivers the essential set of functionality needed to be useful for important work. The product roadmap is ambitious, and new capabilities will be delivered frequently for the foreseeable future, with the ultimate objective of covering almost all kinds of cheminformatics workflows.

There is presently no official documentation for the product, as it is evolving quickly. The Cheminformatics 2.0 blog provides a chronological series of articles detailing enhancements, as each milestone is met: this is currently the best place to look for new developments.

To purchase the product, go to the Mac AppStore:

Alternatively, if you're willing to agree to provide constructive feedback toward the future development of the app, you may want to consider joining the beta testing programme, which is still open. Send an email to:

info@molmatinf.com

Please introduce yourself briefly (e.g. name, any relevant organisational affiliation, or whether you just want to try it out to satisfy your own curiosity). Consider yourself invited no matter where you are in your career: from students to emeritus and everything in between - if you have an interest in software for chemistry data, you are qualified and welcome. Do expect to receive an email from an actual person, as we are interested in following up: we really do want to know what you think. Needless to say you will need to have a a Mac of some kind, and it requires at least macOS 10.10 (Yosemite).

See Also


Mobile Molecular DataSheet (iOS), Products