07:20 wen 

Geo::WebService::Elevation::USGS executes elevation queries against the
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/

19:26 amdmi3 

qtResistors - calculate resistance of resistor by the colors on the resistor

WWW:    http://qt-apps.org/content/show.php/qtResistors?content=118297

PR:             142554
Submitted by:   zloidemon <g.veniamin@googlemail.com>

12:19 wen 

py-DendroPy is a python library for phylogenetic scripting,
simulation, data processing and manipulation.

WWW:    http://packages.python.org/DendroPy/

05:02 pgj 

This is a collection of Haskell 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.

WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/

PR:             ports/142187
Submitted by:   Jacula Modyun <jacula(at)gmail.com>

02:54 wen 

Harminv is a free program (and accompanying library) to solve the problem
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>

13:44 wen 

PyBrain is a modular Machine Learning Library for Python.
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/

11:10 wen 

libkml is a library for use with applications that want to
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)

11:02 miwi 

mol2ps is a freely available command-line utility program which reads
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>

09:53 miwi 

Checkmol is a command-line utility program which reads molecular
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>

20:02 miwi 

libquantum is a C library for the simulation of quantum
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>

05:14 maho 

Remove science/dft++. Not actively maintained the original site. Old
style coding with lots of warnings, and build error with gcc44.

Also suggested by: gerald@

14:07 lwhsu 

Add py-h5py 1.2.0, a general-purpose Python interface to the HDF5
library.

PR:             ports/136096
Submitted by:   TAOKA Fumiyoshi

15:55 amdmi3 

peekabot is a distributed real-time 3D visualization tool for robotics
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>

20:02 erwin 

Remove science/openfoam as it has been marked BROKEN for over 5 months.

20:00 erwin 

Remove science/elmerfront as it has been marked BROKEN over 3 months ago.

22:16 amdmi3 

Avogadro is an advanced molecular editor designed for cross-platform use in
computational chemistry, molecular modeling, bioinformatics, materials science,
and related areas. It offers flexible rendering and a powerful plugin
architecture.

WWW: http://avogadro.openmolecules.net/

PR:             134710
Submitted by:   Troels Kofoed Jacobsen <tkjacobsen@gmail.com>

13:00 miwi 

Chemistry-MacroMol is a toolkit includes basic objects and methods to
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>

12:51 miwi 

p5-Chemistry-File-PDB reads and writes PDB files. The PDB file format
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>

23:29 miwi 

Chemistr-Mol is a toolkit includes basic objects and methods to
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>

17:02 miwi 

Machine Learning PY (mlpy) is a high-performance Python package for
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>

09:58 miwi 

2009-03-22 science/oof: Broken with GCC 4.2 and beyond
2009-04-06 www/raqdevil: Master site gone, distfiles not fetchable

22:09 pav 

- Fix Fortran linking
- Add a slaveport so fortran enabled netcdf can be packaged

PR:             ports/132430
Submitted by:   thierry
Approved by:    maintainer timeout (14 days)

15:18 miwi 

Geo::ReadGRIB is an object Perl module that provides read
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>

06:07 miwi 

Brian is a simulator for spiking neural networks available on almost all
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>

19:58 miwi 

PsychoPy is an open-source package for creating psychology stimuli
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

20:18 miwi 

netCDF version 4 has many features not found in earlier versions of the
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

00:09 miwi 

pydicom is a pure python package for working with DICOM files. It was
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>

18:17 pav 

- Remove science/gchempaint, it has been integrated into science/gchemutils

12:20 chinsan 

- Attach science/netcdf4

05:35 miwi 

- Connect hdf5-18

18:52 miwi 

Modular toolkit for Data Processing (MDP) is a Python data processing
framework. Implemented algorithms include: Principal Component
Analysis (PCA), Independent Component Analysis (ICA), Slow Feature
Analysis (SFA), Independent Slow Feature Analysis (ISFA), Growing Neural
Gas (GNG), Factor Analysis, Fisher Discriminant Analysis (FDA), Gaussian
Classifiers, and Restricted Boltzmann Machines.

WWW: http://mdp-toolkit.sourceforge.net/

PR:             ports/127338
Submitted by:   Li-Lun Wang <llwang at infor.org>

23:21 miwi 

py-hcluster library provides Python functions for
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>

22:35 maho 

liboglappth is a support library packages for science/ghemical
This is for the OpenGL stuff.
See also:
http://www.bioinformatics.org/pipermail/ghemical-devel/2007-September/000688.html

WWW: http://www.uku.fi/~thassine/projects/ghemical/

21:19 beech 

- New port silo-4.6.1

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>

14:00 miwi 

This port installs python bindings for openbabel.

WWW:    http://openbabel.sourceforge.net

PR:             ports/125768
Submitted by:   Max Brazhnikov <makc at issp.ac.ru>

09:41 miwi 

Pycdf is a python interface to the Unidata netCDF library. It provides an
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

06:51 edwin 

[NEW PORT] graphics/2d-rewriter: Fractals generator based on pattern matching
and rewriting

        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>

23:04 miwi 

Jmol is a Java molecular viewer for
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>

21:04 hq 

Colt is a package for scalable scientific and technical computing in Java. It
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>

12:56 tabthorpe 

DTI visualization software from Stanford.

WWW: http://graphics.stanford.edu/projects/dti/

PR:             ports/120129
Submitted by:   Jason W. Bacon <jwbacon at tds.net>

13:29 itetcu 

Move speedcrunch from science to math.
No repo is requiered since there's no history to preserve.

Requsted by:    danfe@

11:40 itetcu 

SpeedCrunch is a multiplatform desktop calculator for power users.
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>

07:10 rafan 

- science/liblr is moved to science/liblinear (project renamed)

21:04 thierry 

Code_Saturne is EDF's general purpose computational fluid dynamics
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/>

14:05 rafan 

Add liblr-1.0, a library for large regularized logistic regression.

22:18 pav 

The chemical-mime-data package is a collection of data files to add support for
various chemical MIME types on Linux/UNIX desktops, such as KDE and GNOME.

WWW: http://chemical-mime.sourceforge.net/

22:16 pav 

The Blue Obelisk Data Repository lists many important chemoinformatics data
such as element and isotope properties, atomic radii, etc. including references
to original literature. Developers can use this repository to make their
software interoperable.

WWW: http://wiki.cubic.uni-koeln.de/bowiki/index.php/DataRepository

13:44 miwi 

Parallel-NetCDF is a library providing high-performance I/O while still
maintaining file-format compatibility with Unidata's NetCDF. NetCDF gives
scientific programmers a space-efficient and portable means for storing data.
However, it does so in a serial manner, making it difficult to achieve high
I/O performance. By making some small changes to the API specified by NetCDF,
we can use MPI-IO and its collective operations.

WWW: http://trac.mcs.anl.gov/projects/parallel-netcdf

PR:             ports/112265
Submitted by:   Chao Shin <quakelee at cn.FreeBSD.org>

10:58 miwi 

NIfTI-1 is a new Analyze-style data format, proposed by the NIfTI DFWG
as a short-term measure to facilitate inter-operation of functional MRI
data analysis software packages.

WWW:    http://nifti.nimh.nih.gov/

PR:             ports/112183
Submitted by:   Jason W. Bacon

17:40 miwi 

2007-03-27 emulators/kmamerun: Project was abandoned 4 years ago and expects an
old version of XMAME, please use other frontends instead (like gxmame)
2007-03-28 graphics/hobbes-icons-xpm: Archaic port
2007-04-10 japanese/firefox-ja: Incomplete pkg-plist
2007-04-10 japanese/lookup-xemacs: Does not install
2007-04-10 lang/linux-hla: Does not compile
2007-04-10 mail/vmailmgr: Incomplete pkg-plist
2007-04-10 multimedia/qvamps: Touches filesystem prior to 'make install'
2007-03-10 net-mgmt/sting: Broken on all supported versions of FreeBSD
2007-04-10 net-mgmt/tas: Incomplete pkg-plist
2007-04-10 net-p2p/verlihub-plugins: Does not configure, it needs at least
verlihub 1.0
2007-04-10 news/inn-stable: Fails to patch
2007-04-10 palm/malsync: Does not build with new pilot-link
2007-04-10 russian/elm.language: Leaves behind files on deinstall
2007-04-10 russian/pine.language: Leaves behind config file on deinstall
2007-04-01 science/py-scipy03: Replaced by py-scipy
2007-04-10 security/php4-cryptopp: Does not compile

09:00 thierry 

The CFD General Notation System (CGNS) provides a standard for recording and
recovering computer data associated with the numerical solution of the equations
of fluid dynamics.

00:39 maho 

GAMESS is freely available ab-initio molecular orbital
calculation program calculates energy, molecular structure,
vibrational frequencies from the basic principle of quantum mechanics.

A site license for GAMESS is available at no cost to both academic
and industrial users. Please refer
http://wwwmsg.fi.ameslab.gov/GAMESS/dist.menu.html
for details.

We also included simple launcher called `gamess'
for your convenience. You don't set any environment variable
to run gamess. Just type
% gamess <somefile.inp>
is enough.

WWW: http://wwwmsg.fi.ameslab.gov/GAMESS/

I also recived an e-mail from Mike Schmidt <mike@si.fi.ameslab.gov>
as my inquery.

> I'm maintaining gamess port for FreeBSD only for myself,
> but I'd like to maintain this program at ports tree so that
> everyone can install gamess for FreeBSD very easily like following:
> obtain gamess-current.tar.gz then, put it to some directory, then:
>
> % mkdir /usr/ports/distfiles/gamess.20060907.4
> % cp gamess-current.tar.gz /usr/ports/distfiles/gamess.20060907.4/
> % cd /usr/ports/science/gamess
> % make
> % sudo make install
> ...
> will finish the compilation and installation.
>
> So I'd like to ask you about it.
>
> Can I put port such a skeleton, which is merely an installation
> instruction for FreeBSD ports tree like MPQC?
> http://www.freebsd.org/cgi/cvsweb.cgi/ports/science/mpqc/
> Everyone can access this instruction publically.
> Of course, I don't expose gamess archive for public, and if gamess =20
> archive
> is not found, make stops like:
>
>> % make
>> =3D=3D=3D>  gamess-20060907.4 You must manually get the source =20
>> distribution from master site. http://www.msg.ameslab.gov/GAMESS/=20
>> dist.menu.html. Please selsect "Source code distribution", and =20
>> check on "running on Intel compatible PC running Linux". You must =20
>> have license, but freely obtainable..
>> *** Error code 1
>

Mike Schmidt <mike@si.fi.ameslab.gov> replied as:
> I do not really object to your idea about "make" for BSD, since
> you don't include source code with it.  but don't really understand
> why it would be necessary.
:)

18:42 miwi 

2007-01-01 graphics/teddy: No new releases in the past 4 years
2007-01-01 net/arla: "does not compile"
2007-01-02 sysutils/lsmlib: distfile and homepage disappeared
2007-01-02 security/ifd-gpr400: distfile and homepage disappeared
2007-01-04 science/mmtk: distfile and homepage disappeared
2007-01-04 print/xtem: distfile and homepage disappeared
2007-01-04 net/mrt: distfile and homepage disappeared

07:41 maho 

Libint is a library for evaluating ERI (electron replusion integral)
over Cartesian Gaussian fuctions for modern atomic and molecular theory;
esp. for science/mpqc and science/psi3.

03:38 ijliao 

add linsmith 0.99.3
Smith charting program

05:54 rafan 

- Reflect repocopy ofscience/py-scipy -> science/py-scipy03

08:59 clsung 

Add g3data 1.5.0, utility for extracting data from graphs.

PR:             ports/103397
Submitted by:   trasz <trasz at pin.if.uz.zgora.pl>

19:17 dinoex 

Paje is a graphical tool that displays traces produced during the
execution of multithreaded programs. Other programs can also generate
traces for this tool.
PR:             103677
Submitted by:   Gürkan Sengün

19:59 dinoex 

GTAMS Analyzer is a complete coding and analysis package. It is a "port" of
TAMS Analyzer for Macintosh OS X. Note, at some point the two projects will
have identical file formats, at which point  the initial G (for GNUstep)
will be dropped. GTAMS stands for GNUstep Text Analysis Markup System, it
is a convention for identifying themes in text. The software offers a wide
range of tools for applying themes to texts and identifying patterns of
themes within and between texts.
PR:             103680
Submitted by:   Gürkan Sengün

23:09 thierry 

Medit is an interactive mesh visualization software, developed by the Gamma
project at INRIA-Rocquencourt.

It is intended to display computation results (in mechanics of the solids or
fluids, thermics, electromagnetism, etc.) on grids 2d (triangles and
quadrangles), 3d (tetrahedrons or hexahedrons) or surfaces (triangles and
quandrangles).

01:24 alepulver 

ITK is an open-source software toolkit for performing registration and
segmentation. Segmentation is the process of identifying and classifying
data found in a digitally sampled representation. Typically the sampled
representation is an image acquired from such medical instrumentation as
CT or MRI scanners. Registration is the task of aligning or developing
correspondences between data. For example, in the medical environment,
a CT scan may be aligned with a MRI scan in order to combine the
information contained in both.

WWW: http://www.itk.org

Port maintainer: Jason W. Bacon
                 bacon@smithers.neuro.mcw.edu

PR:             ports/95166
Submitted by:   bacon at smithers.neuro.mcw.edu

22:34 pav 

Gwyddion is a modular SPM (Scanning Probe Microsopy) data visualization and
analysis tool written with Gtk+.

It can be used for all most frequently used data processing operations
including: leveling, false color plotting, shading, filtering, denoising, data
editing, integral transforms, grain analysis, profile extraction, fractal
analysis, and many more.  The program is primarily focused on SPM data analysis
(e.g. data obtained from AFM, STM, NSOM, and similar microscopes).  However, it
can also be used for analysis of SEM (Scanning Electron Microscopy) data or any
other 2D data.

WWW: http://gwyddion.net/

PR:             ports/101773
Submitted by:   David Necas <yeti@gwyddion.net>

07:29 clsung 

Add p5-Algorithm-SVMLight 0.05, perl interface to SVMLight
Machine-Learning Package.

PR:             ports/101297
Submitted by:   Gea-Suan Lin <gslin at gslin.org>

15:07 clsung 

Add svmlight 6.01, an implementation of Support Vector Machines (SVMs)
in C.

PR:             ports/100944
Submitted by:   Gea-Suan Lin <gslin at gslin.org>

03:38 clsung 

Add crf++ 0.42, yet Another CRF toolkit.

PR:             ports/100909
Submitted by:   Cheng-Lung Sung <clsung at FreeBSD.org>

03:36 clsung 

Add ghmm 0.7.0a, general Hidden Markov Model Library in C.

PR:             ports/100886
Submitted by:   Cheng-Lung Sung <clsung at FreeBSD.org>

03:34 clsung 

Add pcp 2.2, machine learning program for pattern classification.

PR:             ports/100798
Submitted by:   Cheng-Lung Sung <clsung at FreeBSD.org>

19:58 rafan 

Add xmds , XMDS is a code generator that integrates equations;.

PR:             ports/100419
Submitted by:   EelVex

07:30 maho 

Libghemical port. This port installs support libraries of
science/ghemical port. From version 2.0, science/ghemical becomes
large, splitted into two parts. Update of ghemical port will
follow soon.

18:58 itetcu 

Objecto Oriented Finite Element Analysis of Real Material Microstructures
__________________

OOF is designed to help materials scientists calculate macroscopic
properties from images of real or simulated microstructures. It is
composed of two cooperating parts: ppm2oof and oof. ppm2oof reads images
in the ppm (Portable Pixel Map) format and assigns material properties to
features in the image. oof conducts virtual experiments on the data
structures created by ppm2oof to determine the macroscopic properties of
the microstructure. Currently, the programs calculate stresses and
strains, but someday we hope to include thermal, electric, and magnetic
field calculations.

Check the Homepage for online manuals and new versions

WWW:     http://www.ctcms.nist.gov/oof/

PR:             ports/98601
Submitted by:   Pedro F. Giffuni

08:41 pav 

CDO is a collection of command line Operators to manipulate and analyse Climate
model Data. Supported file formats are GRIB, netCDF, SERVICE, EXTRA and IEG.
There are more than 250 operators available. The following table gives a short
overview about the main categories.

* File information (info, sinfo, diff, ...)
* File operations (copy, cat, merge, split*, ...)
* Selection (selcode, selvar, sellevel, seltimestep, ...)
* Missing values (setctomiss, setmisstoc, setrtomiss)
* Arithmetic (add, sub, mul, div, ...)
* Mathematical functions (sqrt, exp, log, sin, cos, ...)
* Comparision (eq, ne, le, lt, ge, gt, ...)
* Conditions (ifthen, ifnotthen, ifthenc, ifnotthenc)
* Field statistic (fldsum, fldavg, fldstd, fldmin, fldmax, ...)
* Vertical statistic (vertsum, vertavg, vertstd, vertmin, ...)
* Time range statistic (timavg, yearavg, monavg, dayavg, ...)
* Ensemble statistic (enssum, ensavg, ensstd, ensmin, ...)
* Regression (detrend)
* Field interpolation (remapbil, remapcon, remapdis, ...)
* Vertical interpolation (ml2pl, ml2hl)
* Time interpolation (inttime, intyear)

WWW: http://www.mpimet.mpg.de/fileadmin/software/cdo/

PR:             ports/98099
Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet@sunpoet.net>

12:05 thierry 

Add science/minc2.

MINC (Medical Imaging NetCDF) is a medical imaging data format and an
associated set of tools and libraries. MINC was created in 1993 by Peter
Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
Institute. Many others have contributed to the design and implementation
MINC over the years.

PR:             ports/93495
Submitted by:   Jason Bacon <bacon (at) smithers.neuro.mcw.edu>
Repocopied by:  marcus

19:55 thierry 

ElmerPost - the Visualization of Numerical Results.

The function of ElmerPost is to visualize the numerical results produced
by ElmerSolver and other finite element programs. ElmerPost operates with
the data specific to the unknown variables (temperature, velocity,
pressure, displacement etc.) defined in the mathematical model. ElmerPost
plots e.g. contours and vector fields, and can manipulate computed data
into another form using the built-in MATC-language (for instance heat
fluxes from temperature distributions).

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:54 thierry 

ElmerFront - the Graphical User Interface.

ElmerFront is a tool for initializing the computational process in Elmer.
It communicates with external software producing geometrical data, i.e.,
CAD files and computational meshes. ElmerFront generates its own finite
element meshes, allows the user to build mathematical models graphically,
and finally produces input data for ElmerSolver.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:54 thierry 

ElmerSolver - the Solution of Partial Differential Equations.

ElmerSolver is thus an independent module that processes the computational
mesh and the model input file containing references to the selected
equations and model parameters. ElmerSolver makes the equations into a
discrete form, handles coupled systems, non-linearities and
time-dependences, and provides output data for visualization.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:53 thierry 

HUTIter library for use in the Elmer FEM package.

Elmer is an open-source computational tool for multi-physics problems.

Elmer includes physical models of fluid dynamics, structural mechanics,
electromagnetics and heat transfer. These are described by partial
differential equations which Elmer solves by the Finite Element Method (FEM).

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:50 thierry 

MATC language library used by Elmer FEM package.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:49 thierry 

Input/Output Data base interface for use in the ELMER FEM package.

Elmer is an open-source computational tool for multi-physics problems.

Elmer includes physical models of fluid dynamics, structural mechanics,
electromagnetics and heat transfer. These are described by partial
differential equations which Elmer solves by the Finite Element Method (FEM)

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:48 thierry 

ElmerGrid is a utility program for fast creation of structured 2D and
extruded and rotated 3D geometries. ElmerGrid is independent but fully
supports ElmerSolver and ElmerPost. It may be used to create linear,
quadratic and cubic triangles and rectangles. It has also versatile
capabilities in mesh manipulation.

ElmerGrid may also be used in grid manipulation. ElmerGrid may, for
example, be used to transfer different mesh formats to that understood by
ElmerSolver or ElmerPost. ElmerGrid also includes mesh partitioning
routines that have been optimized for ElmerSolver. The partitioning may be
done by METIS or by a simple geometric division.

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

19:46 thierry 

A Mesh Generation Utility for use with the ELMER FEM package.

Elmer is an open-source computational tool for multi-physics problems.

Elmer includes physical models of fluid dynamics, structural mechanics,
electromagnetics and heat transfer. These are described by partial
differential equations which Elmer solves by the Finite Element Method (FEM)

Submitted by:   Pedro F. Giffuni <giffunip@asme.org>

20:51 thierry 

A program for doing calculation on Smith Chart, similar in functionality to
xsmc but with a simpler user interface; written with GNU/GTK library and
released under GNU/GPL. Written by Lapo Pieri IK5NAX

WWW: http://www.qsl.net/ik5nax

PR:             ports/93224
Submitted by:   Diane Bruce <db (at) db.net> - VA3DB

10:38 garga 

Add fasthenry , a multipole-accelerated inductance analysis program.

PR:             ports/93969
Submitted by:   Pedro Giffuni <giffunip@asme.org>

10:36 garga 

Add fastcap , a three-dimensional capacitance extraction program.

PR:             ports/93968
Submitted by:   Pedro Giffuni <giffunip@asme.org>

15:30 thierry 

MINC (Medical Imaging NetCDF) is a medical imaging data format and an
associated set of tools and libraries. MINC was created in 1993 by Peter
Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
Institute. Many others have contributed to the design and implementation
MINC over the years.

PR:             ports/91918
Submitted by:   Jason W. Bacon <bacon (at) smithers.neuro.mcw.edu>

11:55 vd 

Remove expired port science/glens

Approved by:    garga (mentor)

22:19 thierry 

Repocopy math/netcdf to science/netcdf, along with cdf, hdf and hdf5.

PR:             92497
Submitted by:   /me
Repocopied by:  marcus

20:40 thierry 

Common Data Format (CDF) is a conceptual data abstraction for storing
multi-dimensional data sets. The basic component of CDF is a software
programming interface that is a device independent view of the CDF data
model. The application developer is insulated from the actual physical
file format for reasons of conceptual simplicity, device independence,
and future expandability. CDF files created on any given platform can
be transported to any other platform on to which CDF is ported and used
with any CDF tools or layered applications.

A comparison between CDF, netCDF, HDF and HDF5 is available at
<http://cdf.gsfc.nasa.gov/html/FAQ.html>.

17:34 vd 

Add new port science/afni

AFNI (Advanced Functional Neuro Imaging) is a tool for analyzing
3 dimensional images, especially functional MRI images used in
brain mapping research.

WWW: http://afni.nimh.nih.gov/

PR:             ports/90752
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu>
Reviewed by:    garga (mentor)
Approved by:    garga (mentor)

10:13 thierry 

The OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate
anything from complex fluid flows involving chemical reactions, turbulence and
heat transfer, to solid dynamics, electromagnetics and the pricing of financial
options.

WWW: http://www.opencfd.co.uk/openfoam/index.html

PR:             ports/91886
Submitted by:   thierry

21:45 thierry 

Add V_Sim, a program to visualize atomic structures such as crystals, grain
boundaries and so on.

18:48 thierry 

GDL - GNU Data Language - is a free IDL (Interactive Data Language)
compatible incremental compiler (i.e.  runs IDL programs).

IDL is a registered trademark of Research Systems Inc.
(see: <http://www.rsinc.com/>)

Remark: slave port for Python module intentionnally not yet committed.

WWW: http://gnudatalanguage.sourceforge.net/

12:45 thierry 

Add gerris 0.6.0, a scientific CFD simulator.

Gerris is an Open Source Free Software library for the solution of partial
differential equations describing fluid flow. Gerris is supported by NIWA
(National Institute of Water and Atmospheric research) and by the
Marsden Fund of the Royal Society of New Zealand. The code is written
entirely in C and uses both the GLib Library and the GTS Library for
geometrical functions and object-oriented programming.

PR:             86297
Submitted by:   Oliver Dunkl <odunkl (at) gmx.net>

16:22 pav 

PAIDA is pure Python scientific analysis package and implements AIDA (Abstract
Interfaces for Data Analysis).

PR:             ports/83599
Submitted by:   Vsevolod Stakhov <vsevolod@highsecure.ru>

05:41 anholt 

New port: ParaView is a powerful scientific visualization application, designed
with the need to visualize large data sets in mind.

15:50 pav 

New port for mbdyn, which is a MultiBody Dynamics simulation software. It comes
with lots of libraries etc.  There are two knobs which are in development at
the moment so I disabled them with an IGNORE message.  They need some work and
maybe some testing.

PR:             ports/81136
Submitted by:   Kay Lehmann <kay_lehmann@web.de>

21:44 thierry 

Add lamprop 1.3.1.

Lamprop takes in input file describing the lay-up and constituent materials
of a fiber-reinforced composite laminate, and calculates some mechanical
and other properties. The submitter is the original author of the software,
and will maintain the port.

PR:             81066
Submitted by:   Roland Smith <rsmith (at) xs4all.nl>

03:20 kris 

Remove mxp

Forgotten by:   maho
Approved by:    portmgr (self)

10:54 maho 

Add mxp (Mandelbrot explorer). Mxp is an X application for computing and
exploring
Mandelbrot sets.  Features of mxp include:
        - zoom and un-zoom
        - dynamic resizing of drawing window
        - setup save/load
        - asynchronous image generation (buttons always work)
        - GIF output
        - animation
        - nine color schemes
        - color rotation
        - color change options
        - detailed statistics

WWW:  http://www.ibiblio.org/pub/Linux/apps/math/fractals/

19:30 glewis 

. Add a port of the Szip scientific compression library, used by current
  versions of HDF:

  "Szip is an implementation of the extended-Rice lossless compression
   algorithm.

   WWW: http://hdf.ncsa.uiuc.edu/doc_resource/SZIP/"

20:26 sem 

DCL is scientific graphic library for geoscience, written in Fortran.

PR:             ports/76856
Submitted by:   Shin'ya Murakami <murakami (at) ahs.scitec.kobe-u.ac.jp>