Sustainable Software Ecosystems: Software Engineers, Domain Scientists, and Engineers Collaborating for Science

The development of scientific software is often a partnership between domain scientists and scientific software engineers. It is especially important to embrace these collaborations when developing advanced scientific software, where sustainability, reproducibility, and extensibility are important. In the ideal case, as discussed in this manuscript, this brings together teams composed of the world's foremost scientific experts in a given field with seasoned software developers experienced in forming highly collaborative teams working on software to further scientific research.Comment: 4 pages, submission for WSSSPE

Sustainable Software Ecosystems for Open Science

Sustainable software ecosystems are difficult to build, and require concerted effort, community norms and collaborations. In science it is especially important to establish communities in which faculty, staff, students and open-source professionals work together and treat software as a first-class product of scientific investigation-just as mathematics is treated in the physical sciences. Kitware has a rich history of establishing collaborative projects in the science, engineering and medical research fields, and continues to work on improving that model as new technologies and approaches become available. This approach closely follows and is enhanced by the movement towards practicing open, reproducible research in the sciences where data, source code, methodology and approach are all available so that complex experiments can be independently reproduced and verified.Comment: Workshop on Sustainable Software: Practices and Experiences, 4 pages, 3 figure

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.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Prevalence and Predictors of Vitamin D Insufficiency in Children: A Great Britain Population Based Study

Objectives To evaluate the prevalence and predictors of vitamin D insufficiency (VDI) in children In Great Britain. Design A nationally representative cross-sectional study survey of children (1102) aged 4–18 years (999 white, 570 male) living in private households (January 1997–1998). Interventions provided information about dietary habits, physical activity, socio-demographics, and blood sample. Outcome measures were vitamin D insufficiency (<50 nmol/L). Results Vitamin D levels (mean = 62.1 nmol/L, 95%CI 60.4–63.7) were insufficient in 35%, and decreased with age in both sexes (p<0.001). Young People living between 53–59 degrees latitude had lower levels (compared with 50–53 degrees, p = 0.045). Dietary intake and gender had no effect on vitamin D status. A logistic regression model showed increased risk of VDI in the following: adolescents (14–18 years old), odds ratio (OR) = 3.6 (95%CI 1.8–7.2) compared with younger children (4–8 years); non white children (OR = 37 [95%CI 15–90]); blood levels taken December-May (OR = 6.5 [95%CI 4.3–10.1]); on income support (OR = 2.2 [95%CI 1.3–3.9]); not taking vitamin D supplementation (OR = 3.7 [95%CI 1.4–9.8]); being overweight (OR 1.6 [95%CI 1.0–2.5]); <1/2 hour outdoor exercise/day/week (OR = 1.5 [95%CI 1.0–2.3]); watched >2.5 hours of TV/day/week (OR = 1.6[95%CI 1.0–2.4]). Conclusion We confirm a previously under-recognised risk of VDI in adolescents. The marked higher risk for VDI in non-white children suggests they should be targeted in any preventative strategies. The association of higher risk of VDI among children who exercised less outdoors, watched more TV and were overweight highlights potentially modifiable risk factors. Clearer guidelines and an increased awareness especially in adolescents are needed, as there are no recommendations for vitamin D supplementation in older children

Use of quercetin in animal feed : effects on the P-gp expression and pharmacokinetics of orally administrated enrofloxacin in chicken

Modulation of P-glycoprotein (P-gp, encoded by Mdr1) by xenobiotics plays central role in pharmacokinetics of various drugs. Quercetin has a potential to modulate P-gp in rodents, however, its effects on P-gp modulation in chicken are still unclear. Herein, study reports role of quercetin in modulation of P-gp expression and subsequent effects on the pharmacokinetics of enrofloxacin in broilers. Results show that P-gp expression was increased in a dose-dependent manner following exposure to quercetin in Caco-2 cells and tissues of chicken. Absorption rate constant and apparent permeability coefficient of rhodamine 123 were decreased, reflecting efflux function of P-gp in chicken intestine increased by quercetin. Quercetin altered pharmacokinetic of enrofloxacin by decreasing area under curve, peak concentration, and time to reach peak concentration and by increasing clearance rate. Molecular docking shows quercetin can form favorable interactions with binding pocket of chicken xenobiotic receptor (CXR). Results provide convincing evidence that quercetin induced P-gp expression in tissues by possible interaction with CXR, and consequently reducing bioavailability of orally administered enrofloxacin through restricting its intestinal absorption and liver/kidney clearance in broilers. The results can be further extended to guide reasonable use of quercetin to avoid drug-feed interaction occurred with co-administered enrofloxacin or other similar antimicrobials.Peer reviewedFinal Published versio

Self-driving Multimodal Studies at User Facilities

Multimodal characterization is commonly required for understanding materials. User facilities possess the infrastructure to perform these measurements, albeit in serial over days to months. In this paper, we describe a unified multimodal measurement of a single sample library at distant instruments, driven by a concert of distributed agents that use analysis from each modality to inform the direction of the other in real time. Powered by the Bluesky project at the National Synchrotron Light Source II, this experiment is a world's first for beamline science, and provides a blueprint for future approaches to multimodal and multifidelity experiments at user facilities.Comment: 36th Conference on Neural Information Processing Systems (NeurIPS 2022). AI4Mat Worksho

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

PMCID: PMC3710212This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

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

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract 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.Peer Reviewe

Excimer formation by steric twisting in carbazole and triphenylamine-based host materials

This paper presents a detailed spectroscopic investigation of luminescence properties of 4,4′-Bis(N-carbazolyl)-1,1′-biphenyl (CBP) and N,N,N’,N’-tetraphenylbenzidine (TAD) in solutions and neat films. These compounds are compared to their derivatives CDBP and TDAD that contain methyl groups in the 2 and 2’ position of the biphenyl core. We find that whereas steric twisting in CDBP and TDAD leads to a high triplet energy of about 3.0 and 3.1 eV, respectively, these compounds also tend to form triplet excimers in a neat film, in contrast to CBP and TAD. By comparison with N-phenylcarbazole (NPC) and triphenylamine (TPA), on which these compounds are based, as well as with the rigid spiro analogs to CBP and TAD we show that the reduced excimer formation in CBP and TAD can be attributed to a localization of the excitation onto the central biphenyl part of the molecule.We acknowledge support from the Federal Ministry of Education and Research (BMBF) through the project ‘Trip-Q’, the German Science Foundation (DFG) through the Research and Training Group GRK 1640 and the UK Engineering and Physical Sciences Research Council (grant number EP/G060738/1).This is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/jp512772j