The last post described the addition of molecules to the BioAssay Express project, and alluded to the near term intention of making this actually useful for something. The first round of utility is now in place: the ability to select columns and download the molecules as a single SDfile, suitable for use as a structure-activity dataset. Continue reading
XMDS
XMDS experiments: quantities, metrics and SVG
The XMDS molecular datasheet editor is steadily marching forward in terms of functionality: the reaction scheme editor has been complemented by separate display panels showing the quantities of each component in blocks, which can be opened up and edited. The green chemistry metrics (PMI, E-factor, atom economy) are also calculated and shown. In the interests of making the data useful for presentations, bitmapped or vector representations can be dragged directly into a graphics package (e.g. Pages, Word, PowerPoint, Keynote, etc.), and generation of SVG images is now supported, so reactions and molecules can be easily touched-up with a vector graphics editor like Inkscape. The XMDS app (for Mac OS X) is still in long beta, so you are welcome to try it out (just ask nicely). Continue reading
Experiment editing in XMDS: dogfooding time
Progress is coming along nicely with the Experiment aspect editor for XMDS, which is essentially the desktop platform playing catchup with mobile and matching the functionality of the Green Lab Notebook (GLN) app. There is now an editor in place for the overall reaction scheme, which allows the components of a multistep reaction to be composed. This is a development milestone because it means that it’s time to switch to using it for data entry to find out what needs to be added or fixed most urgently, rather than implementing essential features that are obviously missing (cf. dogfooding = eating one’s own dogfood, in case anyone is unfamiliar with the term). Continue reading
Reactions in XMDS
After much procrastination, chemical reactions have started to make their way into the OS X Molecular DataSheet (XMDS) beta. The screenshot shows several multistep reactions from my Ph.D. research, and were originally entered using the Green Lab Notebook (GLN) app.
The Mac app and the iOS app both use the same data format, which is based on the extensible aspect protocol for molecular datasheets (see description), which seeks to capture a reaction description that is highly machine readable. As well as representing a multi-step schema, which can handle the non-organic species that are so commonly used as reactants, it also handles stoichiometry and quantities, in a way that can be used to balance the reaction and generate metrics. This has been available on mobile for awhile now, but the desktop analog is catching up.
Editing has yet to be implemented, but there’s a lot of background work that goes into just displaying reaction schemes, so it’s well underway.
Always-on R/S and E/Z stereo labels with XMDS
The most recent addition to the OS X Molecular DataSheet (XMDS) desktop app is calculation of stereochemistry labels as-you-edit, using the Cahn-Ingold-Prelog (CIP) designations (R/S, Z/E). The labelling can be switched off with a menu option, but since most people use software with its factory settings, this is more or less equivalent to having it hardcoded permanently. Continue reading
Aspects and XMDS: higher order metadata for datasheets
Recent progress on the OS X Molecular DataSheet (XMDS) app, which is currently in beta, has involved the inclusion of aspects into the user interface for editing datasheets. The core format that the XMDS desktop app, as well as all the rest of the products from Molecular Materials Informatics, is the datasheet, which is a tabular format made up of rows and columns: like a spreadsheet, except that the columns are strongly typed, so you can’t just abuse it and put in whatever you want wherever you want. The minimalistic table datastructure can be supplemented by any number of aspects, which are directives that impose higher order layers of interpretation, which are often composed of multiple columns (e.g. a chemical reaction which cobbles together multiple molecules for its reactants, reagents and products). One of the fun software engineering challenges has been to make these complex representations fit seemlessly into the grid-based “spreadsheet” editor upon which XMDS operates. Continue reading
XMDS ready for beta phase
The OS X Molecular DataSheet (XMDS) desktop app is now ready for beta testing. And by beta testing, I mean the minimum viable product is done and ready to be used for actual cheminformatics tasks. You can sign up anytime: all it takes is an email (info@molmatinf.com), a Mac with Yosemite-or-later (v10.10), and a Dropbox account. And you get to keep using the app for as long as you want, even after the beta testing programme is wrapped up. Continue reading
XMDS and dragging content into other Mac apps
One of the things that one must become accustomed to when using a Mac regularly is that drag’n’drop is actually an effective way to get real work done. Two main use case scenarios are considered: getting graphics images of molecules into presentation tools (e.g. Pages or Keynote), and getting raw data into another cheminformatics tool (e.g. uploading an SDfile to a browser-based application). Both of these are now functioning in the pre-alpha version of XMDS (the OS X Molecular DataSheet), which essentially brings it to demo-ready status. Continue reading
Ergonomic molecule editing, and praise for Mac-style dialogs
Normally I wouldn’t consider a trivial dialog box to be worthy of a blog post, but it’s as good a time as any for a progress update on XMDS. The sketching interface for editing molecular structures is now somewhat feature complete. There are a few bits to come back to, but in general the methods for adding, deleting, editing and aligning atoms and bonds are available in a highly redundant way. By redundant, I mean that in a good way. The editor is based on a confluence of methodologies that I’ve built out in various products over the years: (1) the conventional way of drawing molecules with a painting-style toolbox (see SketchEl); (2) the “drawing primitives” designed for precise editing when user interaction is expensive, motivated by mobile devices with tiny screens; and (3) keyboard shortcuts, designed so that an expert can draw molecules incredibly quickly without having to reach for the mouse, battle-tested with the BlackBerry version of MMDS back in 2010, when touchscreens were not yet ubiquitous. Continue reading
XMDS: progress toward structure sketcher
Since the last sneak preview, the skunkworks project “XMDS” – the Mac OS X desktop version of the Mobile Molecular DataSheet app – has gained enough functionality to make another screenshot, this time showing what the actual molecular drawing interface might look like once it’s done. Continue reading
Cheminformatics 2.0 