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Trying to squeeze sense out of chemical data

Archive for the ‘cloud’ tag

Software for the “Federation of Independent Scientists”

without comments

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.

Written by Rajarshi Guha

April 14th, 2012 at 9:23 pm

Chemistry, Clouds, Collaboration (Part 1)

with 4 comments

There’s been an interesting discussion sparked by Deepaks post, asking why there is a much smaller showing of chemists and chemistry applications in the cloud compared to other life science areas. This post led to a FriendFeed thread that raised a number of issues.

At a high level one can easily point out factors such as licensing costs for the tools to do chemistry in the cloud, lack of standards in data sets and formats and so on. As Joerg pointed out in the FF thread, IP issues and security are major factors. Even though I’m not a cloud expert, I have read and heard of various cases where financial companies are using clouds. Whether their applications involves sensitive data I don’t know, but it seems that this is one area that is addressable (if not already addressed). As a side note, I was interested in seeing that Lilly seems to be making a move towards an Amazon based cloud infrastructure.

But when I read Deepaks post, the question that occurred to me was: what is the compelling chemistry application that would really make use of the cloud?

While things like molecular dynamics are not going to run too well on a cloud set up, problems that are data parallel can make excellent use of such a set up. Given that, some immediate applications include docking, virtual screening and so on. There have been a number of papers talking about the use of Grids for docking, so one could easily consider docking in the cloud. Virtual screening (using docking, machine learning etc) would be another application.

But the problem I see facing these efforts is that they tend to be project specific. In contrast doing something like BLAST in the cloud is more standardized – you send in a sequence and compare it to the usual standard databases of sequences. On the other hand, each docking project is different, in terms of receptor (though there’s less variation) and ligand libraries. So on the chemistry side, the input is much larger and more variable.

Similarity searching is another example – one usually searches against a public database or a corporate collection. If these are not in the cloud, making use of the cloud is not very practical. Furthermore, how many different collections should be stored and accessed in the cloud?

Following on from this, one could ask, are chemistry datasets really that large? I’d say, no. But I qualify this statement by noting that many projects are quite specific – a single receptor of interest and some focused library. Even if that library is 2 or 3  million compounds, it’s still not very large. For example, while working on the Ugi project with Jean-Claude Bradley I had to dock 500,000 compounds. It took a few days to set up the conformers and then 1.5 days to do the docking, on 8 machines. With the conformers in hand, we can rapidly redock against other targets. But 8 machines is really small. Would I want to do this in the cloud? Sure, if it was set up for me. But I’d still have to transfer 80GB of data (though Amazon has this now). So the data is not big enough that I can’t handle it.

So this leads to the question: what is big enough to make use of the cloud?

What about really large structure databases? Say PubChem and ChemSpider? While Amazon has made progress in this direction by hosting PubChem, chemistry still faces the problem that PubChem is not the whole chemical universe. There will invariably be portions of chemical space that are not represented in a database. On the other hand a community oriented database like ChemSpider could take on this role – it already contains PubChem, so one could consider groups putting in their collections of interest (yes, IP is an issue but I can be hopeful!) and expanding the coverage of chemical space.

So to summarize, why isn’t there more chemistry in the cloud? Some possibilities include

  • Chemistry projects tend to be specific, in the sense that there aren’t a whole lot of “standard” collections
  • Large structure databases are not in the cloud and if they are, still do not cover the whole of chemical space
  • Many chemistry problems are not large in terms of data size, compared to other life science applications
  • Cheminformatics is a much smaller community than bioinformatics, though is applies mainly to non-corporate settings (where the reverse is likely true)

Though I haven’t explicitly talked about the tools – that certainly plays a factor. While there are a number of Open Source solutions to various cheminformatics problems, many people use commercial tools and will want to use them in the cloud. So one factor that will need to be addressed is the vendors coming on board and supporting cloud style setups.

Written by Rajarshi Guha

February 22nd, 2009 at 5:00 pm