TL;DR: publCIF is an application designed for creating, editing and validating crystallographic information files (CIFs) that are used in journal publication and provides a web interface to the checkCIF service of the International Union of Crystallography (IUCr), which provides a full crystallographic analysis of the structural data.
Abstract: publCIF is an application designed for creating, editing and validating crystallographic information files (CIFs) that are used in journal publication. It validates syntax and dictionary-defined data attributes through internal routines, and also provides a web interface to the checkCIF service of the International Union of Crystallography (IUCr), which provides a full crystallographic analysis of the structural data. The graphical interface allows users to edit the CIF either in its `raw' ASCII form (using a text editor with context-sensitive data validation and input facilities) or as a formatted representation of a structure report (using a word-processing environment), as well as via a number of convenience tools (e.g. spreadsheet representations of looped data). Beyond file and data validation, publCIF provides access to resources to facilitate preparation of a structure report (e.g. databases of author details, experimental data, standard references etc., either distributed with the program or collected during its use), along with tools for reference parsing, spell checking, structure visualization and image management. publCIF was commissioned by the IUCr, both as free software for authors and as a tool for in-house journal production; the tool for authors is described here. Binary distributions for Linux, MacOS and Windows operating systems are available.
TL;DR: A web tool called ClustVis that aims to have an intuitive user interface for the Principal Component Analysis and heatmap plots and is freely available at http://biit.cs.ut.ee/clustvis/.
Abstract: The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/.
TL;DR: The ALSCRIPT program was developed specifically to allow the easy formatting and graphical display of large multiple alignments, and should be easy to learn by anyone familiar with plotting graphs.
Abstract: The ALSCRIPT program described in this article was developed specifically to allow the easy formatting and graphical display of large multiple alignments. Although written originally for the author's use, the interface is relatively friendly, and should be easy to learn by anyone familiar with plotting graphs
TL;DR: In this paper, requests from browsing clients are identified which contain information relating to the data itself and the display format for the data, and the data is read and processed so as to combine a representation of the viewable data with executable instructions.
Abstract: Output signals are served from a serving device to a plurality of browsing devices connected to a network. The output signals represent commands executable by each browsable device so as to display viewable data in accordance with specified page formatting. Requests from browsing clients are identified which contain information relating to the data itself and the display format for the data. The data is read and processed so as to combine a representation of the viewable data with executable instructions. The signals are then supplied to requesting browsing devices, after effectively being assembled as a real time on-line process.
TL;DR: In this article, the user is presented with a hierarchy of queries based on wallet-type (basic identification) and non-wallet type (more private) information designed to ensure the identity of the user and prevent fraud, false negatives and other undesirable results.
Abstract: A network authentication system provides verification of the identity or other attributes of a network user to conduct a transaction, access data or avail themselves of other resources. The user is presented with a hierarchy of queries based on wallet-type (basic identification) and non-wallet type (more private) information designed to ensure the identity of the user and prevent fraud, false negatives and other undesirable results. A preprocessing stage may be employed to ensure correct formatting of the input information and clean up routine mistakes (such as missing digits, typos, etc.) that might otherwise halt the transaction. Queries can be presented in interactive, batch processed or other format. The authenticator can be configured to require differing levels of input or award differing levels of authentication according to security criteria.