Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.
Release Notes: The most important changes in this release are some improvements for VPG. A new form allows you to easily create a DSSP file from a PDB file, i.e., have the dsspcmbi program by Kabsch & Sander assign secondary structure information to the atom coordinates in the PDB file. Some fixes, rearranged menus, and new keyboard shortcuts for many VPG features are also new.
Release Notes: This is a maintenance release.
TexMaths is an add-on designed to provide LaTeX support in LibreOffice. LaTeX equations can be inserted as images (SVG or PNG formats), and the LaTeX code is saved into the image attribute for further editing.
Release Notes: This release adds a transparency option for PNG images. A Spanish translation is also provided. Many bugs were fixed, and TexMaths is now working better on Mac OS X.
ZABBIX is an enterprise-class distributed monitoring solution designed to monitor and track performance and availability of network servers, devices, and other IT resources. It supports distributed and Web-based monitoring, auto-discovery, real-time monitoring, SLA assurance, trending, and more.
Release Notes: This release candidate introduces several bugfixes, including a security-related one.
JID is a system which can deserialize, update, and reserialize a map of 100,000 entries in half a millisecond on an i7 at 3.40 GHz. Serialization/reserialization timings are largely independent of the size and complexity of the table entries. Incremental serialization/deserialization is used to achieve high performance.
Release Notes: JID now depends on JActor 3.3.2; benchmark results have been updated.
htmLawed is a PHP script that makes input text more secure, HTML standards-compliant, and suitable in general from the viewpoint of a Web-page administrator, for use in the body of HTML 4 or XHTML 1 or 1.1 documents. It is a customizable HTML/XHTML filter, processor, purifier, and sanitizer. It can ensure that HTML tags are balanced and properly nested tags, neutralize code that may be used for cross-site scripting (XSS) attacks, and limit the allowed HTML elements, tags, attributes, or URL protocols.
Release Notes: A fix for possible segmental loss of incremental indentation during tidying when the configuration parameter 'balance' is disabled. A fix for non-effectuation under some circumstances of a corrective behavior to preserve plain text within elements like 'blockquote' and 'form'.
JActor is a high-performance Java Actor implementation that can send 150 million messages per second, making it one of the fastest Actor implementations in any language.
Release Notes: JLPCActor has been rewritten for greater clarity and to cover previously overlooked corner cases. Additional test cases have been added. The API remains unchanged.
zlog is a reliable, efficient, thread safe, flexible, pure C logging library. It was written because there were no good C logging libraries along the lines of Logback for Java or log4cxx for C++. printf can work, but can not be easily redirected or reformatted, and syslog is slow and designed for system use. It provides a syslog model, log format customization, multiple output, safe run-time reconfiguration, high performance, user-defined log levels, safe log rotation, a log4j-style key-value map, in-built debugging, and no external dependencies.
Release Notes: Pipeline support; now zlog can output logs through programs like cronolog. Full rotation support. Other code compatibility details and bugfixes.
eclim is a set of Eclipse and Vim plugins to integrate the two pieces of software.
Release Notes: This is a bugfix release.
eclim is a set of Eclipse and Vim plugins to integrate the two pieces of software.
Release Notes: This release adds support for Eclipse 4.2 (Juno).
Diagnil is a GUI application to help solvers of diagramless crossword puzzles. It accommodates puzzles distributed electronically using several file formats (puz, jpz, xpf, and ipuz) as well as those distributed in print form. Although software for conventional crosswords has existed for years, the diagramless variant has received little attention. Diagnil attempts to fill that void. It lets you solve puzzles by entering words, placing them on a grid, and moving them around the screen until the final shape is achieved.
Release Notes: The user interface was revamped in several areas. A keystroke-based grid navigation mode was added to complement the mouse-based navigation method. A timer feature for displaying and recording solving time was added. Automatic detection of puzzle completion was improved. Support was added for importing files in the Crossword Solver (jpz) format. A primer on diagramless solving was added to the Help information.
BRL-CAD is a powerful constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing support for rendering and geometric analysis, path-tracing for realistic image synthesis, network distributed framebuffer support, and image and signal-processing tools.
Release Notes: This is a substantial introduction of a new development line encompassing more changes than any prior version since BRL-CAD became free open source software. It has robust solid NURBS ray tracing, fixes everything reported by Coverity, updates several geometry converters, has work on a new physics simulation system, makes several improvements to BRL-CAD's extensive documentation resources, and provides a vastly improved installer for Mac OS X.
nut is nutrition software to record what you eat and analyze your meals for nutrient composition. The database included is the latest USDA Nutrient Database for Standard Reference. This database contains values for vitamins, minerals, fats, calories, protein, carbohydrates, fiber, etc., and includes the essential polyunsaturated fats, Omega-3 and Omega-6. Nutrient levels are expressed as a percentage of the Daily Value, the familiar standard of food labeling in the United States, but also can be fully customized. Foods can be added from recipes or food labels, and nutrient intake can be graphed. The program is completely menu-driven and there are no commands to learn.
Release Notes: This release includes enhancements to make it easier to plan a ketogenic diet and to quickly see the chart and graph for a nutrient from the analysis screen.
The j661 project provides a generic CDS (or ARINC 661 Server) in order to facilitate the understanding of the ARINC 661 standard, prototype ARINC 661 concepts and architectures, and facilitate the reuse of ARINC 661 specifications and artefacts between projects. The CDS architecture is designed to allow defining the Server behavior to be easily modified or extended. This is achieved by a modular plug-in architecture, allowing customization at runtime without changing anything in the Server core itself.
Release Notes: This release fixes some bugs in the Debug Plugin. It fixes the server still taking into account widget commands if the associated layer is not active. It can execute editor scripts on all the opened definition files in the editor. It fixes some bugs in corner cases for copy / paste / delete actions in the editor. It will show the XML definition file binary errors in colors depending on their kind (warnings are black, but errors and fatal errors are red).
SableCC is a parser generator that generates fully featured object-oriented frameworks for building compilers, interpreters, and other text parsers. In particular, generated frameworks include intuitive strictly-typed abstract syntax trees and tree walkers. SableCC also keeps a clean separation between machine-generated code and user-written code, which leads to a shorter development cycle.
Release Notes: This version uses unsigned shift left instead of integer division by 2 for binary search.
SEM2DPACK is a simulator of 2D elastic wave propagation and fracture dynamics that applies the Spectral Element Method (SEM, similar to mass-lumped high-order finite element methods). Flexibility and accuracy are the main goals. Although the emphasis is currently on computational seismology and earthquake source dynamics, this tool might attract a wider audience in computational mechanics, research, and engineering.
Release Notes: This version can read mesh files exported by the mesh generation programs CUBIT and EZ4U, and introduces kinematic fault sources, heterogeneous coefficients for anistropic media, absorbing boundaries with arbitrary orientation, and Gaussian source time function and pre-processing utilities to compute critical time steps. Bugs are fixed in time-weakening friction and handling of fault tip nodes of single-sided faults.
tvpvrd is a PVR daemon for Linux that offers the ability to schedule and manage TV recordings using one or multiple installed analogue TV capture cards, e.g. Hauppauge. The daemon is interfaced either through its full command language via a provided command line shell or through a basic (built-in) Web interface provided by the built in micro Web server. The goal is to provide an advanced recording and transcoding (using ffmpeg) server without the need to configure databases or a complex GUI. The server is completely self-contained and uses an XML DB in plain text format to store future recordings.
Release Notes: This release adds the ability to set manual frequencies in the channel/station list, adds an "lf" command to display frequency tables, updates "ffmpeg" commands to match the latest version, tweaks the profile settings for transcoding, and adds a minor bugfix to make it possible to add extra options to the ffmpeg command from the tvpvrd configuration file.
PdfMasher is a tool to convert PDF files containing text into a ready-for-ebook set of HTML files. Most ebook readers support PDF files natively, but it's often a real pain to read those documents because you can't control the font size of the document and have to resort to the zooming feature instead. Another drawback of PDFs on ebook readers is that annotations are not supported. Unlike other tools that convert PDFs to ebooks, PdfMasher does not try to guess the role of each piece of text in the PDF, and instead asks the user about the role of each piece of text, and does so in an efficient manner.
Release Notes: This release fixes a bug causing crashes on Save Project.
XiX Music Player is a music player for MP3, Ogg, M4A, AAC, FLAC, APE, and OPUS files. It is easy to create and maintain your own playlists. There is an integrated lyric viewer that searches for the lyric of the song you are listening to. If the CD cover is found, it is also shown. You can also rip CD tracks to MP3 or FLAC. Listening to your favorite online radio stations is also possible. The focus is on having fast control of all your music.
Release Notes: This release removes CD Artwork and Lyrics from the cache, loads CD Artwork and Lyrics from files, reloads Lyrics from a chosen site, adds Year and Genre in CD ripping/encoding, adds experimental support for a tray icon, and removes some errors on empty playing queues.
Paludis is a package manager for Gentoo (and derived distributions) and Exherbo. It consists of a core library and a number of console-based clients. Package formats supported include Gentoo ebuilds and kdebuilds (as defined by the Package Manager Specification), the Exherbo exheres-0 format, and various miscellaneous utility pseudo-formats for managing accounts, unwritten and unavailable packages, and packages for which no package exists.
Release Notes: 'cave resolve --explain' output now groups together similar items. Phase skipping now works for uninstalls too. build_options: preserve_work is now build_options: work=preserve, and other values are now possible. Various bugfixes.
GLib is a library containing many useful C routines for things such as trees, hashes, and lists. GLib was previously distributed with the GTK toolkit, but has been split off as of the developers' version 1.1.0.
Release Notes: GIO gained a g_file_delete_async() function. The defaults for GThreadPools max_unused_threads and max_idle_time were changed. Various minor bugs were fixed.
GTK, which stands for the Gimp ToolKit, is a library for creating graphical user interfaces. It is designed to be small and efficient, but still flexible enough to allow the programmer freedom in the interfaces created. GTK provides some unique features over standard widget libraries.
Release Notes: The Wayland backend was improved. GDK thread support was deprecated. Several minor bugs were fixed.
Wnotes are small, self-contained text notes for X Window System desktops. You can create, type, cut-and-paste, and save notes in any combination you like. Wnotes let you store notes and their window configurations using any database which accepts input from the Unix shell. It is compatible with most Linux and Unix desktops. The source code package includes sdb, a simple note database written as a bash script, and other examples of how to use Wnotes.
Release Notes: This release contains mainly internal changes to improve reliability when using Wnotes with other programs, and yet more changes to improve usability when editing text.
Stendhal is a multiplayer online adventure game (MMORPG) developed using the Arianne game development system. It features a rich and expanding world in which you can explore towns, buildings, plains, caves, and dungeons. You will meet NPCs and acquire tasks and quests for valuable experience and cold hard cash. Your character will develop and grow, and with each new level up become stronger and better. With the money you acquire, you can buy new items and improve your armour and weapons. You can also roam the world in search of evil monsters (and kill them).
Release Notes: In addition to new NPCs and quests, "Stendhal 1.02: Overcoming darkness" features amazing light effects, an improved tutorial for new users, and may small improvements.
CorneliOS is an easy-to-use and cross-browser "Web Desktop Environment", "Web Operating System", or "Web Office" that comes with a set of cool applications. It includes a Content Management System (CMS) so that you can easily set up and manage your own website as well as a Database Management System that allows you to rapidly build any kind of database application.
Release Notes: This release offers a new CIOS splash screen feature, various CIOS Web API enhancements and bugfixes, as well as updated system images, language kits, and style sheets.