Scripting language

Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

Abstract: A description and justification of the EXPGUI program is presented. This program implements a graphical user interface and shell for the GSAS single-crystal and Rietveld package. Use of the Tcl/Tk scripting language allows EXPGUI to be platform independent. Also included is a synopsis of how the program is implemented.

Abstract: Recent advances in modern Natural Language Processing (NLP) research have been dominated by the combination of Transfer Learning methods with large-scale Transformer language models. With them came a paradigm shift in NLP with the starting point for training a model on a downstream task moving from a blank specific model to a general-purpose pretrained architecture. Still, creating these general-purpose models remains an expensive and time-consuming process restricting the use of these methods to a small sub-set of the wider NLP community. In this paper, we present Transformers, a library for state-of-the-art NLP, making these developments available to the community by gathering state-of-the-art general-purpose pretrained models under a unified API together with an ecosystem of libraries, examples, tutorials and scripts targeting many downstream NLP tasks. Transformers features carefully crafted model implementations and high-performance pretrained weights for two main deep learning frameworks, PyTorch and TensorFlow, while supporting all the necessary tools to analyze, evaluate and use these models in downstream tasks such as text/token classification, questions answering and language generation among others. Transformers has gained significant organic traction and adoption among both the researcher and practitioner communities. We are committed at Hugging Face to pursue the efforts to develop Transformers with the ambition of creating the standard library for building NLP systems.

Abstract: The ROOT system in an Object Oriented framework for large scale data analysis. ROOT written in C++, contains, among others, an efficient hierarchical OO database, a C++ interpreter, advanced statistical analysis (multi-dimensional histogramming, fitting, minimization, cluster finding algorithms) and visualization tools. The user interacts with ROOT via a graphical user interface, the command line or batch scripts. The command and scripting language is C++ (using the interpreter) and large scripts can be compiled and dynamically linked in. The OO database design has been optimized for parallel access (reading as well as writing) by multiple processes.