Archive for the ‘open source’ tag
A few days back, Derek Lowe posted a comment from a reader who suggested a way to approach the current employment challenges in the pharmaceutical industry would be the formation of a Federation of Independent Scientists. Such a federation would be open to consultants, small companies etc and would use its size to obtain group rates on various things – journal access, health insurance and so on. Obviously, there’s a lot of details left out here and when you go in the nitty gritty a lot of issues arise that don’t have simple answers. Nevertheless, an interesting (and welcome, as evidenced by the comment thread) idea.
One aspect raised by a commenter was access to modeling and docking software by such a group. He mentioned that he’d
… like to see an open source initiative develop a free, open source drug discovery package.Why not, all the underlying force fields and QM models have been published … it would just take a team of dedicated programmers and computational chemists time and passion to create it.
This is the very essence of the Blue Obelisk movement, under whose umbrella there is now a wide variety of computation chemistry and cheminformatics software. There’s certainly no lack of passion in the Open Source chemistry software community. As most of it is based on volunteer effort, time is always an issue. This has a direct effect on the features provided by Open Source chemistry software – such software does not always match up to commercial tools. But as the commenter above pointed out, much of the algorithms underlying proprietrary software is published. It just needs somebody with the time and expertise to implement them. And the combination of these two (in the absence of funding) is not always easy to find.
Of course, having access to the software is just one step. A scientists requires (possibly significant) hardware resources to run the software. Another comment raised this issue and asked about the possibility of a cloud based install of comp chem software.
With regards the sophisticated modelling tools – do they have to be locally installed?
How do the big pharma companies deploy the software now? I would be very suprised if it wasn’t easily packaged, although I guess the number of people using it is limited.
I’m thinking of some kind of virtual server, or remote desktop style operation. Your individual contractor can connect from whereever, and have full access to a range of tools, then transfer their data back to their own location for safekeeping.
Unlike CloudBioLinux, which provides a collection of bioinformatics and structural biology software as a prepackaged AMI for Amazons EC2 platform, I’m not aware of a similarly prepackaged set of Open Source tools for chemistry. And certainly not based on the cloud. (There are some companies that host comp chem software on the cloud and provide access to these installations for a fee). While some Linux distribibutions do package a number of scientific packages (UbuntuScience for example), I don’t think that these would support a computational drug discovery operation. (The above comment does’nt necessarily focus just on Open Source software. One could consider commercial software hosted on remote servers, though I wonder what type of licensing would be involved).
The last component would be the issue of data, primarily for cloud based solutions. While compute cycles on such platforms are usually cheap, bandwidth can be expensive. Granted, chemical data is not as big as biological data (cf. 1000Genomes on AWS), but sending a large collection of conformers over the network may not be very cost-effective. One way to bypass this would be to generate “standard” conformer collections and other such libraries and host them on the cloud. But what is “standard” and who would pay for hosting costs is an open question.
But I do think there is a sufficiently rich ecosystem of Open Source software that could serve much of the computational needs of a “Federation of Independent Scientists”. It’d be interesting to put together a list of Open Source based on requirements from the the commenters in that thread.
I met Viven Marx at the BioIT World conference held in Boston earlier this month, in which I spoke on the topic of Open Source cheminformatics. The result of conversations between myself (and Peter Murray Rust) and here were incorporated into an interesting article. (Though the CDK was started at Notre Dame, but is now an internationally developed project).
I’m in academia and I do cheminformatics. Recent collaborations, papers and funding issues in this field have made me think about the future of this research in this setting. This, and a thread discussing David Leahy’s talk on InkSpot Science at the Soton Open Science Workshop got me started on this post.
There are currently a number of groups and collaborations that are attempting to perform drug discovery without the large centralized infrastructure that is characteristic of this process. Examples of this include Jean Claude Bradley who runs the UsefulChem project and the Synaptic Leap as well as various academic labs. Also see Kozikowski et al
Cheminformatics plays a key role in drug discovery efforts at various stages. For example, identifying or prioritizing compounds from virtual libraries, predicting ADME profiles and side effects (e.g., hERG activation) and so on. I should stress that such computational methods don’t replace bench work – but they can certainly enhance it. More generally, we’re now faced with a deluge of data – and human eyeballs are not going to be able to handle this. And this is exactly the place that cheminformatics does it’s stuff.