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.
OpenChrom provides mass spectrometric analysis of chromatographic data, in a way similar to ChemStation from Agilent Technologies. It handles data files from different LC/MS, GC/MS systems and vendors, such as (*.D) chromatograms from Agilent Technologies, Finnigan ITS40 (*.ms), NetCDF (*.cdf), MzXML (*.mzxml), and other formats. It is flexible and can be extended by plugins.
Beat Back the Horde is a rhythm-time strategy game for Android 2.2 and up, focusing on fast-paced placing of units while tapping to the beat! Build up combos to spawn Über Units! It is playable in single-player mode, or in multi-player mode over Bluetooth, and can be learned in a minute and played for hours. It includes many achievements to unlock, five songs to master, adjustable difficulty single-player AI, and particle effects.
Platform Independent Petri Net Editor (PIPE) creates and analyses Petri Nets quickly, efficiently, and effectively. A key design feature is the modular approach adopted for analysis, enabling new modules to be written easily and powerfully, using built-in data layer methods for standard calculations. Six analysis modules are provided, including Invariant Analysis, State-Space Analysis (deadlock, etc.), and Simulation Analysis and Classification. PIPE adheres to the XML Petri net standard (PNML). The file format for saving and loading Petri Nets is extensible through the use of XSLT, the default being PNML.
Daikon is an implementation of dynamic detection of likely invariants. An invariant is a property (such as "x=2*y+5" or "this.next.prev = this" or "myarray is sorted by <") that holds at a certain point or points in a program. Invariants are often seen in assert statements, documentation, and formal specifications. Invariants can be useful in program understanding and a host of other applications. Daikon runs a program, observes the values that the program computes, and then reports properties that were true over the observed executions. It can detect properties in Java, C, C++, Perl, and IOA programs, in spreadsheet files, and in other data sources.
JagPDF is a library for generating PDF documents in C/C++, Python, and Java. It supports TrueType (subsetting) and standard 14 Type 1 fonts, font metrics, Unicode, UTF-8 and common 8-bit character encodings, images (JPEG, PNG, or custom), paths, color spaces (RGB, CMYK, CIE based, ICC profiles, indexed), encryption, bookmarks, hyperlinks, and more.
AntTask-GenerateXML is an Ant task that uses XMLBeans to create example XML instances from a W3C schema. It is especially useful for looking at pieces of schema, as you can set the element you wish to use as the root one. It will use the values from enumerations as the fixed/default values for attributes and elements if they are set. It obeys the XML type system with the exception of regex/patterns.