10:57 wen 

R-cran-AMORE was born to release the TAO robust neural network algorithm
to the R users. It has grown and I think it can be of interest for
the users wanting to implement their own training algorithms as well as
for those others whose needs lye only in the "user space".

WWW: http://rwiki.sciviews.org/doku.php?id=packages:cran:amore

03:54 wen 

The SciMath project includes packages to support scientific and
mathematical calculations, beyond the capabilities offered by SciPy.
    * enthought.interpolate
    * enthought.mathematics
    * enthought.units

WWW: http://pypi.python.org/pypi/SciMath/

PR:             ports/154351
Submitted by:   Wen Heping (myself)

02:39 wen 

Veusz is a GUI scientific plotting and graphing package. It
is designed to produce publication-ready Postscript or PDF
output. SVG, EMF and bitmap formats export are also supported.
The program runs under Unix/Linux, Windows or Mac OS X, and
binaries are provided. Data can be read from text, CSV or FITS
files, and data can be manipulated or examined from within the
application.

WWW: http://home.gna.org/veusz/

PR:             ports/153686
Submitted by:   Stas Timokhin <devel@stasyan.com>

08:50 wen 

Geo::Coordinates::Converter is a simple converter of geo coordinates, the
format and datum of geo coordinates are simply converted. when it is
insufficient in the coordinate system and the format of the standard, it
is possible to add it easily.

WWW:    http://search.cpan.org/dist/Geo-Coordinates-Converter/

21:41 makc 

Connect py-biolccc

00:26 sahil 

Objects of class Physics::Unit define units of measurement that correspond
to physical quantities.  This module allows you to manipulate these units,
generate new derived units from other units, and convert from one unit
to another.

WWW: http://search.cpan.org/dist/Physics-Unit/

PR:             ports/150245
Submitted by:   Frederic Culot <frederic@culot.org>

03:09 sahil 

epte is a curses-based periodic table of the elements. It provides a
set of examples of the basic sets of constants and procedures needed
to understand the behavior of matter.

WWW: http://www.toddmiller.com/epte/

PR:             ports/150183
Submitted by:   Frederic Culot <frederic@culot.org>

18:15 makc 

Connect kst2

09:53 ashish 

- Remove the port from 'science' category.

PR:             ports/146513
Approved by:    pgj (mentor)

03:27 ashish 

QElectroTech is a Qt4 application to design electric diagrams. It uses XML
files for elements and diagrams, and includes both a diagram editor and an
element editor.

WWW:    http://qelectrotech.org/

PR:             ports/146513
Submitted by:   Gvozdikov Veniamin <g.veniamin at googlemail.com>
Approved by:    tabthorpe (mentor)

01:22 wen 

JStrack is written by and for people who are in areas that are
prone to hits from tropical systems (currently only in the Tropical
Atlantic). It's intended to display the NHC/TPC data and give you
what you need to make decisions, etc.. It does NOT, nor will it ever,
attempt to do any forecasting on its own---I leave that to the gurus
at the NHC/TPC.

WWW: http://www.jstrack.org/jstrack/

PR:             ports/148208
Submitted by:   Chris Rees <utisoft@gmail.com>
Feature safe:   yes

14:21 lwhsu 

Add netcdf3-ftn , netCDF (network Common Data Form), with Fortran
support.

Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net>

09:43 wen 

The massXpert project aims at providing (bio)chemists with a software
package allowing the following:

* User-specific atom definitions and polymer chemistry definitions;
* Powerful sequence editing with user-defined glyphs for each monomer
and monomer chemical modification. Multi-region selections;
* Polymer sequence chemical/enzymatic cleavage;
* Intramolecular cross-linking, like disulfide bonds with total resolution
of the peptides generated upon enzymatic cleavage;
* Gas-phase fragmentation of oligomers;
* Mass-to-charge ratio calculations with inline change of ionization agent;
* Calculation of net electrical charge and of isoelectric point (even by
taking into account monomer modifications if polymer is a protein);
* Simulation of isotopic patterns for any chemical formula and z charge;
* A number of plugins allow 1) translation of the sequence from one format
to another (using a dictionary, like between the 1-letter code and the 3-letter
code of proteins) 2) conversion of number format according to any localized
number format 3) sort mass lists.

PR:             ports/146564
Submitted by:   Gvozdikov Veniamin <g.veniamin@googlemail.com>

05:31 wen 

PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.

WWW: http://neuralensemble.org/trac/PyNN

00:14 wen 

- Remove pyNN and re-add as pynn

Reviewed by:    danfe@

08:14 wen 

PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.

WWW: http://neuralensemble.org/trac/PyNN

PR:             ports/146664
Submitted by:   Ju Pengfei <jupengfei@gmail.com>

13:25 beat 

Bddsolve is a BDD-based tool for solving satisfiability and reachability
problems.  It uses the BDD package Buddy as a backend.

WWW: http://www.win.tue.nl/~wieger/bddsolve/

Submitted by:   ed@

15:36 miwi 

Perl modules for molecular chemistry

WWW:    http://search.cpan.org/dist/PerlMol/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:35 miwi 

Perl module which parses a SMILES (Simplified Molecular Input Line Entry
Specification) string.

WWW:    http://search.cpan.org/dist/Chemistry-File-SMILES/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:35 miwi 

Perl module implements an object class for representing internal
coordinates and provides methods for converting them to Cartesian
coordinates.

WWW:    http://search.cpan.org/dist/Chemistry-InternalCoords/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:34 miwi 

Perl module which will parse a SMARTS (SMiles ARbitrary Target Specification)
string, generating a Chemistry::Pattern object. It is a file I/O driver for
the PerlMol toolkit.

WWW:    http://search.cpan.org/dist/Chemistry-File-SMARTS/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:33 miwi 

Perl module which generates a three-dimensional molecular structure from a
connection table, such as that obtained by a 2D representation of the
molecule or from a SMILES string.

WWW:    http://search.cpan.org/dist/Chemistry-3DBuilder/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net

15:33 miwi 

SLN linear notation parser/writer

WWW:    http://search.cpan.org/dist/Chemistry-File-SLN/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:32 miwi 

Perl module which will parse a SMARTS (SMiles ARbitrary Target Specification)
string, generating a Chemistry::Pattern object. It is a file I/O driver for
the PerlMol toolkit.

WWW:    http://search.cpan.org/dist/Chemistry-File-SMARTS/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:32 miwi 

MOPAC 6 input file reader/writer

WWW:    http://search.cpan.org/dist/Chemistry-File-Mopac/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:32 miwi 

Explicit chemical reactions

WWW:    http://search.cpan.org/dist/Chemistry-Raction/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:31 miwi 

Match molecule by formula

WWW:    http://search.cpan.org/dist/Chemistry-ForumulaPattern/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:29 miwi 

Select atoms in macromolecule

WWW:    http://search.cpan.org/dist/Chemistry-MidasPattern/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:29 miwi 

Perl molecular awk interpreter

WWW:    http://search.cpan.org/dist/Chemistry-Mok/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:28 miwi 

XYZ molecule format reader/writer

WWW:    http://search.cpan.org/dist/Chemistry-File-XYZ/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:28 miwi 

Generate VRML models for molecules

WWW:    http://search.cpan.org/dist/Chemistry-File-VRML/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:27 miwi 

Perl module which provides some basic methods for representing a ring.

WWW:    http://search.cpan.org/dist/Chemistry-Ring/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:26 miwi 

Perl module which contains the exact mass data from the table of the isotopes.

WWW:    http://search.cpan.org/dist/Chemistry-Isotope/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:25 miwi 

Perl module which implements basic pattern matching for molecules.

WWW:    http://search.cpan.org/dist/Chemistry-Pattern/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:25 miwi 

Perl module which provides functions for "canonicalizing" a molecular
structure; that is, to number the atoms in a unique way regardless of the
input order.

WWW:    http://search.cpan.org/dist/Chemistry-Canonicalize/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:24 miwi 

Perl module which provides functions for detecting the bonds in a molecule from
its 3D coordinates by using simple cutoffs, and for guessing the formal bond
orders.

WWW:    http://search.cpan.org/dist/Chemistry-Bond-Find/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

11:21 miwi 

The HDF Java Products include a visual tool for browsing and editing HDF
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

00:27 wen 

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation
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>

06:46 pgollucci 

- remove broken/expired ports@ ports

Approved by: portmgr (miwi)

audio/ccaudio||2010-01-18|Has expired: has been broken for 4 months
audio/py-libmpdclient||2010-01-18|Has expired: has been broken for 3 months
chinese/gbk2uni||2010-01-18|Has expired: has been broken for 6 months
chinese/iiimf-le-xcin||2010-01-18|Has expired: has been broken for 3 months
devel/adabindx||2010-01-18|Has expired: has been broken for 3 months
devel/agide||2010-01-18|Has expired: has been broken for 6 months
devel/asis||2010-01-18|Has expired: has been broken for 3 months
devel/callgrind||2010-01-18|Has expired: Included in devel/valgrind
devel/florist||2010-01-18|Has expired: has been broken for 3 months
editors/xml2rfc-xxe||2010-01-18|Has expired: has been broken for 4 months
graphics/gephex||2010-01-18|Has expired: has been broken for 3 months
graphics/irit||2010-01-18|Has expired: has been broken for 3 months
graphics/pixieplus||2010-01-18|Has expired: has been broken for 6 months
japanese/expect||2010-01-18|Has expired: has been broken for 3 months
lang/pnetc||2010-01-18|Has expired: has been broken for 5 months
mail/libnewmail||2010-01-18|Has expired: has been broken for 3 months
net-mgmt/flowscan||2010-01-18|Has expired: has been broken for 5 months
net/astmanproxy||2010-01-18|Has expired: has been broken for 3 months
palm/prc-tools||2010-01-18|Has expired: has been broken for 4 months
print/latex-msc||2010-01-18|Has expired: has been broken for 3 months
science/xloops-ginac||2010-01-18|Has expired: has been broken for 3 months
shells/bush||2010-01-18|Has expired: has been broken for 3 months
textproc/iiimf-gnome-im-switcher||2010-01-18|Has expired: has been broken for 4
months
textproc/iiimf-gtk||2010-01-18|Has expired: has been broken for 3 months
x11-toolkits/gtkada-devel||2010-01-18|Has expired: has been broken for 3 months
x11-toolkits/gtkada||2010-01-18|Has expired: has been broken for 3 months
x11-wm/ion-2||2010-01-18|Has expired: has been broken for 4 months

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