The applications of graphs in cheminformatics are numerous. From modeling molecules themselves to reaction networks, to ring system indicies, and even scientific paper authorship relationships, graphs are the way most problems get framed.

Wouldn't it be great if your natural mental model of a problem didn't have to change just because you needed persistent storage of the underlying data?

Neo4j, a high-performance, transactional, embedded graph database written in Java, offers what appears to be the best solution to this gnarly problem I've ever seen.

Check out the presentation by Emil Eifrem and see for yourself.

The Chemcaster Web API documentation is now online.

For the unfamiliar, Chemcaster is the cheminformatics Web services platform optimized for rapid creation of chemistry-focussed websites. If you're creating a website that displays and manages chemical structures, or which allows users to search a database by exact structure or substructure, Chemcaster can streamline the process by eliminating the need to maintain cheminformatics software on your servers.

The Chemcaster API uses a REST web architecture in which commands combine a Resource addressable through a unique path with one or more of the four HTTP verbs GET, PUT, POST, and DELETE.

Recently, Noel O'Boyle announced a Python API for Chemcaster. In the weeks ahead, expect to see additional native Chemcaster APIs written in Java, PHP, and Ruby.

Chemcaster is currently in testing and we're looking for developers interested in using the service to build their next application. You can learn more about Chemcaster by applying for an invitation and signing up for a free account.

It's been said before but bears repeating: social networking is a feature, not a destination. One service that demonstrates this principle very well is GitHub, which not only lets you keep track of specific repositories a given developer is maintaining, but their activity on GitHub in general. This can be very useful in finding new software, learning about new approaches, and meeting other developers that share your interests.

Over the last few months, I've noticed a steady increase in cheminformatics developers using GitHub. Because GitHub doesn't make it very easy to find them (searching by 'cheminformatics' doesn't turn up much), I thought it might be useful to compile a list of them here. In no particular order, they are:

Giorgi Lekishvili / giorgil

Duan Lian / chemhack

Geoff Hutchison / ghutchis

Rajarshi Guha / rajarshi

Egon Willighagen egonw

Noel O'Boyle / baoilleach

Rich Apodaca / rapodaca

Tim Vandermeersch / timvdm

David Lonie / dlonie

Marcus D. Hanwell / cryos

Christoph Helma / helma

Charlie Zhu / CharlieZhu

Metamolecular, LLC / metamolecular

Andreas Maunz / amaunz

Craig James / cjames53

Syed Asad Rahman / asad

Gilleain Torrance / gilleain

If I've missed anybody, please feel free to add them in a comment.

Edit: These were added after initial posting:

John Jaeger / goeslightly

After having spent some time recently playing around with Jmol, the thought occurs - is there a setting that enables 3D-effect viewing with those colored glassed used with movies?

For that matter, which of the free 3D molecule viewers currenly available support it?

Image Credit: Dicky

The second beta release of MX is now available for download. MX is a library of essential cheminformatics models and routines. It was created with the goal of providing a clean, well-tested platform for chemistry applications.

This beta release includes a new binary fingerprinter package that was not ready for release in the first beta. Of particular note is the modular system MX uses for creating fingerprints based on interchangeable BloomFilter, Walker, RingFilter, RingFinder, and PathWriter classes.

Unit tests are now augmented by Mockito for stubbing and mocking. The MX test suite now includes over 300 individual tests, all of which pass.

The full list of MX features includes:

• Substructure search and atom mapping based on the VF algorithm

• Exhaustive ring perception based on the Hanser algorithm

• Path-based binary fingerprints

• Flexible query atom support

• Depth-First traversal

• Implicit hydrogen detection

• Complete system of atomic masses and isotopes based on the IUPAC Technical Report.

• Model objects (Molecule, Atom, Bond, Superatom) based on MDL CTfile specification

• Molfile reader and writer

• SD File reader and writer

MX is released under the highly permissive MIT License.

If you find a bug or other issue, please consider filing an bug report.