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This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities. Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also Blast output parsing. Partly implemented single linkage clustering, and multiple alignment. Reading Gene Ontology (GO) annotations (GOA) and definitions hierarchy.

ISAAC (Integrated Solution Algorithm for Arbitrary Configurations) is a compressible Euler/Navier-Stokes computational fluid dynamics code. ISAAC includes the capability of calculating the Euler equations for inviscid flow or the Navier-Stokes equations for viscous flows. ISAAC uses a domain decomposition structure to accomodate complex physical configurations. ISAAC can calculate either steady-state or time dependent flow. ISAAC was designed to test turbulence models. Various two equation turbulence models, explicit algebraic Reynolds stress models, and full differential Reynolds stress models are implemented in ISAAC. Several test cases are documented in the User's Guide.

metaf2xml can download, parse and decode aviation routine weather reports (METAR, SPECI, SAO), aerodrome forecasts (TAF), synoptic observations (SYNOP), observations from buoys (BUOY) and meteorological reports from aircrafts (AMDAR). Data can also be taken from decoded BUFR messages. The extracted data can be written as XML or passed to a user-defined function (all done in Perl). It also provides XSLT style sheets to convert the XML to plain language (text, HTML), or XML with different schemas. A web-based (CGI) user interface can be used to download and display up-to-date weather data from NOAA, Ogimet, and other sources.

FastHenry computes the frequency dependent self and mutual inductances and resistances between conductors of complex shape. The algorithm used in FastHenry is an acceleration of rge mesh formulation approach. The linear system resulting from the mesh formulation is solved using a generalized minimal residual algorithm with a fast multipole algorithm to efficiently compute the iterates. --------------------- Superconductivity Support ------------------------- This version of fasthenry has been modified to support superconducting segments and ground planes by Stephen R. Whiteley of Whitleley Research Inc. The analysis used is based on the London equations and the two-fluid model. Both reactive and lossy components of the superconductor complex conductivity are employed in obtaining the impedance matrix.

The sigrok project aims at creating a portable, cross-platform, Free/Libre/Open-Source signal analysis software suite that supports various device types, such as logic analyzers, MSOs, oscilloscopes, multimeters, LCR meters, sound level meters, thermometers, hygrometers, anemometers, light meters, DAQs, dataloggers, function generators, spectrum analyzers, power supplies, GPIB interfaces, and more. sigrok-cli is a command-line tool written in C, which uses both libsigrok and libsigrokdecode to provide the basic sigrok functionality from the command-line. Among other things, it's useful for scripting purposes.

PGP (Pretty Good Privacy) is a public key encryption pack- age to protect E-mail and data files. It lets you commu- nicate securely with people you've never met, with no secure channels needed for prior exchange of keys. It's well featured and fast, with sophisticated key management, digital signatures, data compression, and good ergonomic design. Contributors: Matthias Bruestle for the myetsid feature. Lutz Donnerhacke for the pgp2.6.3in development. Ingmar Camphausen, Thomas Roessler, a.o. for extensive testing. FTP: ftp://ftp.fu-berlin.de/doc/IN/IN-CA/pgp/pgp263in/files/pgp263in.changes

HotSSH is an interface to Secure Shell, for GNOME and OpenSSH. It intends to be a better experience than simply invoking "ssh" from an existing terminal window. * Fast search-based interface for new connections * Also display and search of local (Avahi) SSH servers * Tabbed display with automatic session saving (Firefox style) * Status bar with information like latency to server and output of remote uptime * Close integration with OpenSSH features like connection sharing (near-instant new tabs) * NetworkManager integration to easily reconnect after a network change, great for laptops

Fast AES cipher implementation with advanced mode of operations. The modes of operations available are ECB (Electronic code book), CBC (Cipher block chaining), CTR (Counter), XTS (XEX with ciphertext stealing), GCM (Galois Counter Mode). The AES implementation uses AES-NI when available (on x86 and x86-64 architecture), but fallback gracefully to a software C implementation. The software implementation uses S-Boxes, which might suffer for cache timing issues. However do notes that most other known software implementations, including very popular one (openssl, gnutls) also uses same implementation. If it matters for your case, you should make sure you have AES-NI available, or you'll need to use a different implementation.

httprint is a web server fingerprinting tool. It relies on web server characteristics to accurately identify web servers, despite the fact that they may have been obfuscated by changing the server banner strings, or by plug-ins such as mod_security or servermask. httprint can also be used to detect web enabled devices which do not have a server banner string, such as wireless access points, routers, switches, cable modems, etc. httprint uses text signature strings and it is very easy to add signatures to the signature database.

A user authentication and authorisation framework plugin for Dancer apps. Makes it easy to require a user to be logged in to access certain routes, provides role-based access control, and supports various authentication methods/sources (config file, database, Unix system users, etc). Designed to support multiple authentication realms and to be as extensible as possible, and to make secure password handling easy (the base class for auth providers makes handling `RFC2307'-style hashed passwords really simple, so you have no excuse for storing plain-text passwords).