BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity. It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems.
Kalyp is a fantasy-based roguelike game written in Java. Its design is based on traditions set by popular roguelike games, especially Nethack. It is single player and runs in a text terminal. The project focuses mostly on the Artificial Intelligence engine for the non-player characters. Most of the game design will be done in scripting, as the core engine written in Java will handle user interface, rulesets, basic actions, and try to hold it all together.
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.
AMLET is software designed to estimate multinomial and mixed logit discrete choices models, which are increasingly popular in econometry. The software supports cross- sectional and panel data, and offers various optimization methods, including the new variable sample-size approach.
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.
Computation Job Management (jobman) is a program that calls executables according to a given program flow. Each executable is run in a separate process. It is useful when a project needs to carry out a series of calculations that are performed by software written in different languages or supplied by third parties, but invoking individual programs manually is error prone and hard to manage. The various individual programs don't communicate with each other except via persistent storage. This is especially the case for some scientific computing, quantitative finance, and prototyped programming.
Jigsaw is an embedded data-store designed for the development of data-warehouse, analytical, and machine learning applications. Jigsaw can perform over one million operations a second, and scale to store tera-bytes of data. The object library contains classes for representing ordered and unordered mappings, highly compressed bit vectors with a range of set theoretic operators, and directly integrates a high performance sort system.
SAOTrace is a suite of software designed to simulate the as-built performance of grazing-angle X-ray optics using the ray-tracing approach. It is derived from portions of the NASA OSAC (Optical Surface Analysis Code) software suite. It can model nested conical as well as flat optical designs, and includes the ability to model arbitrary support structures and baffles. It can model non-ideal multi-layer reflective coatings as well as scattering from the optical surfaces.