cloud-servers

BioAssay Express: converting annotations into prose

The BioAssay Express project is about describing bioassay protocols using machine readable annotations (which are URIs that have been appropriated from semantic web dictionaries). Because almost all currently existing bioassay protocols are represented as text, much of the focus has been on finding ways to streamline the annotation process. Thinking forward to the future, however, we anticipate that once this technology is widely deployed, scientists will find it easier to annotate new protocols using our templates and web-based interface than to write up many pages of prose using a wordprocessor.

For this reason, we are experimenting with running the process in reverse: converting the nicely structured semantic web annotations to scientific English, so that the biologist doesn’t have to do. Continue reading →

MolSync overhaul: back to the web, now with reactions too

molsync_overhaul1Things have been a bit quiet in these parts lately, but not due to inactivity: far from it. In between working on some exciting projects with Collaborative Drug Discovery, I have been quietly making rapid progress on several important key technologies. These include the OS X Molecular DataSheet (XMDS), presiding over a growing collection of reaction data, and most recently a complete overhaul of the MolSync website, which provides cheminformatics support services of various kinds. Continue reading →

Online file sharing with iOS 8: upgrading the Green Lab Notebook app

picker_gln02Mobile apps for iOS have always been able to share files by a variety of different mechanisms, but many of these were limited in ways that were very detrimental to the user experience. The Green Lab Notebook app is now catching up to the new technology introduced with iOS 8: using the “document picker” interface to import and export files to document providers, which immediately makes it fully interoperable with iCloud, and file sharing services like Dropbox. Continue reading →

MetaSearch options: and stealth OpenPHACTS prefilter

metasearch_optionsThe 1.5 release of the Mobile Molecular DataSheet (MMDS) introduced a couple of major features, including a minimum viable feature deployment of OpenPHACTS assay integration. That is being quite liberal with the meaning of viable: building this into a practical scientific workflow is more of an ongoing campaign than a specific new piece of functionality, and so other features are being improved in lock step. The next one to get an upgrade is the searching capability, which has an additional preflight configuration block (shown to the right). Continue reading →

Cheminformatics workflows using the mobile + cloud platform: NETTAB 2013

cover_nettab2013Yesterday I returned from a truly delightful trip to Europe, the primary purpose of which was to deliver a presentation to the 2013 NETTAB meeting. The slides are now available on slideshare:

http://www.slideshare.net/aclarkxyz/alex-clark-nettab-2013

For the benefit of the audience at the conference, I wanted to make sure that everyone present could easily access the apps that I was talking about, and so rather than handing out promotional codes on scraps of paper, I decided to simply drop the price of the non-free apps that I described in the presentation to zero for a few days. I didn’t tell anyone else about this, and figured that a few dozen people would accidently get a freebie or two. That’s not quite the way it worked out: in actuality more like a few tens of thousands of people got in while the going was good. Next time I pull a stunt like that, I might just shorten the window of opportunity a little bit, but if anyone out there is reading this, and you made the best of it, please consider popping by the iTunes AppStore and putting in a favourable review and/or rating!

Besides having the opportunity to meet a lot of bioinformaticians and semantic web experts (two adjacent fields that I have not been paying as much attention to as I should have), it certainly didn’t hurt that the conference was held at the Lido of Venice. This being my first time ever to visit any place along the mediterranean, I have to say the location is quite amazing. For a rustic colonial who doesn’t normally bother taking photographs, well lets just say I snapped several hundred of them in the Lido and main city of Venice. It’s one of those places that isn’t overhyped: it really is a must-see.

Nonetheless, there’s now a lot of work to catch up on. My list of cool ideas to try to prioritise was already pretty long, but many brainstorming sessions later, it’s grown a whole lot. So much to do, before or after the next trip, to the 9th German Conference on Cheminformatics.