Open Babel: An open chemical toolbox.

BACKGROUND: A 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. RESULTS: We 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. CONCLUSIONS: Open 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.

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.

BACKGROUND: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. RESULTS: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. CONCLUSIONS: We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

Drug Guru: a computer software program for drug design using medicinal chemistry rules.

Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.

Quality management and the work environment: an empirical investigation in a public sector organization.

The integration of quality management initiatives, particularly total quality management (TQM), and ergonomics has received increasing attention from scholars and practitioners. Above all, the question of how TQM programs relate to ergonomic aspects of organizational design and culture is at the center of this discussion. This study examines how elements of a "typical", Deming-inspired, TQM program in the public sector interact with the work environment. Elements of the TQM program were defined and measured using the Malcom Baldridge Award criteria. The specific elements examined were "Management Support of Quality", "Information and Analysis", "Human Resources", "Processes and Quality Results", and "Customer Focus and Satisfaction". The relationship between these TQM elements and the work environment were defined through five separate hypotheses. The work environment was described by the constructs "Supervisor Support", "Task Clarity", "Task Orientation", and "Innovation". Data were obtained through survey questionnaires administered to employees of four departments in a municipal government organization. Results supported three of the hypotheses, but produced some unanticipated outcomes with regard to the other two. Namely, "Management Support of Quality" was significantly related to "Supervisor Support", "Task Orientation", "Task Clarity" and "Innovation"; "Human Resources" was significantly related to "Supervisor Support"; "Processes and Quality Results" was significantly related to "Task Orientation" and "Innovation". Contrary to predicted "Information and Analysis" was negatively related to "Innovation", and "Customer Focus" was unrelated to any of the outcome variables. The relationships between these TQM elements and work environment dimensions are discussed. Implications for TQM and ergonomic practice are analyzed, and directions for future research proposed.