Marcus D. Hanwell

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

BackgroundThe Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.ResultsThe work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.ConclusionsAvogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

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

BackgroundThe 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.ResultsThis 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.ConclusionsWe 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.

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon which their works are built. To highlight some of these issues and share experiences, the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) was held in November 2013 in conjunction with the SC13 Conference. The workshop featured keynote presentations and a large number (54) of solicited extended abstracts that were grouped into three themes and presented via panels. A set of collaborative notes of the presentations and discussion was taken during the workshop. Unique perspectives were captured about issues such as comprehensive documentation, development and deployment practices, software licenses and career paths for developers. Attribution systems that account for evidence of software contribution and impact were also discussed. These include mechanisms such as Digital Object Identifiers, publication of “software papers”, and the use of online systems, for example source code repositories like GitHub. This paper summarizes the issues and shared experiences that were discussed, including cross-cutting issues and use cases. It joins a nascent literature seeking to understand what drives software work in science, and how it is impacted by the reward systems of science. These incentives can determine the extent to which developers are motivated to build software for the long-term, for the use of others, and whether to work collaboratively or separately. It also explores community building, leadership, and dynamics in relation to successful scientific software.

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

BackgroundMultidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinformation. In this paper an end-to-end use of semantically rich data incomputational chemistry is demonstrated utilizing the Chemical MarkupLanguage (CML) framework. Semantically rich data is generated by the NWChemcomputational chemistry software with the FoX library and utilized by theAvogadro molecular editor for analysis and visualization.ResultsThe NWChem computational chemistry software has been modified and coupled tothe FoX library to write CML compliant XML data files. The FoX library wasexpanded to represent the lexical input files and molecular orbitals used bythe computational chemistry software. Draft dictionary entries and a formatfor molecular orbitals within CML CompChem were developed. The Avogadroapplication was extended to read in CML data, and display molecular geometryand electronic structure in the GUI allowing for an end-to-end solutionwhere Avogadro can create input structures, generate input files, NWChem canrun the calculation and Avogadro can then read in and analyse the CML outputproduced. The developments outlined in this paper will be made available infuture releases of NWChem, FoX, and Avogadro.ConclusionsThe production of CML compliant XML files for computational chemistrysoftware such as NWChem can be accomplished relatively easily using the FoXlibrary. The CML data can be read in by a newly developed reader in Avogadroand analysed or visualized in various ways. A community-based effort isneeded to further develop the CML CompChem convention and dictionary. Thiswill enable the long-term goal of allowing a researcher to run simple“Google-style” searches of chemistry and physics and have theresults of computational calculations returned in a comprehensible formalongside articles from the published literature.

A hybrid visualization system for molecular models

Nowadays, 3D visualization is part of our everyday lives and remains an important tool for understanding complex structures, dynamic simulations, and research discoveries. In the meantime, the complexity of the visualization often requires specific hardware, including visualization clusters, as well as dedicated software tools. Several efforts, such as WebGL and remote visualization, have been pushing visualization to the web browser. However, technical limitations have constrained the adoption of web browsers as a means of rendering 3D datasets. To surpass these limitations, prospective action has been recently initiated with the development of a web application based on two innovative technologies: WebGL and ParaViewWeb. This application combines the benefits of local and remote rendering, therefore allowing a user to visualize small to massive 3D molecular datasets on a large number of devices. To demonstrate this approach a prototype has been developed, and in this paper we present the hybrid architecture of the proposed system, the initial implementation experiment, and a comparison with current technologies. Finally, we discuss the future work and potential improvements of the application.

Photochemical fabrication of three-dimensional micro- and nano-structured surfaces from a C60 monoadduct

Exposure of Langmuir–Blodgett (LB) films of a C60 adduct supported on silicon wafers to UV light leads to cross-linking of the C60 moieties, which are resistant to removal by solvent exposure, whereas unexposed moieties are readily removed. This process provides a convenient and simple route for the fabrication of highly conjugated surface-attached structures, with dimensions ranging from micrometres (using masks) to a few tens of nanometres using light emitted from a scanning near-field optical microscope (SNOM). The SNOM writing velocity was found to significantly affect the lateral resolution and the height of the three-dimensional nanostructures. Increasing the writing velocity from 0.3 to 2 μm s−1 resulted in a decrease in the width of the structures from 240 nm to 70 nm (corresponding to the SNOM aperture diameter), respectively, and a reduction in the height from 8 nm (the thickness of the original film) to 3 nm, respectively. This approach provides a simple, direct route to surface-bound nanometre scale assemblies of C60.

Repeatable and Transferable Processing for Electron Tomography: An Open Platform for Visualization and Reconstruction of 3D Materials

Three-dimensional (3D) characterization of materials at the nanoand meso-scale has become possible with transmission and scanning transmission electron tomography[1-2]. This process requires advanced software tools where the final 3D visualization is critically dependent on the reconstruction algorithm and the parameters used to render the 3D image. Exacerbating this variability, electron tomography lacks the standards and tools for repeatable, transferable scientific analysis—the field requires open data formats, reconstruction algorithms, 3D visualization, and most importantly a way to share all processing steps from start to finish.

Evidence of collinear ferrimagnetism in (Fe, Tb)B metallic glasses from polarized beam neutron scattering

The atomic-scale magnetic structures of two terbium-substituted (Fe0.83?xTbx)B0.17 metallic glasses have been determined by polarized beam neutron scattering measurements using the IN20 spectrometer at the Institut Laue-Langevin, Grenoble. The four spin-dependent, neutron scattering cross-sections were measured in absolute units for the two glasses. The spin-flip cross-sections and were found to be small; they were independent of the scattering vector Q, independent of the temperature and were also of the same magnitude as the nuclear incoherent cross-section, within experimental errors. These observations indicate that the magnetic structure in these glasses must be collinear. The non-spin-flip cross-sections were found to have a hitherto unobserved shift of the first peak between the and channels. A (collinear) ferrimagnetic state which is consistent with the spin-flip cross-sections is therefore proposed for these glasses. The magnetic moments on the terbium atoms are aligned antiparallel to those on the iron atoms, and the values of both moments reduce to zero by x = 0.50 terbium, in agreement with magnetization data. A calculation of the non-spin-flip cross-sections based on this model correctly predicts the shift of the first peaks. This behaviour arises because of the ferrimagnetic correlations between the magnetic moments and the very strong magnetic scattering from the terbium atoms.

Advanced Platform for 3D Visualization, Reconstruction, and Segmentation with Electron Tomography

Three-dimensional (3D) characterization of materials at the nanoand meso-scale has become possible with electron tomography (ET) [1-2]. The typical workflow consists of raw data collection with a (scanning) transmission electron microscope, tilt series processing/alignment, tomographic reconstruction, post processing, visualization and analysis. Each step often requires distinct software and has a significant impact to final results. This makes the workflow inefficient and impedes sharing of published or working data among researchers. To address this problem, we have developed an open and extendable platform, tomviz (www.tomviz.org), which integrates the entire ET workflow by providing essential tools from basic image filters to 3D animations (Figure 1).