So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘database’ tag

Chemistry, Clouds, Collaboration (Part 1)

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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

Annotating Bioassays

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I’ve been working for some time with the PubChem Bioassay collection – a set of 1293 assays that cover a range of techniques (enzymatic, phenotypic etc.), targets and sizes (from 20 molecules to 200,000 molecules). In addition, some assays are primary, high-throughput assays whereas a number of them are smaller, confirmatory assays. While an extremely valuable collection, one of the drawbacks is the lack of curation. This has led to some people saying that the data is too noisy to be useful. Yes, the noise is a problem, but I think there’s still useful data to extract and model.

One of the problems that I have faced is that while one can perform a full text search for assays on PubChem, there is no form of annotations on the assays themselves. One effect of this is that it is difficult to link an assay to other biological resources (though for enzymatic assays, one can determine a Pubmed protein identifier). While working on my bioassay network project, I needed annotations and I didn’t want to do it manually.

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Written by Rajarshi Guha

January 25th, 2009 at 5:03 pm

Quick Comments on an Analysis of Antithrombotics

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Joerg has made a nice blog post on the use of Open Source software and data to analyse the occurence of antithrombotics. More specifically he was trying to answer the question

Which XRay ligands are closest to the Fontaine et al. structure-activity relationship data for allowing structure-based drug design?

Using Blue Obelisk tools and ChemSpider and where Fontaine et al. refers to the Fontaine Factor Xa dataset. You should read his post for a nice analysis of the problem. I just wanted to consider two points he had raised.

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Written by Rajarshi Guha

January 5th, 2009 at 1:36 am

Brute Force – Inelegant, But Sometimes Useful

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A few days back I posted on improving query times in Pub3D by going from a monolithic database (17M rows), to a partitioned version (~ 3M rows in 6 separate databases) and then performing queries in parallel. I also noted that we were improving query times by making use of an R-tree spatial index.

Andrew Dalke posted a comment:

I’ve wondered about this quote from the ANN page at .

Computing exact nearest neighbors in dimensions much higher than 8 seems to be a very difficult task. Few methods seem to be significantly better than a brute-force computation of all distances.”

Since you’re in 12-D space, this suggests that a linear search would be faster. The times I’ve done searches for near neighbors in higher dimensional property space have been with a few thousand molecules at most, so I’ve never worried about more complicated data structures.

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Written by Rajarshi Guha

November 20th, 2008 at 5:42 pm

Multi-threaded Database Access with Python

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Pub3D contains about 17.3 million 3D structures for PubChem compounds, stored in a Postgres database. One of the things we wanted to do was 3D similarity searching and to achieve that we’ve been employing the Ballester and Graham-Richards method. In this post I’m going to talk about performance – how we went from a single monolithic database with long query times, to multiple databases and significantly faster  multi-threaded queries.

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Written by Rajarshi Guha

November 14th, 2008 at 4:46 pm