Andrew S. I. D. Lang

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.

The Spectral Game: leveraging Open Data and crowdsourcing for education

We report on the implementation of the Spectral Game, a web-based game where players try to match molecules to various forms of interactive spectra including 1D/2D NMR, Mass Spectrometry and Infrared spectra. Each correct selection earns the player one point and play continues until the player supplies an incorrect answer. The game is usually played using a web browser interface, although a version has been developed in the virtual 3D environment of Second Life. Spectra uploaded as Open Data to ChemSpider in JCAMP-DX format are used for the problem sets together with structures extracted from the website. The spectra are displayed using JSpecView, an Open Source spectrum viewing applet which affords zooming and integration. The application of the game to the teaching of proton NMR spectroscopy in an undergraduate organic chemistry class and a 2D Spectrum Viewer are also presented.

Chemistry in second life.

This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.

Modeling Basketball Free Throws

This paper presents a mathematical model for basketball free throws. It is intended to be a supplement to an existing calculus course and could easily be used as a basis for a calculus project. Students will learn how to apply calculus to model an interesting real-world problem, from problem identification all the way through to interpretation and verification. Along the way we will introduce topics such as optimization (univariate and multiobjective), numerical methods, and differential equations.

Determination of Abraham model solute descriptors for the monomeric and dimeric forms of trans-cinnamic acid using measured solubilities from the Open Notebook Science Challenge

AbstractBackgroundCalculating Abraham descriptors from solubility values requires that the solute have the same form when dissolved in all solvents. However, carboxylic acids can form dimers when dissolved in non-polar solvents. For such compounds Abraham descriptors can be calculated for both the monomeric and dimeric forms by treating the polar and non-polar systems separately. We illustrate the method of how this can be done by calculating the Abraham descriptors for both the monomeric and dimeric forms of trans-cinnamic acid, the first time that descriptors for a carboxylic acid dimer have been obtained.ResultsAbraham descriptors were calculated for the monomeric form of trans-cinnamic acid using experimental solubility measurements in polar solvents from the Open Notebook Science Challenge together with a number of water-solvent partition coefficients from the literature. Similarly, experimental solubility measurements in non-polar solvents were used to determine Abraham descriptors for the trans-cinnamic acid dimer.ConclusionAbraham descriptors were calculated for both the monomeric and dimeric forms of trans-cinnamic acid. This allows for the prediction of further solubilities of trans-cinnamic acid in both polar and non-polar solvents with an error of about 0.10 log units. Graphical abstractMolar concentration of trans-cinnamic acid in various polar and non-polar solvents.

Predicting Abraham model solvent coefficients

AbstractBackgroundThe Abraham general solvation model can be used in a broad set of scenarios involving partitioning and solubility, yet is limited to a set of solvents with measured Abraham coefficients. Here we extend the range of applicability of Abraham’s model by creating open models that can be used to predict the solvent coefficients for all organic solvents.ResultsWe created open random forest models for the solvent coefficients e, s, a, b, and v that had out-of-bag R2 values of 0.31, 0.77, 0.92, 0.47, and 0.63 respectively. The models were used to suggest sustainable solvent replacements for commonly used solvents. For example, our models predict that propylene glycol may be used as a general sustainable solvent replacement for methanol.ConclusionThe solvent coefficient models extend the range of applicability of the Abraham general solvation equations to all organic solvents. The models were developed under Open Notebook Science conditions which makes them open, reproducible, and as useful as possible. Graphical AbstractChemical space for solvents with known Abraham coefficients.

Teaching calculus with Wolfram|Alpha

This article describes the benefits and drawbacks of using Wolfram|Alpha as the platform for teaching calculus concepts in the lab setting. It is a result of our experiences designing and creating an entirely new set of labs using Wolfram|Alpha. We present the reasoning behind our transition from using a standard computer algebra system (CAS) to Wolfram|Alpha in our differential and integral calculus labs, together with the positive results from our experience. We also discuss the current limitations of Wolfram|Alpha, including a discussion on why we still use a CAS for our multivariate calculus labs.

The frequency spectrum of the Casimir effect

The frequency spectrum of the Casimir effect between parallel plates is studied. Calculations are performed for both the massless scalar field and the electromagnetic field cases, first using a spectral weight function, and then via the Fourier transform of the renormalized expectation of the Casimir energy-momentum operator. The Casimir force is calculated using the spectrum for two plates which are perfectly transparent in a frequency band. The result of this calculation suggests a way to detect the frequency spectrum of the Casimir effect.

Precipitation Forecasting with Gamma Distribution Models for Gridded Precipitation Events in Eastern Oklahoma and Northwestern Arkansas

AbstractAn elegant and easy to implement probabilistic quantitative precipitation forecasting model that can be used to estimate the probability of exceedance (POE) is presented. The model was built using precipitation data collected across eastern Oklahoma and northwestern Arkansas from late 2005 through early 2013. The dataset includes precipitation analyses at 4578 contiguous, 4 km × 4 km grid cells for 1800 precipitation events of 12 h. The dataset is unique in that the meteorological conditions for each 12-h event were relatively homogeneous when contrasted with single-point data obtained over months or years where the meteorological conditions for each rain event could have varied widely. Grid cells were counted and stratified by precipitation amount in increments of 0.05 in. (1.27 mm) up to 10 in. (254 mm), yielding histograms for each event. POEs were computed from the observed precipitation distributions and compared to POEs computed from two gamma probability density functions ( and ). The error...

Prediction of 1-octanol solubilities using data from the Open Notebook Science Challenge.

Background1-Octanol solubility is important in a variety of applications involving pharmacology and environmental chemistry. Current models are linear in nature and often require foreknowledge of either melting point or aqueous solubility. Here we extend the range of applicability of 1-octanol solubility models by creating a random forest model that can predict 1-octanol solubilities directly from structure.ResultsWe created a random forest model using CDK descriptors that has an out-of-bag (OOB) R2 value of 0.66 and an OOB mean squared error of 0.34. The model has been deployed for general use as a Shiny application.ConclusionThe 1-octanol solubility model provides reasonably accurate predictions of the 1-octanol solubility of organic solutes directly from structure. The model was developed under Open Notebook Science conditions which makes it open, reproducible, and as useful as possible.Graphical abstract: