files, a Java package providing an object-oriented interface to HDF data
objects, and Java Native Interfaces to the standard HDF libraries.
WWW: http://www.hdfgroup.org/hdf-java-html/index.html
PR: ports/143859
Submitted by: rfarmer at predatorlabs.net
software package developed at MIT to model electromagnetic systems,
along with our MPB eigenmode package.
WWW: http://ab-initio.mit.edu/wiki/index.php/Meep
PR: ports/142158
Submitted by: Stas Timokhin <devel@stasyan.com>
Approved by: portmgr (miwi)
audio/ccaudio||2010-01-18|Has expired: has been broken for 4 months
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United States Geological Survey's web server. You provide the latitude
and longitude in degrees, with south latitude and west longitude being
negative. The return is typically a hash containing the data you want.
Query errors are exceptions by default, though the object can be configured
to signal an error by an undef response, with the error retrievable from
the 'error' attribute.
WWW: http://search.cpan.org/dist/Geo-WebService-Elevation-USGS/
building bioinformatics-related tools and utilities.
Current list of features includes: a Sequence data type supporting
protein and nucleotide sequences and conversion between them.
WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
PR: ports/142187
Submitted by: Jacula Modyun <jacula(at)gmail.com>
of harmonic inversion - given a discrete-time, finite-length signal
that consists of a sum of finitely-many sinusoids (possibly exponentially
decaying) in a given bandwidth, it determines the frequencies, decay
constants, amplitudes, and phases of those sinusoids.
WWW: http://ab-initio.mit.edu/wiki/index.php/Harminv
PR: ports/142154
Submitted by: Stas Timokhin <devel@stasyan.com>
It's goal is to offer flexible, easy-to-use yet still powerful
algorithms for Machine Learning Tasks and a variety of
predefined environments to test and compare your algorithms.
PyBrain is short for Python-Based Reinforcement Learning,
Artificial Intelligence and Neural Network Library. In fact,
we came up with the name first and later reverse-engineerer
this quite descriptive "Backronym".
WWW: http://pybrain.org/
parse, generate and operate on KML. It is an implementation
of the OGC KML 2.2 standard.
WWW: http://code.google.com/p/libkml/
Approved by: miwi(mentor)
molecular structure files in different formats and generates
Postscript output for 2D display. The Postscript file can then be used
e.g. for creating a bitmap file, using a Postscript interpreter like
Ghostscript.
WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html
PR: ports/138673
Feature safe: yes
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar>
structure files in different formats and analyzes the input
molecule for the presence of various functional groups and structural
elements. At present, approx. 200 different functional groups are
recognized. This output can be easily placed into a database table,
permitting the creation of chemical databases with a functional group
search option. Checkmol also outputs a set of statistical values derived
from a given molecule, which can also be used for quick retrieval from a
database. These values include: the number of atoms, bonds, and rings,
the number of differently hybridized carbon, oxgen, and nitrogen atoms,
the number of C=O double bonds, the number of rings of different sizes,
the number of rings containing nitrogen, oxygen, sulfur, the number of
aromatic rings, the number of heterocyclic rings, etc. The combination
of all of these values for a given molecule represents some kind of
"fingerprint" which is useful for rapid pre-selection in a database
structure/substructure search prior to a full atom-by-atom match.
WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html
PR: ports/138670
Feature safe:yes
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar>
mechanics, with a special focus laid to quantum computing.
It started as a pure quantum computer simulator, but
support for general quantum simulation has been recently
added.
WWW: http://www.libquantum.de/
PR: ports/137468
Submitted by: Wen Heping <wenheping at gmail.com>
researchers and developers, written in C++.
Its purpose is to simplify the visualization needs faced by a roboticist
daily - using visualization as a debugging aid or making fancy slides for
a presentation, for example.
Chris Petrik (chris@officialunix.com)
WWW: http://www.peekabot.org
PR: 135892
Submitted by: Chris Petrik <c.petrik.sosa@gmail.com>
describe macromolecules, a macromolecule is just a molecule that
consists of several "domains". For example, a protein consists
of aminoacid residues, or a nucleic acid consists of bases. Therefore
Chemistry::MacroMol is derived from Chemistry::Mol, with additional
methods to handle the domains.
WWW: http://search.cpan.org/dist/Chemistry-MacroMol/
PR: ports/134609
Submitted by: Wen Heping <wenheping at gmail.com>
is commonly used to describe proteins, particularly those stored in the
Protein Data Bank.
WWW: http://search.cpan.org/dist/Chemistry-File-PDB/
PR: ports/134612
Submitted by: Wen Heping <wenheping at gmail.com>
describe molecules. It consists of several modules: Chemistry::Mol,
Chemistry::Atom, Chemistry::Bond, and Chemistry::File.
WWW: http://search.cpan.org/dist/Chemistry-Mol/
PR: ports/134462
Submitted by: Wen Heping <wenheping at gmail.com>
predictive modeling. It makes extensive use of numpy (http://scipy.org)
to provide fast N-dimensional array manipulation and easy integration of
C code. mlpy provides high level procedures that support, with few lines
of code, the design of rich Data Analysis Protocols (DAPs) for
preprocessing, clustering, predictive classification and feature
selection. Methods are available for feature weighting and ranking, data
resampling, error evaluation and experiment landscaping.The package
includes tools to measure stability in sets of ranked feature lists.
WWW: http://mlpy.fbk.eu/
PR: ports/133932
Submitted by: Wen Heping <wenheping at gmail.com>
access to data distributed in GRIB files. Specifically,
it is wrote to access NOAA Wavewatch III marine weather
model forecasts which are packaged as GRIB.
WWW: http://search.cpan.org/dist/Geo-ReadGRIB/
PR: ports/132776
Submitted by: Wen Heping <wenheping at gmail.com>
platforms. The motivation for this project is that a simulator should
not only save the time of processors, but also the time of scientists.
Brian is easy to learn and use, highly flexible and easily extensible.
The Brian package itself and simulations using it are all written in
the Python programming language, which is an easy, concise and highly
developed language with many advanced features and development tools,
excellent documentation and a large community of users providing support
and extension packages.
WWW: http://www.briansimulator.org/
PR: ports/132155
Submitted by: Wen Heping <wenheping@gmail.com>
in Python (A real and free alternative to Matlab). PsychoPy combines
the graphical strengths of OpenGL with the easy Python syntax to give
psychophysics a free and simple stimulus presentation and control
package.
The goal is to provide, for the busy scientist (including me!), tools
to control timing and windowing and a simple set of pre-packaged
stimuli and methods. The code is platform independent, using Python
and C libraries that are widely available.
WWW: http://www.psychopy.org/
PR: ports/132156
Submitted by: wenheping at gmail.com
library and is implemented on top of HDF5. This module can read and
write files in both the new netCDF 4 and the old netCDF 3 format, and
can create files that are readable by HDF5 clients. The API modelled
after Scientific.IO.NetCDF, and should be familiar to users of that
module.
Many new features of netCDF 4 are implemented, such as multiple
unlimited dimensions, groups and zlib data compression. All the new
primitive data types (such as 64 bit and unsigned integer types) are
implemented, except variable-length strings (NC_STRING). User defined
data types (compound, vlen, enum etc.) are not supported.
WWW: http://code.google.com/p/netcdf4-python/
PR: ports/131866
Submitted by: wenheping at gmail.com
made for inspecting and modifying DICOM files in an easy "pythonic"
way. The modifications can be written again to a new file. As a pure
python package, it should run anywhere python runs without any other
requirements.
WWW: http://code.google.com/p/pydicom/
PR: ports/130492
Submitted by: Wen Heping <wenheping at gmail.com>
agglomerative clustering. Its features include
* generating hierarchical clusters from distance matrices
* computing distance matrices from observation vectors
* computing statistics on clusters
* cutting linkages to generate flat clusters
* and visualizing clusters with dendrograms.
The interface is very similar to MATLAB's Statistics
Toolbox API to make code easier to port from MATLAB to
Python/Numpy. The core implementation of this library
is in C for efficiency.
WWW: http://code.google.com/p/scipy-cluster/
PR: ports/127515
Submitted by: Wen Heping <wenheping at gmail.com>
A mesh and field I/O library and scientific database
Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files. The files Silo produces and the data within
them can be easily shared and exchanged between wholly independently
developed applications running on disparate computing platforms.
Consequently, Silo facilitates the development of general purpose tools
for processing scientific data. One of the more popular tools that process
Silo data files is the VisIt visualization tool.
Silo supports gridless (point) meshes, structured meshes, unstructured-zoo
and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes,
constructive solid geometry (CSG) meshes, piecewise-constant (e.g.
zone-centered) and piecewise-linear (e.g. node-centered) variables defined
on the node, edge, face or volume elements of meshes as well as the
decomposition of meshes into arbitrary subset hierarchies including
materials and mixing materials. In addition, Silo supports a wide variety
of other useful objects to address various scientific computing
application needs.Although the Silo library is a serial library, it has
some key features which enable it to be applied quite effectively and
scalably in parallel.
PR: ports/125725
Submitted by: Pedro F. Giffuni <giffunip at tutopia.com>
almost complete coverage of the netCDF C API, wrapping it inside easy to
use python classes.
WWW: http://pysclint.sourceforge.net/pycdf/
PR: ports/123303
Submitted by: wenheping at gmail.com
2d-rewriter is fractals generator based on pattern matching
and rewriting. The program takes input containing initial
object placement and rewriting rules and keeps applying
rules to the data field until it reaches an arrangement
where no rules can be applied.
PR: ports/118906
Submitted by: Igor Serikov <bt@turtle.freedns.us>
three-dimensional chemical structures.
Features include reading a variety
of file types and output from quantum
chemistry programs, and animation of
multi-frame files and computed normal
modes from quantum programs.
WWW: http://sourceforge.net/projects/jmol/
PR: ports/123631
Submitted by: Wen heping <wenheping at gmail.com>
consists of several free Java libraries, for user convenience bundled under one
single uniform umbrella. Namely the Colt library, the Jet library, the CoreJava
library, and the Concurrent library.
The Colt library provides fundamental general-purpose data structures optimized
for numerical data, such as resizable arrays, dense and sparse matrices
(multi-dimensional arrays), linear algebra, associative containers and buffer
management.
WWW: http://dsd.lbl.gov/~hoschek/colt/
PR: 122913
Submitted by: Wen heping <wenheping@gmail.com>
It is designed to be enjoyed using keyboard. Result is shown in
scrollable display, history of expressions is available with up
and down arrow.
Some other features:
optional keypad, syntax highlight, matched parenthesis indicator,
just-in-time calculation (show result even before you finish typing)
and autocomplete for variables.
WWW: http://speedcrunch.digitalfanatics.org/
PR: ports/114969
Submitted by: Yinghong.Liu <relaxbsd at gmail.com>
software. Developed since 1997 at EDF R&D, it is based on a co-located
Finite Volume approach that accepts meshes with any type of
cell (tetrahedral, hexahedral, prismatic, pyramidal, polyhedral, ...)
and any type of grid structure (unstructured, blockstructured, hybrid,
conforming or with hanging nodes, ...).
Its basic capabilities enable the handling of either incompressible or
expandable flows with or without heat transfer and turbulence (mixing
length, 2-equation models, v2f, Reynolds stress models, Large Eddy
Simulations, ...).
<http://rd.edf.com/code_saturne/>
