BackgroundA frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.ResultsWe discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.ConclusionsOpen Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

BackgroundComputational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches.Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large.Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together.ResultsThis report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities.ConclusionsHackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

A collaborative experimental and theoretical study of the electronic spectrum and excited-state photochemistry of H(2)CN has been carried out. The absorption spectrum, in the range of 287-278 nm, was measured through cavity ring-down spectroscopy. The radical was prepared by 193 nm photolysis of monomeric formaldoxime vapor. Two diffuse features were observed in the 34800-35800 cm(-1) spectral range, along with the A-X (1,0) band of the OH cofragment. The broad features were assigned through high-level ab initio calculations as vibronic transitions to the ground and 2b(1) (umbrella mode) levels of the second excited B (2)A(1) state from the ground X (2)B(2) state of H(2)CN. Rotational constants for the lower and upper levels of these transitions were computed from the expectation values of the moments of inertia tensor, using the appropriate vibrational wave functions. Experimental and simulated rotational profiles of these bands agree extremely well with each other for an assumed type-B electric dipole-allowed (2)A(1) <-- (2)B(2) transition appropriate to this transition. The former assignment to the dipole-forbidden (2)B(1) <-- (2)B(2) transition can be ruled out by these results. A theoretical investigation of the dissociation pathways for electronically excited H(2)CN is also presented. The upper states of the observed bands cannot dissociate directly but rather decay through internal conversion and subsequent dissociation to H + HCN fragments; higher b(1) levels are above the excited-state dissociation limit.

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