The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific ...communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.
An overview of Mercury 4.0, an analysis, design and prediction platform that acts as a hub for the entire Cambridge Structural Database software suite, is presented.
Green analytical chemistry focuses on making analytical procedures more environmentally benign and safer to humans. The amounts and toxicity of reagents, generated waste, energy requirements, the ...number of procedural steps, miniaturization, and automation are just a few of the multitude of criteria considered when assessing an analytical methodology's greenness. The use of greenness assessment criteria requires dedicated tools. We propose the Analytical GREEnness calculator, a comprehensive, flexible, and straightforward assessment approach that provides an easily interpretable and informative result. The assessment criteria are taken from the 12 principles of green analytical chemistry (SIGNIFICANCE) and are transformed into a unified 0-1 scale. The final score is calculated based on the SIGNIFICANCE principles. The result is a pictogram indicating the final score, performance of the analytical procedure in each criterion, and weights assigned by the user. Freely available software makes the assessment procedure straightforward. It is open-source and downloadable from https://mostwiedzy.pl/AGREE.
CrystalExplorer is a native cross‐platform program supported on Windows, MacOS and Linux with the primary function of visualization and investigation of molecular crystal structures, especially ...through the decorated Hirshfeld surface and its corresponding two‐dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. Over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the Gaussian and NWChem programs to calculate quantum‐mechanical properties of molecules. The current version, CrystalExplorer21, incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.
CrystalExplorer is a native cross‐platform program for the visualization and investigation of molecular crystal structures.
strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time‐scale phylogenies ...of fossil taxa; (2) to plot those time‐scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time‐scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: Stratigraphic Consistency Index (SCI), Manhattan Stratigraphic Measure (MSM*) and the gap excess ratio (GER; including GERt and GER*), as well as the pseudocongruence measure, the Relative Completeness Index (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a user‐defined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets.
Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship ...information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface.
The Generic Mapping Tools Version 6 Wessel, P.; Luis, J. F.; Uieda, L. ...
Geochemistry, geophysics, geosystems : G3,
November 2019, 2019-11-00, 20191101, Volume:
20, Issue:
11
Journal Article
Peer reviewed
Open access
The Generic Mapping Tools (GMT) software is ubiquitous in the Earth and ocean sciences. As a cross‐platform tool producing high‐quality maps and figures, it is used by tens of thousands of scientists ...around the world. The basic syntax of GMT scripts has evolved very slowly since the 1990s, despite the fact that GMT is generally perceived to have a steep learning curve with many pitfalls for beginners and experienced users alike. Reducing these pitfalls means changing the interface, which would break compatibility with thousands of existing scripts. With the latest GMT version 6, we solve this conundrum by introducing a new “modern mode” to complement the interface used in previous versions, which GMT 6 now calls “classic mode.” GMT 6 defaults to classic mode and thus is a recommended upgrade for all GMT 5 users. Nonetheless, new users should take advantage of modern mode to make shorter scripts, quickly access commonly used global data sets, and take full advantage of the new tools to draw subplots, place insets, and create animations.
Plain Language Summary
The Generic Mapping Tools software is widely used in Earth and ocean sciences to process data and make maps and illustrations. This new version simplifies usage, adds quick access to key data sets, and provides a tool for making scientific animations.
Key Points
A new version of the Generic Mapping Tools (GMT) is released
A new modern mode, complementing the existing classic mode, greatly simplifies GMT scripting
Easy access to remote data sets and advanced animation building facilitate science communication
Superhuman AI for multiplayer poker Brown, Noam; Sandholm, Tuomas
Science (American Association for the Advancement of Science),
08/2019, Volume:
365, Issue:
6456
Journal Article
Peer reviewed
Open access
In recent years there have been great strides in artificial intelligence (AI), with games often serving as challenge problems, benchmarks, and milestones for progress. Poker has served for decades as ...such a challenge problem. Past successes in such benchmarks, including poker, have been limited to two-player games. However, poker in particular is traditionally played with more than two players. Multiplayer games present fundamental additional issues beyond those in two-player games, and multiplayer poker is a recognized AI milestone. In this paper we present Pluribus, an AI that we show is stronger than top human professionals in six-player no-limit Texas hold'em poker, the most popular form of poker played by humans.
Analyzing Social Media Networks with NodeXL: Insights from a Connected World, Second Edition, provides readers with a thorough, practical and updated guide to NodeXL, the open-source social network ...analysis (SNA) plug-in for use with Excel. The book analyzes social media, provides a NodeXL tutorial, and presents network analysis case studies, all of which are revised to reflect the latest developments. Sections cover history and concepts, mapping and modeling, the detailed operation of NodeXL, and case studies, including e-mail, Twitter, Facebook, Flickr and YouTube. In addition, there are descriptions of each system and types of analysis for identifying people, documents, groups and events. This book is perfect for use as a course text in social network analysis or as a guide for practicing NodeXL users.
PDF
