Dotmatics UGM 27 April 2010
I was at the Dotmatics User Group Meeting recently and I thought I’d post a few thoughts and comments.
Dotmatics are a relatively small (but growing) scientific informatics company that was formed as a spinout from a major pharmaceutical company. I’ve known the founders as colleagues and friends for many years and followed their progress with interest. They now provide informatics solutions for over 50 clients around the world. I’ve written a review of Vortex previously and I thought I’d focus on a few of their other products in this summary.
One of the most difficult tasks on any major project is keeping track of information, particularly if the data is generated by different labs often in varied geographical regions, Gateway is a web-based project/document management tool that allows scientist to store and share information. This can be the latest biological results, presentations and minutes from meetings, notes from conferences, details of competitors activities, links to literature etc. The real beauty is that everything is indexed and can be searchable. If you have ever spent days searching through shared folders or worse someone’s hard drive trying to find a critical report than I think you can see how valuable this can be. Whilst there are other Enterprise level project management tools many require specific software on your machines (and often have poor support for Macs), Gateway like the majority of the Dotmatics software requires nothing more than a web browser, and thus runs on most platforms even your iPhone or iPad! Talking to a few of the users one of the attractions of Gateway is that they can securely share information with third parties working on a project, no need to install anything on the clients just send them a URL and a password. With companies increasingly collaborating on projects this seems to be very useful.
Whilst Gateway provides a document centric view of a project, Browser is a web-based tool for querying and browsing small and large biological and chemical databases. Many people will be familiar with ISISbase type solutions or Excel spreadsheets, however there are significant limitations with these solutions. Excel while the major workhorse for accountants was never designed to support structure-based searching and all the solutions I’ve seen always seem to break after any updates and become dreadfully slow as soon as any reasonably sized data-set is involved. Desktop clients are usually difficult to customize or modify and often don’t support the sort of functionality that the current internet brought up scientists expect to have, such as popups, display of graphs, movies etc. In addition from a Mac user point of view they rarely offer good Mac compatibility. By focussing their effort on web-based tools Dotmatics can leverage the rapidly evolving web technologies, and because you don’t have to install anything on clients desktops there is a huge IT overhead saving. By sticking to common standards they can support all major browsers and multiple platforms.
All the data is stored in a SQL database (Oracle, SQLserver, MYSQL etc..) and Dotmatics provide Nucleus a web-based tool for importing, mapping and storing data from existing sources. Excel, SDF, XML, CSV, TSV, sequence data, database data etc. Alternatively Browser can be integrated with existing solutions. It is then possible to use the power of the SQL database to index and provide really, really fast searching. Searching supports Boolean logic allowing the construction of complex queries.