Ycarus Gentoo ebuild

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app
- app-admin
  - anaconda - 11.2 (A graphical interface for modifying system date and time)
  - collectd - 4.4.1 (A small daemon to collect system statistics into RRD files.)
  - syslog-ng - 3.0.3 (syslog replacement with advanced filtering features)
  - system-config-boot - 0.2.12 (A graphical interface for configuring the boot loader)
  - system-config-netboot - 0.1.41 (A network booting/install configuration utility)
- app-doc
  - bashdoc - 1.0 (bashdoc is a tool to make documentation from bash scripts.)
- app-editors
  - gobby - 0.4.5-r1 (GTK-based collaborative editor)
- app-emacs
  - ropemacs - 0.6 (Emacs interface for rope)
- app-emulation
  - virtualbox-modules - 4.1.6 (Kernel Modules for Virtualbox)
  - vmware-modules - 1.0.0.15-r3 ()
  - xen - 3.2.1 (The Xen virtual machine monitor)
- app-laptop
  - tp_smapi - 0.40-r3 (IBM ThinkPad SMAPI BIOS driver)
- app-misc
  - gcalcli - 1.2 (CLI interface to Google Calendar)
  - labyrinth - 9999 (Mind mapping tool for the GNOME desktop)
- app-office
  - rescuetime-linux-uploader - 99 (Data uploader for the RescueTime time tracker)
- app-pda
  - barry - 9999 (Barry is an Open Source Linux application that will allo)
  - ipheth-pair - 9999 (iPhone USB Ethernet Driver for Linux pairing helper)
- app-shells
  - heirloom-sh - 050706 (A portable version of the OpenSolaris Bourne Shell)
- app-text
  - acroread - 9.4.6 (Adobe's PDF reader)
  - pastebin - 0.5 (CLI to pastebin.com)
dev
- dev-java
  - diffmk - 2.0_beta2 (An application for highlighting the differences between two XML documents)
  - fop - 0.92_beta (Formatting Objects Processor is a print formatter driven by XSL)
- dev-lang
  - python - 2.5.2 (Python is an interpreted, interactive, object-oriented programming language.)
  - sunstudio - 12_p200709 (Sun Studio Compilers for Linux)
- dev-libs
  - DirectFB - 1.1.0 (Thin library on top of the Linux framebuffer devices)
  - string_f - 1.0 (A small library to interchange strings between C and Fortran)
- dev-python
  - aggdraw - 1.2_alpha3 (Python library for high-quality drawing, with anti-aliasing and alpha compositing)
  - cocos2d - 0.3.0 (cocos2d: A framework for building 2D games)
  - greenlet - 0.2 (Lightweight in-process concurrent programming)
  - jpype - 0.5.4.1 (Allows Python programs full access to Java class libraries)
  - multitask - 0.2.0 (Allows Python programs to use generators (a.k.a. coroutines) to perform cooperative multitasking and asynchronous I/O.)
  - pandas - 0.4.0 (Powerful data structures for data analysis and statistics)
  - pycallgraph - 0.4.1 (Python library that creates call graphs for Python programs.)
  - pycogent - 1.5.1 (A software library for genomic biology, including sequence alignments, phylogeny, clustering, etc.)
  - pymedia - 1.3.7.3 (This is a sample skeleton ebuild file)
  - pystache - 0.3.1 (Mustache in Python.)
  - python-biggles - 1.6.5 (A Python module for creating publication-quality 2D scientific plots.)
  - pyvnc2swf - 0.9.3 (This is a sample skeleton ebuild file)
  - rdfalchemy - 0.2_beta2 (Provides intuitive access to RDF values through dot notation.)
  - requests - 0.8.3 (Requests is an ISC Licensed HTTP library, written in Python, for human beings.)
  - scientificpython - 2.7.8 (Scientific Module for Python)
  - spasmoidal - 0.1.1 (Spasmodic Engine)
  - statlib - 1.1 (The goal of the project is to combine several Python statistics modules into a single package.)
  - suds - 0.4 (Lightweight SOAP client)
  - tweepy - 1.7.1 (Twitter library for python)
- dev-scheme
  - guile-lib - 0.1.6 (An accumulation place for pure-scheme Guile modules)
- dev-tcltk
  - tktreectrl - 2.2.5 (TkTreeCtrl is a flexible listbox widget for Tk)
- dev-util
  - latrace - 0.5 (A frontend to the LD_AUDIT tracing framework in glibc)
  - oprofile - 0.9.3-r1 (A transparent low-overhead system-wide profiler)
  - oprofileui - 0.1.1 (A user interface to the stochastic system profiler OProfile)
  - rstudio-bin - 0.94.92 (RStudioâ„¢ is a new integrated development environment (IDE) for R.)
eclass
- eclass
  - useful.eclass - ()
mail
- mail-client
  - mutt - 1.5.21-r3 (A small but very powerful text-based mail client)
media
- media-gfx
  - fly - 2.0.0 (Creates GIF images on the fly from CGI and other programs)
- media-libs
  - libv4l - 0.5.8-r1 (V4L userspace libraries)
  - swfdec - 0.4.3 (Swfdec is a decoder/renderer for Macromedia Flash animations.)
  - swfdec-mozilla - 0.4.3 (Swfdec-mozilla is a decoder/renderer netscape style plugin for Macromedia Flash animations.)
- media-video
  - gxine - 0.5.901 (GTK+ Front-End for libxine)
  - v4l2ucp - 9999 (A universal control panel for all Video for Linux Two (V4L2) devices)
net
- net-libs
  - webkit-gtk - 0_p35005 (Open source web browser engine)
- net-misc
  - ntp - 4.2.2_p3 (Network Time Protocol suite/programs)
- net-wireless
  - iw - 9999 (nl80211 based CLI configuration utility for wireless devices)
  - kismet - 2007.10.1 (IEEE 802.11 wireless LAN sniffer)
- net-www
  - bottle - 0.8.5 (Fast and simple WSGI-framework for small web-applications.)
sci
- sci-biology
  - TMalign - 9999 (Computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix)
  - biopython - 1.54_beta (Biopython - Python modules for computational molecular biology)
  - biskit - 9999 (This is a sample skeleton ebuild file)
  - ce - 20040716 (3-D protein structure comparison and alignment using the Combinatorial Extension (CE) method)
  - cytoscape - 2.7.0 (A visualization platform for molecular interaction networks)
  - foldx-bin - 2.5.2 (A force field for energy calculations in proteins)
  - imagej - 1.44n (Image Processing and Analysis in Java)
  - mmult - 1.0 (MAtching Molecular Models Obtained from THeory)
  - probalign - 1.3_beta (Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments)
  - sap - 1.0.0 (Pairwise protein structure alignment via double dynamic programming)
  - surfaceracer - 5.0 (Calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules)
- sci-chemistry
  - autodock-vina - 1.1.1 (Program for drug discovery, molecular docking and virtual screening)
  - cclib - 0.91 (Library for parsing and interpreting the results of computational chemistry packages)
  - ccp1gui - 0.7.1 (A free, extensible Graphical User Interface (GUI) for community chemistry programs)
  - ccp4mg - 0.12.1 (This is a sample skeleton ebuild file)
  - dssp - 20070831 (The protein secondary structure standard)
  - dsv - 1.5 (Discovery Studio Visualizer)
  - epmr - 8.10 (Crystallographic molecular replacement by evolutionary search)
  - espresso - 4.0_pre2 (opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization)
  - gridzilla - 0.5_beta (A GUI-based application designed to create grid screens for protein crystal optimization)
  - imosflm - 1.0.5 (A new GUI for the Mosflm crystallographic data processing tool)
  - kincontour - 1.12.030213 (Read value/coordinate lists to produce contour maps in kinemage format)
  - king - 1.53.060628 (An interactive system for 3D graphics (primarily molecular))
  - mage - 6.44.060606 (Mage is a 3D vector display program which shows 'kinemage' graphics)
  - mole-bin - 1.2 (A toolkit for automated location channels, tunnels and pores in molecular structures)
  - mopac2007-bin - 8.032 (Powerful, fast semi-empirical package)
  - mopro-bin - 1 (Crystallographic structure or charge density refinement)
  - mosflm - 7.0.7 (A program for integrating single crystal diffraction data from area detectors)
  - mustang - 3.2 (MUltiple STructural AligNment AlGorithm.)
  - namd - 2.8 (A powerful and highly parallelized molecular dynamics code)
  - open3dqsar - 1.304 (Pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs))
  - pmb - 20060606 (Automated structure refinement tools for CNS)
  - prekin - 6.42.060120 (Prepares molecular kinemages (input files for Mage and KiNG) from PDB-format coordinate files)
  - profit - 2.5.3.1 (Designed to be the ultimate protein least squares fitting program)
  - pyitc - 1.0.2 (Software for processing isothermal titration calorimetry (ITC) data)
  - pymss - 0.8.4 (Multiple superposition of proteins, using a genetic algorithm for optimization)
  - pyrx - 0.6 (GUI for Virtual Screening with AutoDock)
  - qutemol - 0.4 (High quality molecular visualization system that exploits GPU capabilites through OpenGL shaders)
  - rasmol - 2.7.4.2 (Free program that displays molecular structure.)
  - rdkit - 2010.2.1 (www.rdkit.org/)
  - reduce - 3.14.080821 (Adds hydrogens to a Protein Data Bank (PDB) molecule structure file)
  - refmac - ()
  - shakerr - 0.2.17 (Macromolecular crystal structure precision calculator)
  - solve-resolve-bin - 2.13 (Automated crystallographic structure solution for MIR, SAD, and MAD)
  - theseus - 1.4.3 (Maximum likelihood superpositioning and analysis of macromolecular structures)
  - usf-rave-bin - 0.1 (The tools package from USF for macromolecular crystallography)
  - usf-voidoo-bin - 0.1 (The tools package from USF for macromolecular crystallography)
  - vasco - 1.0.2 (Calculates and visualizes annotated protein surfaces)
  - zodiac - 0.5 (Software for molecular modelling - computer-aided drug design)
- sci-libs
  - ann - 1.1.1 (Data structures and algorithms for both exact and approximate nearest neighbor searching in arbitrarily high dimensions.)
  - bigdft - 1.2.0 (DFT electronic structure code using a wavelet basis set)
  - cctbx - 2005.12.29.2029 (Computational Crystallography Toolbox)
  - etsf_io - 1.0.2 (A library of Fortran90 routines to read/write the ETSF file format)
  - fox - 4.0.3 (A library designed to allow the easy use of XML from Fortran)
  - libxc - 0.9 (A library of exchange-correlation functionals for use in DFT)
  - mmdb - 1.0.10 (The Coordinate Library is designed to assist CCP4 developers in working with coordinate files)
  - mmtk - 2.5.23 (Molecular Modeling ToolKit for Python)
  - pgd-utils - 0.4.2 (Protein Geometry Database library and Python modules)
  - pymc - 2.0 (Markov chain Monte Carlo for Python)
  - pymmlib - 1.2.0 (Toolkit and library for the analysis and manipulation of macromolecular structural models)
  - starparse - 9999 (Library for parsing NMR star files (peak-list format) and CIF files)
  - vcg - 9999 (A portable C++ templated library for manipulation, processing and displaying triangle and tetrahedral meshes with OpenGL)
  - wannier90 - 1.1 (Calculates maximally localized Wannier functions (MLWFs))
- sci-mathematics
  - elefant - 0.4.0 (Efficient learning large-scale inference optimization toolkit (machine learning))
  - mlpy - 3.5.0 (Machine Learning PYthon (mlpy) is a high-performance Python library for predictive modeling)
  - orange - 2010.01.01 (Data visualization and analysis; data mining through visual programming or Python scripting)
  - pybrain - 0.3.1 (A modular machine learning library for Python)
  - pyquante - 1.6.3 (a quantum chemistry package written in Python.)
- sci-physics
  - abinit - 5.7.3 (Find total energy, charge density and electronic structure using density functional theory)
  - ape - 1.0.1 (DFT atomic program and pseudo-potential generator)
  - campos-asap - 2.14 (ASAP is a calculator for campos-ase, implementing the Effective Medium Potential)
  - campos-ase - 3.0.0.657 (The Atomistic Simulation Environment is the core of the CampOS simulation software. There are Python modules for: building atomic structures, molecular dynamics, structure optimization, analysis and much more.)
  - campos-dacapo - 2.7.7 (Dacapo is a plane-wave based Density Functional Theory program)
  - campos-gridpaw - 0.4.2734 (Real-spaced implementation of Density Functional Theory with Projector-Augmented Waves)
  - exciting - 0.9.74 (A full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features)
  - octopus - 3.0.0 (A first principles, electronic structure, excited states, time-dependent density functional theory program)
- sci-visualization
  - gnuplot - 9999 (Command-line driven interactive plotting program)
sys
- sys-apps
  - asmutils - 0.18 (A set of miscellaneous utilities written in assembly language, targeted on embedded systems and small distributions)
  - shadow - 4.0.18.1-r1 (Utilities to deal with user accounts)
- sys-boot
  - grub - 9999 (GNU GRUB 2 boot loader)
- sys-cluster
  - charm - 6.2.1 (Charm++ is a message-passing parallel language and runtime system.)
  - parallel - 20100922 (A shell tool for executing jobs in parallel locally or using remote machines)
- sys-kernel
  - homebrew-sources - 2.6.99 ()
- sys-power
  - powertop - 9999 (tool that helps you find what software is using the most power)
www
- www-apps
  - trac-git - 9999 (Experimental git plugin for Trac)
- www-client
  - netrik - 1.15.7 (A text based web browser with no ssl support.)
- www-plugins
  - mozplugger - 1.14.0 (Streaming media plugin for Mozilla, based on netscape-plugger)
x11
- x11-drivers
  - nvidia-drivers - 280.11 (NVIDIA X11 driver and GLX libraries)
  - xf86-video-intel - 2.15.901 (X.Org driver for Intel cards)
- x11-libs
  - agg - 2.5-r3 (Anti-Grain Geometry - A High Quality Rendering Engine for C++)