A recent post described preliminary integration of the Molecular Materials Informatics toolkit with KNIME. Further to that objective, some more developments are coming through within the toolkit itself, being used independently of any third party tools: in particular, a way to execute pre-existing workflows with the benefit of a visual interface. Continue reading
Month: February 2016
Minor side project: PDFBoxLite
My latest contribution to GitHub is PDFBoxLite, which represents a few hours work. Basically, all of my software efforts that involve creating chemical graphics are leaning toward pushing PDF as the format of choice for creating inline figures. Everyone knows PDF as the Portable Document Format – things you look at before sending to the printer. But what you may not know is that PDF files with just a single page, of arbitrary size, are a very well supported as a way to get pictures into a larger document (Word, Pages, PowerPoint, Keynote, Excel, etc.). This is particularly true within the Apple ecosystem. Unlike SVG, correct rendering is essentially universal; and unlike WMF/EMF, it works on platforms other than Windows. And unlike PNG, it isn’t a trainwreck when you try to print/zoom/convert your document. Continue reading
Fullscreen mode in the Green Lab Notebook app
The Green Lab Notebook (GLN) app has a little feature coming up in the next release: a mode for full screen display of an experiment, which consists of the reaction scheme and associated quantities. Continue reading
Tox21 toxicity measurements and PolyPharma
The PolyPharma app is currently getting some major new content added to it, namely a bunch of new models for toxicity. The models are derived from measurements made on the EPA’s Tox21 collection, recently published in nature, and released via PubChem. Continue reading
Adventures with KNIME: pipeline wrapping
One of the items that has been on my to-do list for quite some time is to dig back into the KNIME universe, and interface it with the growing collection of cheminformatics algorithms that I have been assembling over the last few years. Given that my company’s software stack has its own workflow/pipelining infrastructure, but no user interface, it makes a certain amount of sense to look into connecting them together. Continue reading
Cheminformatics 2.0 