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Add new categories science and ukrainian.
2001-03-24 22:40:17 +01:00
# $FreeBSD$
#
Sort entries.
2001-09-21 07:59:19 +02:00
Remove category pkg/COMMENT files in favour of a COMMENT variable in the category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651
2004-04-02 09:29:48 +02:00
COMMENT = Scientific ports
[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>
2008-05-24 08:51:36 +02:00
SUBDIR += 2d-rewriter
Added a Numerical Hartree-Fock Program for Diatomic Molecules. This program package calcluates virtually exact solution of the Hartree-Fock and Hartree-Fock-Salter equations for diatomic molecules (distributed under GPL).
2003-07-24 11:50:24 +02:00
SUBDIR += 2dhf
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
2006-09-07 03:24:33 +02:00
SUBDIR += InsightToolkit
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 11:57:09 +01:00
SUBDIR += R-cran-AMORE
- Add a new port: science/R-cran-DCluster A set of functions for the detection of spatial clusters of disease using count data. Bootstrap is used to estimate sampling distributions of statistics. WWW: http://cran.r-project.org/web/packages/DCluster/
2011-09-18 04:47:50 +02:00
SUBDIR += R-cran-DCluster
- Add a new port: science/R-cran-Epi Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, including interval censored data and representation of multistate data. Also some useful functions for tabulation and plotting. Contains some epidemiological datasets. WWW: http://www.pubhealth.ku.dk/~bxc/Epi/
2011-09-17 08:55:27 +02:00
SUBDIR += R-cran-Epi
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 13:04:35 +01:00
SUBDIR += R-cran-bayesm
- Add a new port: science/R-cran-e1071 Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ... WWW: http://cran.r-project.org/web/packages/e1071/
2012-02-11 03:26:29 +01:00
SUBDIR += R-cran-e1071
eco is a publicly available R package that implements the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008) for ecological inference in $2 \times 2$ tables as well as the method of bounds introduced by Duncan and Davis (1953). WWW: http://imai.princeton.edu/software/eco.html
2011-09-28 09:33:03 +02:00
SUBDIR += R-cran-eco
R-cran-epicalc is functions making R easy for epidemiological calculation. WWW: http://cran.r-project.org/web/packages/epicalc/ Feature safe: yes
2011-12-15 02:20:35 +01:00
SUBDIR += R-cran-epicalc
- Add a new port: science/R-cran-snow The snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls makeCluster to start a cluster of worker processes; the master process then uses functions such as clusterCall and clusterApply to execute R code on the worker processes and collect and return the results on the master. This framework supports many forms of "embarrassingly parallel" computations. Snow can use one of four communications mechanisms: sockets, PVM, MPI, or NetWorkSpaces (NWS). NWS support was provided by Steve Weston. PVM clusters use the rpvm package; MPI clusters use package Rmpi; NWS clusters use package nws. If pvm is used, then pvm must be started, either using a pvm console (e.g the pvm text console or the graphical xpvm console, both available with pvm) or from R using functions provided by rpvm. Similarly, LAM-MPI must be started, e.g. using lamboot, for MPI clusters that use Rmpi and LAM-MPI. If NWS is used, the NetWorkSpaces server must be running. SOCK clusters are the easiest approach for using snow on a single multi-core computer as they require no additional software. WWW: http://cran.r-project.org/web/packages/snow/
2012-01-31 14:14:19 +01:00
SUBDIR += R-cran-snow
Add abinit, calculates total energy, charge density and electronic structure of systems.
2004-08-14 10:45:42 +02:00
SUBDIR += abinit
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)
2006-01-25 18:34:35 +01:00
SUBDIR += afni
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>
2009-05-23 00:16:46 +02:00
SUBDIR += avogadro
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 15:25:37 +02:00
SUBDIR += bddsolve
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/>
2007-06-17 23:04:54 +02:00
SUBDIR += bft
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
2007-05-25 00:16:03 +02:00
SUBDIR += bodr
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>
2009-03-16 07:07:37 +01:00
SUBDIR += brian
Add buddy 2.4, a Binary Decision Diagram library. PR: 71221 Submitted by: Leland Wang
2005-01-22 16:01:02 +01:00
SUBDIR += buddy
Add cdcl, a scientific graphic library for geoscience PR: ports/62871 Submitted by: Shin'ya Murakami <murashin@edamame.summing.com>
2004-02-27 23:35:23 +01:00
SUBDIR += cdcl
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>.
2006-01-28 21:40:56 +01:00
SUBDIR += cdf
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>
2006-06-11 10:41:34 +02:00
SUBDIR += cdo
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.
2007-04-01 11:00:23 +02:00
SUBDIR += cgnslib
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>
2009-09-19 11:53:55 +02:00
SUBDIR += checkmol
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/
2007-05-25 00:18:10 +02:00
SUBDIR += chemical-mime-data
add chemtool Chemtool is a program for drawing organic molecules easily and store them as an Postscript, X-Bitmap, LaTeX and XFig file ps. first science ports ?
2001-03-30 21:23:00 +02:00
SUBDIR += chemtool
Remove # chemtool-devel is now real developer version of chemtool.
2003-10-04 04:30:06 +02:00
SUBDIR += chemtool-devel
Fix broken ordering and remove sample directory.
2001-05-08 02:03:05 +02:00
SUBDIR += clhep
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>
2008-05-01 23:04:57 +02:00
SUBDIR += colt
Add crf++ 0.42, yet Another CRF toolkit. PR: ports/100909 Submitted by: Cheng-Lung Sung <clsung at FreeBSD.org>
2006-07-28 05:38:04 +02:00
SUBDIR += crf++
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>
2005-02-24 21:26:31 +01:00
SUBDIR += dcl
DeViSoR is abbreviated for "Design and Visualization of Software Resource". The DeViSoRGrid application is part of that software family and is primarily used for the following tasks, so far in 2D only: * Geometry generation * Manual coarse mesh generation * Grid visualisation at all levels All of this can be done in a very confortable manner using a simple point and click interface like in common vector-based image processing software. Both the reliable FEAT file format and the new FEAST format with integrated parallelism are supported. WWW: http://www.featflow.de/ PR: 75973 Submitted by: Pedro F. Giffuni <giffunip@asme.org>
2005-01-21 20:03:52 +01:00
SUBDIR += devisor
DTI visualization software from Stanford. WWW: http://graphics.stanford.edu/projects/dti/ PR: ports/120129 Submitted by: Jason W. Bacon <jwbacon at tds.net>
2008-02-25 13:56:17 +01:00
SUBDIR += dtiquery
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/>
2007-06-17 23:04:54 +02:00
SUBDIR += ecs
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>
2006-04-24 21:49:57 +02:00
SUBDIR += elmer-eio
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>
2006-04-24 21:53:14 +02:00
SUBDIR += elmer-hutiter
MATC language library used by Elmer FEM package. Submitted by: Pedro F. Giffuni <giffunip@asme.org>
2006-04-24 21:50:53 +02:00
SUBDIR += elmer-matc
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>
2006-04-24 21:46:15 +02:00
SUBDIR += elmer-meshgen2d
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>
2006-04-24 21:48:58 +02:00
SUBDIR += elmergrid
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>
2006-04-24 21:55:43 +02:00
SUBDIR += elmerpost
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 05:09:31 +02:00
SUBDIR += epte
add euler 1.60.4 A program computes with real and complex numbers and matrices
2002-05-14 05:59:02 +02:00
SUBDIR += euler
Add fastcap , a three-dimensional capacitance extraction program. PR: ports/93968 Submitted by: Pedro Giffuni <giffunip@asme.org>
2006-03-15 11:36:29 +01:00
SUBDIR += fastcap
Add fasthenry , a multipole-accelerated inductance analysis program. PR: ports/93969 Submitted by: Pedro Giffuni <giffunip@asme.org>
2006-03-15 11:38:00 +01:00
SUBDIR += fasthenry
. Welcome felt to the science category. PR: 58178 Submitted by: Pedro F. Giffuni <giffunip@yahoo.com>
2003-11-08 10:08:52 +01:00
SUBDIR += felt
add flounder 0.32a A quick way to visualize regularly spaced 4D data
2002-10-14 22:11:17 +02:00
SUBDIR += flounder
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/>
2007-06-17 23:04:54 +02:00
SUBDIR += fvm
Add g3data 1.5.0, utility for extracting data from graphs. PR: ports/103397 Submitted by: trasz <trasz at pin.if.uz.zgora.pl>
2006-10-02 10:59:12 +02:00
SUBDIR += g3data
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. :)
2007-03-13 01:39:58 +01:00
SUBDIR += gamess
Add gchemutils a set of C++ class and GTK+-2 widgets related to chemistry. PR: 50538 Submitted by: Pav Lucistnik <pav@oook.cz>
2003-04-08 02:04:57 +02:00
SUBDIR += gchemutils
add gdis 0.73.3 Display and manipulation of isolated molecules and periodic systems
2002-03-05 04:36:20 +01:00
SUBDIR += gdis
Add getdp 1.0.0, a rather general finite element solver using mixed finite elements. Suggested by: Pedro F. Giffuni.
2004-11-15 23:18:09 +01:00
SUBDIR += getdp
Add new port science/ghemical a computational chemistry software package
2003-05-04 04:33:52 +02:00
SUBDIR += ghemical
Add ghmm 0.7.0a, general Hidden Markov Model Library in C. PR: ports/100886 Submitted by: Cheng-Lung Sung <clsung at FreeBSD.org>
2006-07-28 05:36:25 +02:00
SUBDIR += ghmm
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/
2005-10-31 19:48:23 +01:00
SUBDIR += gnudatalanguage
Gramps (Genealogical Research and Analysis Management Programming System) is an open source genealogy program. It is written in Python, using the GTK/GNOME interface. WWW: http://gramps.sourceforge.net PR: ports/62171 Submitted by: Andreas Fehlner <fehlner@gmx.de>
2004-02-01 04:09:52 +01:00
SUBDIR += gramps
New port science/gromacs GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles, and also the World's fastest Molecular Dynamics under GPL. PR: 71211 Submitted by: Stephen Montgomery-Smith <stephen@math.missouri.edu> Reviewed by: Bruno Afonso <brunomiguel@dequim.ist.utl.pt>
2004-10-19 03:36:11 +02:00
SUBDIR += gromacs
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
2006-03-19 21:51:14 +01:00
SUBDIR += gsmc
Add gsystem, a virtual reality simulation framework, specialised on life and evolution simulation. I'm a main developer of this framework and I will also keep the FreeBSD port up-to-date, as I'm using FreeBSD as my primary platform. See http://www.g-system.at for details. PR: ports/75466 Submitted by: Raphael Langerhorst <raphael-langerhorst@gmx.at>
2004-12-29 00:30:00 +01:00
SUBDIR += gsystem
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
2006-09-27 21:59:46 +02:00
SUBDIR += gtamsanalyzer
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>
2006-08-13 00:34:57 +02:00
SUBDIR += gwyddion
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 20:42:35 +01:00
SUBDIR += h5utils
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>
2010-01-02 03:54:00 +01:00
SUBDIR += harminv
Unhook hdf* ports in graphics, hook them in science.
2004-02-25 23:55:01 +01:00
SUBDIR += hdf
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 12:21:53 +01:00
SUBDIR += hdf-java
Unhook hdf* ports in graphics, hook them in science.
2004-02-25 23:55:01 +01:00
SUBDIR += hdf5
- Connect hdf5-18
2008-11-24 06:35:04 +01:00
SUBDIR += hdf5-18
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>
2010-01-03 06:02:13 +01:00
SUBDIR += hs-bio
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/>
2007-06-17 23:04:54 +02:00
SUBDIR += ics
Add isaac-cfd 4.2, Integrated Solution Algorithm for Arbitrary Configuration. PR: 75529 Submitted by: Pedro F. Giffuni
2004-12-29 21:46:47 +01:00
SUBDIR += isaac-cfd
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>
2008-05-18 01:04:44 +02:00
SUBDIR += jmol
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 03:22:16 +02:00
SUBDIR += jstrack
The KDE/FreeBSD team is pleased to announce KDE Software Compilation 4.7.2. The official release notes can be found at: http://kde.org/announcements/announce-4.7.2.php This release ships with many improvements. Read more about them here: http://FreeBSD.kde.org/news.php#itemKDESC472availableinports We'd like to say thanks to all testers and contributors, especially to lwhsu@ for his effort on hosting our test packages. PR: 156293 [1] 159219 [2] 160164 [3] Submitted by: Oleg Sidorkin <osidorkin@gmail.com> [1] Alvaro Castillo <gobledb@gmail.com> [2] dkeav04@gmail.com [3] Tested by: exp-run via pav
2011-10-17 02:03:42 +02:00
SUBDIR += kalzium
add kmovisto 0.5.1 A real 3-D molecule viewer
2003-10-24 06:19:28 +02:00
SUBDIR += kmovisto
Add kst 0.97. kst is a program for looking at data streams. It can plot: - x-y plots - power spectra - histograms - equations (including equations of data streams). - data in files which are being updated as data is being logged, in which case it can act as a plotter for a chart recorder. - much more You can use the mouse to rapidly zoom into interesting parts of the plots. In addition to a complete GUI, kst has a convenient command line interface for rapid access to plotting data in files. kst can read data from stdin. It provides a DCOP interface for remote manipulation, and supports several file formats in use in scientific projects around the world. WWW: http://omega.astro.utoronto.ca/kst/ WWW: http://extragear.kde.org/apps/kst.php
2004-04-30 17:44:32 +02:00
SUBDIR += kst
Connect kst2
2010-08-23 20:15:03 +02:00
SUBDIR += kst2
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>
2005-05-15 23:44:02 +02:00
SUBDIR += lamprop
add libctl 2.2 Control Language Library
2003-04-04 09:28:22 +02:00
SUBDIR += libctl
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.
2006-07-03 09:30:45 +02:00
SUBDIR += libghemical
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.
2006-12-29 08:41:44 +01:00
SUBDIR += libint
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)
2009-10-07 13:10:21 +02:00
SUBDIR += libkml
- science/liblr is moved to science/liblinear (project renamed)
2007-07-28 09:10:54 +02:00
SUBDIR += liblinear
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/
2008-08-21 00:35:40 +02:00
SUBDIR += liboglappth
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>
2009-08-14 22:02:07 +02:00
SUBDIR += libquantum
Add libsvm 2.33, a library for Support Vector Machines. PR: 32997 Submitted by: Chia-Hsing Yu <davidyu@oio.cx>
2001-12-19 04:44:59 +01:00
SUBDIR += libsvm
Slave port to science/libsvm PR: ports/73981 Submitted by: Rong-En Fan <rafan(at)infor.org>
2004-12-11 05:52:40 +01:00
SUBDIR += libsvm-python
add linsmith 0.99.3 Smith charting program
2006-12-22 04:38:47 +01:00
SUBDIR += linsmith
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 11:43:14 +02:00
SUBDIR += massxpert
add mayavi 1.1 The MayaVi Data Visualizer
2002-03-09 11:58:55 +01:00
SUBDIR += mayavi
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>
2005-05-22 17:50:06 +02:00
SUBDIR += mbdyn
McStas - Monte Carlo simulation of neutron instruments McStas is an ongoing project to create a general tool for simulating neutron scattering instruments. The project is conducted at Risoe National Laboratory in cooperation with the ILL. McStas is based on a compiler that reads a high-level specification language defining the instrument to be simulated and produces C code that performs the Monte Carlo Simulation. WWW: http://neutron.risoe.dk/ PR: ports/66031 Submitted by: Joerg Pulz <Joerg.Pulz@frm2.tum.de>
2005-02-18 15:17:20 +01:00
SUBDIR += mcstas
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).
2006-09-25 01:09:26 +02:00
SUBDIR += medit
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 01:27:10 +01:00
SUBDIR += meep
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>
2006-02-12 16:30:03 +01:00
SUBDIR += minc
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
2006-04-30 14:05:08 +02:00
SUBDIR += minc2
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>
2009-09-19 13:02:46 +02:00
SUBDIR += mol2ps
add mpb 1.4.2 MIT Photonic-Bands
2003-04-04 12:22:55 +02:00
SUBDIR += mpb
New port: xmakemol - a motif molecule viewer program PR: ports/27981 Submitted by: Chi Zhang <chizhang@midway.uchicago.edu>
2001-09-12 18:36:24 +02:00
SUBDIR += mpqc
add mpqc-mpich PR: 40631 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
2002-07-16 08:53:52 +02:00
SUBDIR += mpqc-mpich
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/>
2007-06-17 23:04:54 +02:00
SUBDIR += ncs
Repocopy math/netcdf to science/netcdf, along with cdf, hdf and hdf5. PR: 92497 Submitted by: /me Repocopied by: marcus
2006-01-30 23:19:24 +01:00
SUBDIR += netcdf
- 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)
2009-03-22 23:09:27 +01:00
SUBDIR += netcdf-ftn
Add netcdf3-ftn , netCDF (network Common Data Form), with Fortran support. Submitted by: Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net>
2010-05-20 16:21:43 +02:00
SUBDIR += netcdf3-ftn
- Attach science/netcdf4
2009-01-01 13:20:36 +01:00
SUBDIR += netcdf4
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
2007-04-28 12:58:01 +02:00
SUBDIR += nifticlib
Add omnetpp, a public-source, component-based, modular and open-architecture simulation environment with strong GUI support and an embeddable simulation kernel. Its primary application area is the simulation of communication networks and because of its generic and flexible architecture, it has been successfully used in other areas like the simulation of IT systems, queueing networks, hardware architectures and business processes as well. PR: ports/73920 Submitted by: Bjoern Koenig <bkoenig@cs.tu-berlin.de>
2004-11-15 23:53:44 +01:00
SUBDIR += omnetpp
add openbabel 1.100.0 Chemistry file translation program
2003-01-05 18:04:59 +01:00
SUBDIR += openbabel
Add ovt 2.3, the Orbit Visualization Tool. PR: 57860 Submitted by: Mykola Khotyaintsev <ko@nest.irfu.se>
2004-03-24 00:34:29 +01:00
SUBDIR += ovt
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>
2006-08-03 09:29:03 +02:00
SUBDIR += p5-Algorithm-SVMLight
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 17:33:52 +02:00
SUBDIR += p5-Chemistry-3DBuilder
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 17:24:14 +02:00
SUBDIR += p5-Chemistry-Bond-Find
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 17:25:12 +02:00
SUBDIR += p5-Chemistry-Canonicalize
Add p5-Chemistry-Elements 0.91, perl extension for working with Chemical Elements. PR: 33412 Submitted by: Seamus Venasse <svenasse@polaris.ca>
2002-02-08 07:15:14 +01:00
SUBDIR += p5-Chemistry-Elements
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 17:32:52 +02:00
SUBDIR += p5-Chemistry-File-MDLMol
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 17:32:24 +02:00
SUBDIR += p5-Chemistry-File-Mopac
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>
2009-05-17 14:51:49 +02:00
SUBDIR += p5-Chemistry-File-PDB
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 17:33:24 +02:00
SUBDIR += p5-Chemistry-File-SLN
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 17:34:39 +02:00
SUBDIR += p5-Chemistry-File-SMARTS
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 17:35:47 +02:00
SUBDIR += p5-Chemistry-File-SMILES
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 17:28:04 +02:00
SUBDIR += p5-Chemistry-File-VRML
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 17:28:42 +02:00
SUBDIR += p5-Chemistry-File-XYZ
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 17:31:34 +02:00
SUBDIR += p5-Chemistry-FormulaPattern
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 17:35:23 +02:00
SUBDIR += p5-Chemistry-InternalCoords
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 17:26:37 +02:00
SUBDIR += p5-Chemistry-Isotope
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>
2009-05-17 15:00:50 +02:00
SUBDIR += p5-Chemistry-MacroMol
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 17:29:58 +02:00
SUBDIR += p5-Chemistry-MidasPattern
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 17:29:35 +02:00
SUBDIR += p5-Chemistry-Mok
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>
2009-05-17 01:29:15 +02:00
SUBDIR += p5-Chemistry-Mol
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 17:25:56 +02:00
SUBDIR += p5-Chemistry-Pattern
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 17:32:03 +02:00
SUBDIR += p5-Chemistry-Reaction
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 17:27:22 +02:00
SUBDIR += p5-Chemistry-Ring
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 07:15:55 +01:00
SUBDIR += p5-Geo-BUFR
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 09:50:40 +01:00
SUBDIR += p5-Geo-Coordinates-Converter
- Add p5-Geo-Coordinates-Converter-iArea 0.14 Geo::Coordinates::Converter::iArea is utilities for DoCoMo iArea. WWW: http://search.cpan.org/dist/Geo-Coordinates-Converter-iArea/
2011-06-12 18:18:59 +02:00
SUBDIR += p5-Geo-Coordinates-Converter-iArea
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>
2009-03-22 16:18:46 +01:00
SUBDIR += p5-Geo-ReadGRIB
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 08:20:43 +01:00
SUBDIR += p5-Geo-WebService-Elevation-USGS
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 17:36:26 +02:00
SUBDIR += p5-PerlMol
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 02:26:13 +02:00
SUBDIR += p5-Physics-Unit
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
2006-09-28 21:17:57 +02:00
SUBDIR += paje
New port: ParaView is a powerful scientific visualization application, designed with the need to visualize large data sets in mind.
2005-06-14 07:41:20 +02:00
SUBDIR += paraview
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>
2009-06-22 17:55:11 +02:00
SUBDIR += peekabot
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>
2007-04-30 15:44:51 +02:00
SUBDIR += pnetcdf
The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Molecular point-group symmetry is utilized throughout to maximize efficiency.
2004-03-19 10:32:49 +01:00
SUBDIR += psi3
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
2009-02-28 20:58:19 +01:00
SUBDIR += psychopy
py-DendroPy is a python library for phylogenetic scripting, simulation, data processing and manipulation. WWW: http://packages.python.org/DendroPy/
2010-01-09 13:19:58 +01:00
SUBDIR += py-DendroPy
Connect py-biolccc
2010-11-13 22:41:03 +01:00
SUBDIR += py-biolccc
Add py-h5py 1.2.0, a general-purpose Python interface to the HDF5 library. PR: ports/136096 Submitted by: TAOKA Fumiyoshi
2009-07-13 16:07:16 +02:00
SUBDIR += py-h5py
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>
2008-09-27 01:21:54 +02:00
SUBDIR += py-hcluster
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>
2008-09-27 20:52:29 +02:00
SUBDIR += py-mdp
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>
2009-04-23 19:02:20 +02:00
SUBDIR += py-mlpy
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
2009-02-23 21:18:45 +01:00
SUBDIR += py-netCDF4
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 09:46:36 +01:00
SUBDIR += py-obspy-core
The obspy.db package contains a waveform indexer collecting metadata from a file based waveform archive and storing in into a standard SQL database. Supported waveform formats depend on installed ObsPy packages. WWW: http://www.obspy.org/ Feature safe: yes
2011-12-09 09:59:34 +01:00
SUBDIR += py-obspy.db
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 15:05:40 +01:00
SUBDIR += py-obspy.gse2
obspy.imaging provides tools for displaying features used in seismology. WWW: http://www.obspy.org/
2011-06-29 10:18:07 +02:00
SUBDIR += py-obspy.imaging
The obspy.iris package contains a client for the DMC Web services provided by IRIS (http://www.iris.edu/ws/). WWW: http://www.obspy.org/ Feature safe: yes
2011-12-13 07:24:57 +01:00
SUBDIR += py-obspy.iris
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 14:08:04 +01:00
SUBDIR += py-obspy.mseed
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 15:09:29 +01:00
SUBDIR += py-obspy.signal
The obspy.taup package contains Python wrappers for iaspei-tau - a travel time library by Arthur Snoke (http://www.iris.edu/pub/programs/iaspei-tau/). The library iaspei-tau is written in Fortran and interfaced via Python ctypes. WWW: http://www.obspy.org/
2012-01-16 07:55:05 +01:00
SUBDIR += py-obspy.taup
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 07:28:57 +01:00
SUBDIR += py-obspy.wav
The obspy.xseed package contains methods in order to read, write and convert seismological meta data files in the Dataless SEED, RESP and XML-SEED format. WWW: http://www.obspy.org/
2011-06-29 10:13:17 +02:00
SUBDIR += py-obspy.xseed
This port installs python bindings for openbabel. WWW: http://openbabel.sourceforge.net PR: ports/125768 Submitted by: Max Brazhnikov <makc at issp.ac.ru>
2008-07-19 16:00:33 +02:00
SUBDIR += py-openbabel
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>
2005-07-18 18:22:48 +02:00
SUBDIR += py-paida
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>
2009-01-16 01:09:20 +01:00
SUBDIR += py-pydicom
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 04:54:04 +01:00
SUBDIR += py-scimath
add py-scipy 0.3 Scientific tools for Python
2004-08-26 10:37:09 +02:00
SUBDIR += py-scipy
- New port science/py-ws2300 Ws2300 manipulates the LaCrosse WS-2300 weather station via its RS232 interface. It can read and write values, and can continuously log data from WS-2300 to a file or SQL database. WWW: http://ace-host.stuart.id.au/russell/files/ws2300/ PR: ports/153452 Submitted by: Stefan Bethke <stb@lassitu.de> Approved by: gabor (mentor)
2011-07-01 22:23:41 +02:00
SUBDIR += py-ws2300
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/
2009-11-19 14:44:38 +01:00
SUBDIR += pybrain
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
2008-06-03 11:41:36 +02:00
SUBDIR += pycdf
PyNN(pronounced 'pine') is a simulator-independent language for building neuronal network models. WWW: http://neuralensemble.org/trac/PyNN
2010-05-19 07:31:44 +02:00
SUBDIR += pynn
- Move emulators/qcl -> science/qcl on maintainer's request. Repocopy by: marcus
2005-02-10 09:44:55 +01:00
SUBDIR += qcl
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>
2010-01-13 20:26:59 +01:00
SUBDIR += qtresistors
Add ruby-dcl, a ruby interface to DCL, a scienific graphical library. Add ruby-dcl-gtk, a slave port for ruby-dcl with gtk patches. PR: ports/62873, ports/62874 Submitted by: <murashin@edamame.summing.com>
2004-02-28 00:54:14 +01:00
SUBDIR += ruby-dcl
Add ruby-gphys, a multi-purpose class to handle gridded physical quantities for Ruby. PR: ports/64248 Submitted by: Shin'ya Murakami <murakami@ahs.scitec.kobe-u.ac.jp>
2004-03-14 17:34:51 +01:00
SUBDIR += ruby-gphys
AI4R is a collection of ruby algorithms implementations, covering several Artificial intelligence fields. It implements: * Genetic algorithms * Self-organized maps (SOM) * Neural Networks - Multilayer perceptron with Backpropagation learning - Hopfield net * Automatic classifiers (Machine Learning) - ID3 (Decision Trees) - PRISM (J. Cendrowska, 1987) - Multilayer Perceptron - OneR (AKA One Attribute Rule, 1R) - ZeroR - Hyperpipes - Naive Bayes - IB1 (D. Aha, D. Kibler - 1991) * Data clustering - K-means - Bisecting k-means - Single linkage - Complete linkage - Average linkage - Weighted Average linkage - Centroid linkage - Median linkage - Ward's method linkage - Diana (Divisive Analysis) WWW: http://ai4r.rubyforge.org/ PR: ports/155699 Submitted by: Eric Freeman <freebsdports at chillibear.com>
2011-03-25 13:08:20 +01:00
SUBDIR += rubygem-ai4r
- 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>
2008-07-20 23:19:13 +02:00
SUBDIR += silo
SIMLIB/C++ is the SIMulation LIBrary for C++ programming language. You can create models directly in C++ language with the use of predefined simulation tools from the library. SIMLIB allows object-oriented description of models based on simulation abstractions. Current version allows a description of continuous, discrete, combined, 2D/3D vector, and fuzzy models. Requested by: Roman Divacky
2004-11-27 22:38:03 +01:00
SUBDIR += simlib
The KDE/FreeBSD team is pleased to announce KDE Software Compilation 4.7.2. The official release notes can be found at: http://kde.org/announcements/announce-4.7.2.php This release ships with many improvements. Read more about them here: http://FreeBSD.kde.org/news.php#itemKDESC472availableinports We'd like to say thanks to all testers and contributors, especially to lwhsu@ for his effort on hosting our test packages. PR: 156293 [1] 159219 [2] 160164 [3] Submitted by: Oleg Sidorkin <osidorkin@gmail.com> [1] Alvaro Castillo <gobledb@gmail.com> [2] dkeav04@gmail.com [3] Tested by: exp-run via pav
2011-10-17 02:03:42 +02:00
SUBDIR += step
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>
2006-08-01 17:07:54 +02:00
SUBDIR += svmlight
. 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/"
2005-03-17 20:30:00 +01:00
SUBDIR += szip
Add a port of udunits: The Unidata units library, udunits, supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of unit specifications, and conversion of values between compatible scales of measurement. WWW: http://www.unidata.ucar.edu/packages/udunits/ Obtained from: Gentoo (partially)
2005-01-14 22:52:08 +01:00
SUBDIR += udunits
Add V_Sim, a program to visualize atomic structures such as crystals, grain boundaries and so on.
2005-12-10 22:45:28 +01:00
SUBDIR += v_sim
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 03:39:32 +01:00
SUBDIR += veusz
add vis5d+ 1.2.1 An OpenGL-based volumetric visualization program for scientific datasets
2002-01-09 15:51:38 +01:00
SUBDIR += vis5d+
Add vmd, a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. PR: ports/70509 Submitted by: Stephen Montgomery-Smith <stephen@math.missouri.edu>
2004-08-21 18:34:57 +02:00
SUBDIR += vmd
Add x11iraf 1.3.1, which provides graphical tools to work with IRAF. PR: 70816 Submitted by: David Syphers.
2004-12-27 00:08:06 +01:00
SUBDIR += x11iraf
New port: xmakemol - a motif molecule viewer program PR: ports/27981 Submitted by: Chi Zhang <chizhang@midway.uchicago.edu>
2001-09-12 18:36:24 +02:00
SUBDIR += xmakemol
Add xmds , XMDS is a code generator that integrates equations;. PR: ports/100419 Submitted by: EelVex
2006-07-19 21:58:28 +02:00
SUBDIR += xmds
Add new categories science and ukrainian.
2001-03-24 22:40:17 +01:00
.include <bsd.port.subdir.mk>
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