Commit graph

211 commits

Author SHA1 Message Date
Wen Heping
bb12e102f3 The obspy.wav package contains methods in order to read and write
seismogram files in the WAV(audio) format. The data are squeezed to
audible frequencies.

ObsPy is an open-source project dedicated to provide a Python framework
for processing seismological data. It provides parsers for common
file formats and seismological signal processing routines which allow
the manipulation of seismological time series (see Beyreuther et. al.
2010). The goal of the ObsPy project is to facilitate rapid application
development for seismology.

WWW: http://www.obspy.org/
2011-03-21 06:28:57 +00:00
Steve Wills
cae009169c h5utils is a set of utilities for visualization and conversion of
scientific data in the free, portable HDF5 format.

Besides providing a simple tool for batch visualization as PNG images,
h5utils also includes programs to convert HDF5 datasets into the formats
required by other free visualization software (e.g. plain text, Vis5d,
and VTK).

WWW: http://ab-initio.mit.edu/wiki/index.php/H5utils

PR:		ports/155482
Submitted by:	Klaus Aehlig <aehlig at linta.de>
2011-03-18 19:42:35 +00:00
Wen Heping
f56fbc67a7 - Remove py-obspy.core because the default cvsupd configuration (cvsignore to be exact) prevents the download of files named *.core, use py-obspy-core instead
Thanks to:	dougb@, cperciva@, demelier.david@gmail.com
2011-03-16 09:56:38 +00:00
Wen Heping
3eabb018e9 The obspy.core package contains common methods and classes
for ObsPy. It includes UTCDateTime, Stats, Stream and Trace
classes and methods for reading seismograms.

ObsPy is an open-source project dedicated to provide a Python
framework for processing seismological data. It provides
parsers for common file formats and seismological signal
processing routines which allow the manipulation of
seismological time series (see Beyreuther et. al. 2010).
The goal of the ObsPy project is to facilitate rapid application
development for seismology.

WWW: http://www.obspy.org/
2011-03-16 08:46:36 +00:00
Wen Heping
ac49b69bf5 The obspy.signal package contains signal processing routines
for seismology. Capabilities include filtering, triggering,
rotation, instrument correction and coordinate transformations.

ObsPy is an open-source project dedicated to provide a Python
framework for processing seismological data. It provides parsers
for common file formats and seismological signal processing
routines which allow the manipulation of seismological time
series (see Beyreuther et. al. 2010). The goal of the ObsPy
project is to facilitate rapid application development for seismology.

WWW: http://www.obspy.org/
2011-03-14 14:09:29 +00:00
Wen Heping
53ab78064b This module contains Python wrappers for gse_functions - The GSE2 library
of Stefan Stange (http://www.orfeus-eu.org/Software/softwarelib.html#gse).
Currently CM6 compressed GSE2 files are supported, this should be sufficient
for most cases. Gse_functions are written in C and interfaced via Python
ctypes.

WWW: http://www.obspy.org/
2011-03-14 14:05:40 +00:00
Wen Heping
beaa8282a4 This module contains Python wrappers for libmseed - The MiniSeed
library of Chad Trabant. Libmseed is written in C and interfaced
via Python ctypes.

WWW: http://www.obspy.org/
2011-03-14 13:08:04 +00:00
Wen Heping
a84b4427a2 The obspy.core package contains common methods and classes
for ObsPy. It includes UTCDateTime, Stats, Stream and Trace
classes and methods for reading seismograms.

ObsPy is an open-source project dedicated to provide a Python
framework for processing seismological data. It provides
parsers for common file formats and seismological signal
processing routines which allow the manipulation of
seismological time series (see Beyreuther et. al. 2010).
The goal of the ObsPy project is to facilitate rapid application
development for seismology.

WWW: http://www.obspy.org/
2011-03-14 13:04:03 +00:00
Wen Heping
ca7b73fa17 BUFR = Binary Universal Form for the Representation of meteorological data.
BUFR is approved by WMO (World Meteorological Organization) as the standard
universal exchange format for meteorological observations, gradually
replacing a lot of older alphanumeric data formats.

This module provides methods for decoding and encoding BUFR messages, and
for displaying information in BUFR B and D tables and in BUFR flag and code
tables.

Installing this module also installs some programs: bufrread.pl,
bufrresolve.pl, bufrencode.pl, bufr_reencode.pl and bufralter.pl. See
https://wiki.met.no/bufr.pm/start for examples of use. For the majority of
potential users of Geo::BUFR I would expect these programs to be all that
you will need Geo::BUFR for.

WWW: http://search.cpan.org/dist/Geo-BUFR/
2011-03-10 06:15:55 +00:00
Wen Heping
267e104201 bayesm covers many important models used in marketing and micro-econometrics
applications. The package includes: Bayes Regression (univariate or
multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
Mixtures of Normals (including clustering), Dirichlet Process Prior Density
Estimation with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals prior and
covariates, Hierarchical Multinomial Logits with a mixture of normals prior
and covariates, Hierarchical Multinomial Logits with a Dirichlet Process
prior and covariates, Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear
instrumental variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).

WWW: http://www.perossi.org/home/bsm-1
2011-03-07 12:04:35 +00:00
Wen Heping
a850098cd5 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
2011-03-07 10:57:09 +00:00
Wen Heping
ba88c81733 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)
2011-02-20 03:54:04 +00:00
Wen Heping
90d4a1b864 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>
2011-01-06 02:39:32 +00:00
Wen Heping
7aaaa71110 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/
2010-12-29 08:50:40 +00:00
Max Brazhnikov
10979612c2 Connect py-biolccc 2010-11-13 21:41:03 +00:00
Sahil Tandon
807ae2afd6 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>
2010-09-09 00:26:13 +00:00
Sahil Tandon
a5408a406d 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>
2010-09-08 03:09:31 +00:00
Max Brazhnikov
3ef6616777 Connect kst2 2010-08-23 18:15:03 +00:00
Ashish SHUKLA
7d375bc1fd - Remove the port from 'science' category.
PR:		ports/146513
Approved by:	pgj (mentor)
2010-07-21 09:53:14 +00:00
Ashish SHUKLA
d976a44c9c 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)
2010-07-21 03:27:25 +00:00
Wen Heping
3bc13a27ce 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
2010-06-29 01:22:16 +00:00
Li-Wen Hsu
e4d1bb5df1 Add netcdf3-ftn , netCDF (network Common Data Form), with Fortran
support.

Submitted by:	Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net>
2010-05-20 14:21:43 +00:00
Wen Heping
cc8da973ab 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>
2010-05-20 09:43:14 +00:00
Wen Heping
8d3cf83cc4 PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.

WWW: http://neuralensemble.org/trac/PyNN
2010-05-19 05:31:44 +00:00
Wen Heping
d85961f518 - Remove pyNN and re-add as pynn
Reviewed by:	danfe@
2010-05-19 00:14:14 +00:00
Wen Heping
e424150d98 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>
2010-05-18 08:14:12 +00:00
Beat Gaetzi
d717f25f58 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@
2010-05-12 13:25:37 +00:00
Martin Wilke
83e3ba00ba Perl modules for molecular chemistry
WWW:	http://search.cpan.org/dist/PerlMol/

PR:		ports/145143
Submitted by:	Steve Wills <steve at mouf.net>
2010-04-02 15:36:26 +00:00
Martin Wilke
a6af1d634f 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>
2010-04-02 15:35:47 +00:00
Martin Wilke
e576408592 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>
2010-04-02 15:35:23 +00:00
Martin Wilke
4af115e4ea 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>
2010-04-02 15:34:39 +00:00
Martin Wilke
4eb372dfc7 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
2010-04-02 15:33:52 +00:00
Martin Wilke
7edfd85264 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>
2010-04-02 15:33:24 +00:00
Martin Wilke
4deddb544f 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>
2010-04-02 15:32:52 +00:00
Martin Wilke
31412b24c1 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>
2010-04-02 15:32:24 +00:00
Martin Wilke
0c0fc43cf8 Explicit chemical reactions
WWW:	http://search.cpan.org/dist/Chemistry-Raction/

PR:		ports/145143
Submitted by:	Steve Wills <steve at mouf.net>
2010-04-02 15:32:03 +00:00
Martin Wilke
e686fdf65d Match molecule by formula
WWW:	http://search.cpan.org/dist/Chemistry-ForumulaPattern/

PR:		ports/145143
Submitted by:	Steve Wills <steve at mouf.net>
2010-04-02 15:31:34 +00:00
Martin Wilke
c85c1cf3b1 Select atoms in macromolecule
WWW:	http://search.cpan.org/dist/Chemistry-MidasPattern/

PR:		ports/145143
Submitted by:	Steve Wills <steve at mouf.net>
2010-04-02 15:29:58 +00:00
Martin Wilke
c19a7ca028 Perl molecular awk interpreter
WWW:	http://search.cpan.org/dist/Chemistry-Mok/

PR:		ports/145143
Submitted by:	Steve Wills <steve at mouf.net>
2010-04-02 15:29:35 +00:00
Martin Wilke
4b9751f871 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>
2010-04-02 15:28:42 +00:00
Martin Wilke
3e051c0a76 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>
2010-04-02 15:28:04 +00:00
Martin Wilke
b0bc65a895 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>
2010-04-02 15:27:22 +00:00
Martin Wilke
2f7bf2888c 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>
2010-04-02 15:26:37 +00:00
Martin Wilke
be4a09a2d8 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>
2010-04-02 15:25:56 +00:00
Martin Wilke
b9c5628b0d 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>
2010-04-02 15:25:12 +00:00
Martin Wilke
5fd8c153ed 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>
2010-04-02 15:24:14 +00:00
Martin Wilke
3ab2c72352 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
2010-02-13 11:21:53 +00:00
Wen Heping
551d43b724 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>
2010-01-25 00:27:10 +00:00
Philip M. Gollucci
5eccbb21e0 - 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
2010-01-18 06:46:44 +00:00
Wen Heping
dd998fd1cb 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/
2010-01-15 07:20:43 +00:00