CVS log for ports/science/Makefile
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Revision 1.233: download - view: text, markup, annotated - select for diffs
Fri Feb 3 12:04:14 2012 UTC (7 days, 5 hours ago) by tota
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- Remove science/R-cran-survival which has been already included in math/R Reported by: pointyhat (pav)
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Tue Jan 31 13:22:44 2012 UTC (10 days, 3 hours ago) by tota
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- Add a new port: science/R-cran-survival survival analysis: descriptive statistics, two-sample tests, parametric accelerated failure models, Cox model. Delayed entry (truncation) allowed for all models; interval censoring for parametric models. Case-cohort designs. WWW: http://cran.r-project.org/web/packages/survival/
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Tue Jan 31 13:14:19 2012 UTC (10 days, 3 hours ago) by tota
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- 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/
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Mon Jan 16 06:55:05 2012 UTC (3 weeks, 4 days ago) by wen
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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/
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Thu Dec 15 01:20:35 2011 UTC (8 weeks, 1 day ago) by wen
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R-cran-epicalc is functions making R easy for epidemiological calculation. WWW: http://cran.r-project.org/web/packages/epicalc/ Feature safe: yes
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Tue Dec 13 06:24:57 2011 UTC (8 weeks, 3 days ago) by wen
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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
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Fri Dec 9 08:59:33 2011 UTC (2 months ago) by wen
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CVS tags: RELEASE_9_0_0
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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
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Wed Nov 2 01:35:39 2011 UTC (3 months, 1 week ago) by dougb
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Remove ports@ ports that have been DEPRECATED for at least 1 month audio/shoutcast Unfetchable; website rearranged audio/linux-shoutcast Unfetchable; website rearranged chinese/scim-chewing Does not configure converters/py-cjkcodecs Integrated into every python version in the tree databases/kpogre Does not compile deskutils/mhc Does not fetch deskutils/org-mode.el6 Does not fetch deskutils/gemcal Does not fetch devel/erlang-thrift Does not build dns/domtools Does not fetch editors/richtext Does not compile games/vultures-claw Does not fetch games/bomb Does not fetch games/lgeneral-data Bad plist games/linux-enemyterritory-jaymod Does not fetch games/xphotohunter Does not fetch graphics/gimpshop Fails to patch graphics/lightspark-devel Does not compile graphics/xmms-plazma Does not fetch graphics/py-cgkit Does not fetch, does not compile on ia64, powerpc, or sparc64 japanese/rxvt Does not fetch, fails to build with new utmpx japanese/epic4 Some distfiles do not fetch java/jde Does not fetch java/kaffe Does not fetch korean/gdick HTMLs from the Yahoo! Korea Dictionary cannot be parsed, other runtime problems korean/hanterm-xf86 Does not compile korean/stardict2-dict-kr Does not fetch lang/p5-JavaScript Does not fetch lang/TenDRA Website disappeared; last release 2006, Does not compile on recent FreeBSD-9 mail/freepops Does not build mail/itraxp Does not build misc/tellico Leaves file behind on deinstall net/gsambad Does not fetch net/nocatauth-gateway Uses a UID registered to another port net/nocatauth-server Uses a UID registered to another port net/libosip2 Does not fetch net/kmuddy Does not fetch net/netboot Does not build net-mgmt/jffnms Does not fetch net-p2p/frostwire Does not fetch net-p2p/azureus Does not fetch news/cleanscore Does not fetch news/nntpswitch Does not fetch news/p5-NewsLib Does not fetch russian/cyrproxy Does not fetch science/gerris Does not fetch security/opensaml Does not fetch sysutils/wmbattery Does not fetch sysutils/cpuburn No more public distfiles textproc/tei-guidelines-p4 Does not fetch textproc/tei-p4 Does not fetch textproc/py-hyperestraier Does not fetch textproc/tdtd.el Does not fetch textproc/tei-lite Does not fetch www/phpwiki13 Does not fetch www/p5-Apache-Scoreboard Depends on mod_perl www/p5-B-LexInfo Broken due the new mod_perl2 API www/phpwiki Does not fetch www/smb2www Apache13 is deprecated, migrate to 2.2.x+ now www/spip Checksum is changing daily www/monkey Does not fetch x11-toolkits/jdic Does not fetch x11-toolkits/py-kde Does not compile
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Mon Oct 17 00:03:07 2011 UTC (3 months, 3 weeks ago) by avilla
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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
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Sun Oct 9 02:47:49 2011 UTC (4 months ago) by dougb
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Remove ports maintainted by ports@ which have passed their EXPIRATION_DATE astro/gkrellsun Abandonware astro/xrmap No more distfiles audio/midimountain Abandonware audio/gkrellmss Abandonware audio/gnapster Abandonware databases/xbase No more public distfiles databases/xbsql No more public distfiles games/gtkabale No more public distfiles games/battleball No more public distfiles, does not compile on ia64 or sparc64 games/race No more public distfiles games/stvef-paks No more public distfiles games/stvef-server No more public distfiles games/tome No more public distfiles games/qkmj No more public distfiles games/oilwar No more public distfiles games/xbaby No more public distfiles games/xword Abandonware games/kslide No more public distfiles graphics/xmrm No more public distfiles, does not compile on amd64 or sparc64 graphics/giftrans Upstream disappeared and distfile is not available graphics/wildmagic BROKEN for more than 6 months, does not fetch irc/ircd-rusnet No more public distfiles irc/tkirc No more public distfiles korean/mizifont No more public distfiles lang/freetxl No more public distfiles math/nsc2ke No more public distfiles misc/mgp-mode.el No more public distfiles multimedia/p5-RIFF-Info No more public distfiles net/p5-Net-OpenDHT No more public distfiles net/mudix No more public distfiles net-im/newsbot No more public distfiles net-im/libicq2000 Abandonware net-im/gossip No longer maintain by upstream, use net-im/empathy instead net-im/ickle Abandonware net-mgmt/nipper BROKEN for more than 6 month, does not fetch net-p2p/mldonkey-serverspy No more public distfiles news/p5-Gateway No more public distfiles print/epsmerge No more public distfiles science/at No more public distfiles science/pyvox No more public distfiles security/p5-Email-Obfuscate No more public distfiles security/libparanoia No more public distfiles security/execwrap No more public distfiles
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Wed Sep 28 07:33:03 2011 UTC (4 months, 1 week ago) by wen
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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
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Sun Sep 18 02:47:50 2011 UTC (4 months, 3 weeks ago) by tota
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- 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/
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Sat Sep 17 06:55:27 2011 UTC (4 months, 3 weeks ago) by tota
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- 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/
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Tue Aug 2 06:31:28 2011 UTC (6 months, 1 week ago) by bapt
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Remove some expired ports 2011-08-01 audio/rio: Look like an abandonware, no more public distfile 2011-08-02 audio/ruby-musicextras: Upcoming ruby-gnome removes dependencies 2011-08-02 deskutils/sshmenu: Upcoming ruby-gnome removes dependencies 2011-08-02 japanese/gsuica: Upcoming ruby-gnome removes dependencies 2011-08-02 science/gave: Upcoming ruby-gnome removes dependencies 2011-08-02 x11-themes/gnome-art: Upcoming ruby-gnome removes dependencies 2011-08-02 x11-themes/gnome-splashscreen-manager: Upcoming ruby-gnome removes dependencies
Revision 1.219: download - view: text, markup, annotated - select for diffs
Thu Jul 28 09:56:33 2011 UTC (6 months, 2 weeks ago) by bf
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remove science/bblimage; attach science/pyvox to build; add an entry to MOVED PR: 158562
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Fri Jul 1 20:23:41 2011 UTC (7 months, 1 week ago) by stephen
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- 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)
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Wed Jun 29 08:18:06 2011 UTC (7 months, 1 week ago) by wen
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obspy.imaging provides tools for displaying features used in seismology. WWW: http://www.obspy.org/
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Wed Jun 29 08:13:17 2011 UTC (7 months, 1 week ago) by wen
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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/
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Sun Jun 12 16:18:59 2011 UTC (7 months, 4 weeks ago) by sunpoet
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- 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/
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Tue May 3 13:05:07 2011 UTC (9 months, 1 week ago) by bapt
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Another bunch of expired ports removal 2011-05-01 audio/albumart: Upstream disapear and distfile is no more available 2011-05-01 audio/aylet: Upstream disapear and distfile is no more available 2011-05-01 audio/cantus: Upstream disapear and distfile is no more available 2011-05-01 audio/xaylet: Upstream disapear and distfile is no more available 2011-05-01 science/oases: Upstream disapear and distfile is no more available 2011-05-01 shells/pash: Upstream disapear and distfile is no more available
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Mon Apr 18 22:25:34 2011 UTC (9 months, 3 weeks ago) by rene
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Remove most expired ports: 2011-04-17 cad/tclspice: has been broken for more than a year 2011-04-17 comms/hcfmdm: does not compile on 7.X or higher 2011-04-17 databases/mysqlcc: has been broken for almost a year 2011-04-17 devel/ruby-rjudy: does not compile on FreeBSD 7.x or newer 2011-04-17 devel/xfc: does not compile on FreeBSD 7.x or newer 2011-04-17 devel/lamson: has been broken for a half year 2011-04-17 devel/cocktail: does not build on FreeBSD 7.x or newer 2011-04-17 devel/djgpp-gcc: has been broken for half a year 2011-04-17 devel/gauche-sdl: has been broken for a year 2011-04-17 devel/gdb53-act: does not compile on FreeBSD 7.x and up 2011-04-17 editors/zed: does not compile on FreeBSD 7.x or newer 2011-04-17 games/aqbubble: does not compile on FreeBSD 7.x or newer 2011-04-17 graphics/libvisual-plugins: has been broken for 3 years 2011-04-17 japanese/roundcube: has been broken for almost a year 2011-04-17 japanese/tkstep80: does not compile on FreeBSD 7.x or newer 2011-04-17 lang/u++: has been broken for over a half year 2011-04-17 lang/pugs: has been broken for over a year 2011-04-17 lang/mozart: does not compile on FreeBSD 7.x or newer 2011-04-17 math/linalg: does not build on FreeBSD 7.x or newer 2011-04-17 math/R-cran-igraph: has been broken for over a half year 2011-04-17 misc/ftree: has been broken for over a half year 2011-04-17 multimedia/katchtv: has been broken for a half year 2011-04-17 multimedia/libomxil-bellagio: has been broken for almost a year 2011-04-17 multimedia/banshee-mirage: has been broken for over a half year 2011-04-17 net-p2p/trackerbt: has been broken for a half year 2011-04-17 net/cap: does not compile on FreeBSD 7.x or newer 2011-04-17 net/ggsd: does not compile on FreeBSD 7.x or newer 2011-04-17 net/b2bua: does not compile on FreeBSD 7.x or newer 2011-04-17 net/penguintv: has been broken for a half year 2011-04-17 news/openftd: has been broken for almost a year 2011-04-17 palm/romeo: does not compile on FreeBSD 7.x or newer 2011-04-17 science/pcp: does not compile on FreeBSD 7.x or newer 2011-04-17 science/elmer-fem: has been broken for over a year 2011-04-17 security/newpki-lib: does not compile on FreeBSD 7.x or newer 2011-04-17 security/newpki-server: does not compile on FreeBSD 7.x or newer 2011-04-17 security/xmlsec: does not compile on FreeBSD 7.x or newer 2011-04-17 security/f-protd: has been broken for over a year 2011-04-17 sysutils/xwlans: does not compile on FreeBSD 7.x or newer 2011-04-17 www/bk_edit: does not compile on FreeBSD 7.x and newer 2011-04-17 www/bricolage: has been broken for a half year 2011-04-17 x11-toolkits/gauche-gtk: has been broken for a year 2011-04-17 x11-toolkits/gambas2-gb-qt: has been broken for over a year 2011-04-17 x11-toolkits/php-gtk2: has been broken for over a half year 2011-04-17 x11-toolkits/p5-Tcl-Tk: has been broken for 2 year 2011-04-17 x11/metisse: has been broken for over a half year
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Fri Mar 25 12:08:20 2011 UTC (10 months, 2 weeks ago) by miwi
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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>
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Mon Mar 21 06:28:57 2011 UTC (10 months, 3 weeks ago) by wen
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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/
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Fri Mar 18 19:42:35 2011 UTC (10 months, 3 weeks ago) by swills
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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>
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Wed Mar 16 09:56:38 2011 UTC (10 months, 3 weeks ago) by wen
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- 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
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Wed Mar 16 08:46:36 2011 UTC (10 months, 3 weeks ago) by wen
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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/
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Mon Mar 14 14:09:29 2011 UTC (10 months, 4 weeks ago) by wen
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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/
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Mon Mar 14 14:05:40 2011 UTC (10 months, 4 weeks ago) by wen
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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/
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Mon Mar 14 13:08:04 2011 UTC (10 months, 4 weeks ago) by wen
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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/
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Mon Mar 14 13:04:03 2011 UTC (10 months, 4 weeks ago) by wen
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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/
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Thu Mar 10 06:15:55 2011 UTC (11 months ago) by wen
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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/
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Mon Mar 7 12:04:35 2011 UTC (11 months ago) by wen
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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
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Mon Mar 7 10:57:09 2011 UTC (11 months ago) by wen
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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
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Sun Feb 20 03:54:04 2011 UTC (11 months, 2 weeks ago) by wen
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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)
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Thu Jan 6 02:39:32 2011 UTC (13 months ago) by wen
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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>
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Wed Dec 29 08:50:40 2010 UTC (13 months, 1 week ago) by wen
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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/
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Sat Nov 13 21:41:03 2010 UTC (14 months, 3 weeks ago) by makc
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Connect py-biolccc
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Thu Sep 9 00:26:13 2010 UTC (17 months ago) by sahil
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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>
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Wed Sep 8 03:09:30 2010 UTC (17 months ago) by sahil
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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>
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Mon Aug 23 18:15:03 2010 UTC (17 months, 2 weeks ago) by makc
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Connect kst2
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Wed Jul 21 09:53:14 2010 UTC (18 months, 3 weeks ago) by ashish
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- Remove the port from 'science' category. PR: ports/146513 Approved by: pgj (mentor)
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Wed Jul 21 03:27:25 2010 UTC (18 months, 3 weeks ago) by ashish
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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)
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Tue Jun 29 01:22:15 2010 UTC (19 months, 1 week ago) by wen
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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
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Thu May 20 14:21:43 2010 UTC (20 months, 3 weeks ago) by lwhsu
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Add netcdf3-ftn , netCDF (network Common Data Form), with Fortran support. Submitted by: Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net>
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Thu May 20 09:43:14 2010 UTC (20 months, 3 weeks ago) by wen
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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>
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Wed May 19 05:31:44 2010 UTC (20 months, 3 weeks ago) by wen
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PyNN(pronounced 'pine') is a simulator-independent language for building neuronal network models. WWW: http://neuralensemble.org/trac/PyNN
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Wed May 19 00:14:14 2010 UTC (20 months, 3 weeks ago) by wen
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- Remove pyNN and re-add as pynn Reviewed by: danfe@
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Tue May 18 08:14:12 2010 UTC (20 months, 3 weeks ago) by wen
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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>
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Wed May 12 13:25:37 2010 UTC (21 months ago) by beat
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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@
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Fri Apr 2 15:36:25 2010 UTC (22 months, 1 week ago) by miwi
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Perl modules for molecular chemistry WWW: http://search.cpan.org/dist/PerlMol/ PR: ports/145143 Submitted by: Steve Wills <steve at mouf.net>
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Fri Apr 2 15:35:47 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:35:23 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:34:39 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:33:52 2010 UTC (22 months, 1 week ago) by miwi
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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
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Fri Apr 2 15:33:24 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:32:52 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:32:24 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:32:03 2010 UTC (22 months, 1 week ago) by miwi
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Explicit chemical reactions WWW: http://search.cpan.org/dist/Chemistry-Raction/ PR: ports/145143 Submitted by: Steve Wills <steve at mouf.net>
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Fri Apr 2 15:31:33 2010 UTC (22 months, 1 week ago) by miwi
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Match molecule by formula WWW: http://search.cpan.org/dist/Chemistry-ForumulaPattern/ PR: ports/145143 Submitted by: Steve Wills <steve at mouf.net>
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Fri Apr 2 15:29:58 2010 UTC (22 months, 1 week ago) by miwi
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Select atoms in macromolecule WWW: http://search.cpan.org/dist/Chemistry-MidasPattern/ PR: ports/145143 Submitted by: Steve Wills <steve at mouf.net>
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Fri Apr 2 15:29:35 2010 UTC (22 months, 1 week ago) by miwi
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Perl molecular awk interpreter WWW: http://search.cpan.org/dist/Chemistry-Mok/ PR: ports/145143 Submitted by: Steve Wills <steve at mouf.net>
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Fri Apr 2 15:28:41 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:28:03 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:27:21 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:26:37 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:25:56 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:25:11 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Fri Apr 2 15:24:14 2010 UTC (22 months, 1 week ago) by miwi
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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>
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Sat Feb 13 11:21:53 2010 UTC (23 months, 3 weeks ago) by miwi
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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
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Mon Jan 25 00:27:09 2010 UTC (2 years ago) by wen
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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>
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Mon Jan 18 06:46:39 2010 UTC (2 years ago) by pgollucci
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- 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
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Fri Jan 15 07:20:43 2010 UTC (2 years ago) by wen
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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/
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Wed Jan 13 19:26:59 2010 UTC (2 years ago) by amdmi3
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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>
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Sat Jan 9 12:19:57 2010 UTC (2 years, 1 month ago) by wen
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py-DendroPy is a python library for phylogenetic scripting, simulation, data processing and manipulation. WWW: http://packages.python.org/DendroPy/
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Sun Jan 3 05:02:13 2010 UTC (2 years, 1 month ago) by pgj
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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>
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Sat Jan 2 02:53:59 2010 UTC (2 years, 1 month ago) by wen
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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>
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Thu Nov 19 13:44:37 2009 UTC (2 years, 2 months ago) by wen
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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/
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Wed Oct 7 11:10:20 2009 UTC (2 years, 4 months ago) by wen
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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)
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Sat Sep 19 11:02:46 2009 UTC (2 years, 4 months ago) by miwi
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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>
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Sat Sep 19 09:53:55 2009 UTC (2 years, 4 months ago) by miwi
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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>
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Fri Aug 14 20:02:07 2009 UTC (2 years, 5 months ago) by miwi
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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>
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Tue Aug 11 05:14:52 2009 UTC (2 years, 6 months ago) by maho
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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@
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Mon Jul 13 14:07:16 2009 UTC (2 years, 6 months ago) by lwhsu
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Add py-h5py 1.2.0, a general-purpose Python interface to the HDF5 library. PR: ports/136096 Submitted by: TAOKA Fumiyoshi
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Mon Jun 22 15:55:10 2009 UTC (2 years, 7 months ago) by amdmi3
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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>
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Sat Jun 13 20:02:44 2009 UTC (2 years, 7 months ago) by erwin
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Remove science/openfoam as it has been marked BROKEN for over 5 months.
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Sat Jun 13 20:00:38 2009 UTC (2 years, 7 months ago) by erwin
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Remove science/elmerfront as it has been marked BROKEN over 3 months ago.
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Fri May 22 22:16:45 2009 UTC (2 years, 8 months ago) by amdmi3
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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>
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Sun May 17 13:00:50 2009 UTC (2 years, 8 months ago) by miwi
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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>
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Sun May 17 12:51:49 2009 UTC (2 years, 8 months ago) by miwi
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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>
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Sat May 16 23:29:15 2009 UTC (2 years, 8 months ago) by miwi
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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>
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Thu Apr 23 17:02:20 2009 UTC (2 years, 9 months ago) by miwi
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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>
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Sat Apr 11 09:58:38 2009 UTC (2 years, 10 months ago) by miwi
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2009-03-22 science/oof: Broken with GCC 4.2 and beyond 2009-04-06 www/raqdevil: Master site gone, distfiles not fetchable
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Sun Mar 22 22:09:27 2009 UTC (2 years, 10 months ago) by pav
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- 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)
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Sun Mar 22 15:18:46 2009 UTC (2 years, 10 months ago) by miwi
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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>
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Mon Mar 16 06:07:37 2009 UTC (2 years, 10 months ago) by miwi
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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>
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Sat Feb 28 19:58:19 2009 UTC (2 years, 11 months ago) by miwi
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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
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Mon Feb 23 20:18:45 2009 UTC (2 years, 11 months ago) by miwi
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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
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Fri Jan 16 00:09:20 2009 UTC (3 years ago) by miwi
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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>
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Tue Jan 13 18:17:29 2009 UTC (3 years ago) by pav
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- Remove science/gchempaint, it has been integrated into science/gchemutils
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Thu Jan 1 12:20:36 2009 UTC (3 years, 1 month ago) by chinsan
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- Attach science/netcdf4
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Mon Nov 24 05:35:04 2008 UTC (3 years, 2 months ago) by miwi
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- Connect hdf5-18
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Sat Sep 27 18:52:29 2008 UTC (3 years, 4 months ago) by miwi
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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>
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Fri Sep 26 23:21:54 2008 UTC (3 years, 4 months ago) by miwi
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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>
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Wed Aug 20 22:35:40 2008 UTC (3 years, 5 months ago) by maho
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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/
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Sun Jul 20 21:19:13 2008 UTC (3 years, 6 months ago) by beech
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- 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>
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Sat Jul 19 14:00:33 2008 UTC (3 years, 6 months ago) by miwi
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This port installs python bindings for openbabel. WWW: http://openbabel.sourceforge.net PR: ports/125768 Submitted by: Max Brazhnikov <makc at issp.ac.ru>
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Tue Jun 3 09:41:36 2008 UTC (3 years, 8 months ago) by miwi
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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
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Sat May 24 06:51:36 2008 UTC (3 years, 8 months ago) by edwin
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[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>
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Sat May 17 23:04:44 2008 UTC (3 years, 8 months ago) by miwi
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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>
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Thu May 1 21:04:57 2008 UTC (3 years, 9 months ago) by hq
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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>
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Mon Feb 25 12:56:17 2008 UTC (3 years, 11 months ago) by tabthorpe
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DTI visualization software from Stanford. WWW: http://graphics.stanford.edu/projects/dti/ PR: ports/120129 Submitted by: Jason W. Bacon <jwbacon at tds.net>
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Tue Aug 14 13:29:49 2007 UTC (4 years, 5 months ago) by itetcu
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Move speedcrunch from science to math. No repo is requiered since there's no history to preserve. Requsted by: danfe@
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Tue Aug 14 11:40:35 2007 UTC (4 years, 5 months ago) by itetcu
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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>
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Sat Jul 28 07:10:53 2007 UTC (4 years, 6 months ago) by rafan
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- science/liblr is moved to science/liblinear (project renamed)
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Sun Jun 17 21:04:52 2007 UTC (4 years, 7 months ago) by thierry
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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/>
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Sun May 27 14:05:54 2007 UTC (4 years, 8 months ago) by rafan
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Add liblr-1.0, a library for large regularized logistic regression.
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Thu May 24 22:18:10 2007 UTC (4 years, 8 months ago) by pav
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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/
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Thu May 24 22:16:02 2007 UTC (4 years, 8 months ago) by pav
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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
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Mon Apr 30 13:44:51 2007 UTC (4 years, 9 months ago) by miwi
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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>
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Sat Apr 28 10:58:00 2007 UTC (4 years, 9 months ago) by miwi
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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
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Tue Apr 10 17:40:50 2007 UTC (4 years, 10 months ago) by miwi
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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
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Sun Apr 1 09:00:23 2007 UTC (4 years, 10 months ago) by thierry
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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.
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Tue Mar 13 00:39:57 2007 UTC (4 years, 11 months ago) by maho
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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. :)
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Fri Jan 5 18:42:54 2007 UTC (5 years, 1 month ago) by miwi
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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
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Fri Dec 29 07:41:43 2006 UTC (5 years, 1 month ago) by maho
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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.
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Fri Dec 22 03:38:47 2006 UTC (5 years, 1 month ago) by ijliao
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add linsmith 0.99.3 Smith charting program
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Wed Nov 15 05:54:59 2006 UTC (5 years, 2 months ago) by rafan
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- Reflect repocopy ofscience/py-scipy -> science/py-scipy03
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Mon Oct 2 08:59:12 2006 UTC (5 years, 4 months ago) by clsung
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Add g3data 1.5.0, utility for extracting data from graphs. PR: ports/103397 Submitted by: trasz <trasz at pin.if.uz.zgora.pl>
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Thu Sep 28 19:17:56 2006 UTC (5 years, 4 months ago) by dinoex
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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
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Wed Sep 27 19:59:45 2006 UTC (5 years, 4 months ago) by dinoex
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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
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Sun Sep 24 23:09:25 2006 UTC (5 years, 4 months ago) by thierry
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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).
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Thu Sep 7 01:24:33 2006 UTC (5 years, 5 months ago) by alepulver
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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
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Sat Aug 12 22:34:57 2006 UTC (5 years, 6 months ago) by pav
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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>
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Thu Aug 3 07:29:02 2006 UTC (5 years, 6 months ago) by clsung
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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>
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Tue Aug 1 15:07:54 2006 UTC (5 years, 6 months ago) by clsung
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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>
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Fri Jul 28 03:38:03 2006 UTC (5 years, 6 months ago) by clsung
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Add crf++ 0.42, yet Another CRF toolkit. PR: ports/100909 Submitted by: Cheng-Lung Sung <clsung at FreeBSD.org>
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Fri Jul 28 03:36:24 2006 UTC (5 years, 6 months ago) by clsung
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Add ghmm 0.7.0a, general Hidden Markov Model Library in C. PR: ports/100886 Submitted by: Cheng-Lung Sung <clsung at FreeBSD.org>
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Fri Jul 28 03:34:54 2006 UTC (5 years, 6 months ago) by clsung
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Add pcp 2.2, machine learning program for pattern classification. PR: ports/100798 Submitted by: Cheng-Lung Sung <clsung at FreeBSD.org>
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Wed Jul 19 19:58:28 2006 UTC (5 years, 6 months ago) by rafan
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Add xmds , XMDS is a code generator that integrates equations;. PR: ports/100419 Submitted by: EelVex
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Mon Jul 3 07:30:44 2006 UTC (5 years, 7 months ago) by maho
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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.
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Mon Jun 12 18:58:44 2006 UTC (5 years, 8 months ago) by itetcu
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Objecto Oriented Finite Element Analysis of Real Material Microstructures __________________ OOF is designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. It is composed of two cooperating parts: ppm2oof and oof. ppm2oof reads images in the ppm (Portable Pixel Map) format and assigns material properties to features in the image. oof conducts virtual experiments on the data structures created by ppm2oof to determine the macroscopic properties of the microstructure. Currently, the programs calculate stresses and strains, but someday we hope to include thermal, electric, and magnetic field calculations. Check the Homepage for online manuals and new versions WWW: http://www.ctcms.nist.gov/oof/ PR: ports/98601 Submitted by: Pedro F. Giffuni
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Sun Jun 11 08:41:34 2006 UTC (5 years, 8 months ago) by pav
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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>
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Sun Apr 30 12:05:08 2006 UTC (5 years, 9 months ago) by thierry
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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
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Mon Apr 24 19:55:42 2006 UTC (5 years, 9 months ago) by thierry
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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>
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Mon Apr 24 19:54:49 2006 UTC (5 years, 9 months ago) by thierry
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ElmerFront - the Graphical User Interface. ElmerFront is a tool for initializing the computational process in Elmer. It communicates with external software producing geometrical data, i.e., CAD files and computational meshes. ElmerFront generates its own finite element meshes, allows the user to build mathematical models graphically, and finally produces input data for ElmerSolver. Submitted by: Pedro F. Giffuni <giffunip@asme.org>
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Mon Apr 24 19:54:02 2006 UTC (5 years, 9 months ago) by thierry
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ElmerSolver - the Solution of Partial Differential Equations. ElmerSolver is thus an independent module that processes the computational mesh and the model input file containing references to the selected equations and model parameters. ElmerSolver makes the equations into a discrete form, handles coupled systems, non-linearities and time-dependences, and provides output data for visualization. Submitted by: Pedro F. Giffuni <giffunip@asme.org>
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Mon Apr 24 19:53:14 2006 UTC (5 years, 9 months ago) by thierry
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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>
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Mon Apr 24 19:50:53 2006 UTC (5 years, 9 months ago) by thierry
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MATC language library used by Elmer FEM package. Submitted by: Pedro F. Giffuni <giffunip@asme.org>
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Mon Apr 24 19:49:57 2006 UTC (5 years, 9 months ago) by thierry
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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>
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Mon Apr 24 19:48:57 2006 UTC (5 years, 9 months ago) by thierry
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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>
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Mon Apr 24 19:46:15 2006 UTC (5 years, 9 months ago) by thierry
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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>
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Sun Mar 19 20:51:14 2006 UTC (5 years, 10 months ago) by thierry
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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
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Wed Mar 15 10:38:00 2006 UTC (5 years, 10 months ago) by garga
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Add fasthenry , a multipole-accelerated inductance analysis program. PR: ports/93969 Submitted by: Pedro Giffuni <giffunip@asme.org>
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Wed Mar 15 10:36:29 2006 UTC (5 years, 10 months ago) by garga
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Add fastcap , a three-dimensional capacitance extraction program. PR: ports/93968 Submitted by: Pedro Giffuni <giffunip@asme.org>
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Sun Feb 12 15:30:03 2006 UTC (5 years, 11 months ago) by thierry
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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>
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Wed Feb 8 11:55:08 2006 UTC (6 years ago) by vd
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Remove expired port science/glens Approved by: garga (mentor)
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Mon Jan 30 22:19:20 2006 UTC (6 years ago) by thierry
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Repocopy math/netcdf to science/netcdf, along with cdf, hdf and hdf5. PR: 92497 Submitted by: /me Repocopied by: marcus
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Sat Jan 28 20:40:56 2006 UTC (6 years ago) by thierry
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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>.
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Wed Jan 25 17:34:35 2006 UTC (6 years ago) by vd
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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)
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Sun Jan 22 10:13:05 2006 UTC (6 years ago) by thierry
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The OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options. WWW: http://www.opencfd.co.uk/openfoam/index.html PR: ports/91886 Submitted by: thierry
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Sat Dec 10 21:45:28 2005 UTC (6 years, 2 months ago) by thierry
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Add V_Sim, a program to visualize atomic structures such as crystals, grain boundaries and so on.
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Mon Oct 31 18:48:23 2005 UTC (6 years, 3 months ago) by thierry
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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/
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Sun Sep 25 12:45:46 2005 UTC (6 years, 4 months ago) by thierry
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Add gerris 0.6.0, a scientific CFD simulator. Gerris is an Open Source Free Software library for the solution of partial differential equations describing fluid flow. Gerris is supported by NIWA (National Institute of Water and Atmospheric research) and by the Marsden Fund of the Royal Society of New Zealand. The code is written entirely in C and uses both the GLib Library and the GTS Library for geometrical functions and object-oriented programming. PR: 86297 Submitted by: Oliver Dunkl <odunkl (at) gmx.net>
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Mon Jul 18 16:22:48 2005 UTC (6 years, 6 months ago) by pav
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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>
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Tue Jun 14 05:41:20 2005 UTC (6 years, 7 months ago) by anholt
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New port: ParaView is a powerful scientific visualization application, designed with the need to visualize large data sets in mind.
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Sun May 22 15:50:05 2005 UTC (6 years, 8 months ago) by pav
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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>
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Sun May 15 21:44:02 2005 UTC (6 years, 8 months ago) by thierry
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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>
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Sun Mar 27 03:20:32 2005 UTC (6 years, 10 months ago) by kris
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Remove mxp Forgotten by: maho Approved by: portmgr (self)
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Sat Mar 19 10:54:36 2005 UTC (6 years, 10 months ago) by maho
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Add mxp (Mandelbrot explorer). Mxp is an X application for computing and exploring
Mandelbrot sets. Features of mxp include:
- zoom and un-zoom
- dynamic resizing of drawing window
- setup save/load
- asynchronous image generation (buttons always work)
- GIF output
- animation
- nine color schemes
- color rotation
- color change options
- detailed statistics
WWW: http://www.ibiblio.org/pub/Linux/apps/math/fractals/
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Thu Mar 17 19:30:00 2005 UTC (6 years, 10 months ago) by glewis
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. 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/"
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Thu Feb 24 20:26:31 2005 UTC (6 years, 11 months ago) by sem
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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>
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Thu Feb 24 20:14:59 2005 UTC (6 years, 11 months ago) by sem
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science/cdcl -> update to 5.3 and use gtk by default science/cdcl-gtk -> delete science/ruby-dcl -> update to 1.5 and use gtk by default science/ruby-dcl-gtk -> delete science/ruby-gphys -> update to 0.3.5 and fix dependency science/gave -> update to 1.1.3 and fix dependency PR: ports/76853 Submitted by: maintainer
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Fri Feb 18 14:17:20 2005 UTC (6 years, 11 months ago) by pav
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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>
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Thu Feb 10 08:44:55 2005 UTC (7 years ago) by pav
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- Move emulators/qcl -> science/qcl on maintainer's request. Repocopy by: marcus
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Sat Jan 22 15:01:02 2005 UTC (7 years ago) by thierry
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Add buddy 2.4, a Binary Decision Diagram library. PR: 71221 Submitted by: Leland Wang
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Fri Jan 21 19:03:52 2005 UTC (7 years ago) by hq
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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>
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Fri Jan 14 21:52:08 2005 UTC (7 years ago) by glewis
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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)
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Wed Dec 29 20:46:47 2004 UTC (7 years, 1 month ago) by thierry
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Add isaac-cfd 4.2, Integrated Solution Algorithm for Arbitrary Configuration. PR: 75529 Submitted by: Pedro F. Giffuni
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Tue Dec 28 23:30:00 2004 UTC (7 years, 1 month ago) by pav
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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>
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Sun Dec 26 23:08:06 2004 UTC (7 years, 1 month ago) by thierry
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Add x11iraf 1.3.1, which provides graphical tools to work with IRAF. PR: 70816 Submitted by: David Syphers.
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Sat Dec 11 04:52:40 2004 UTC (7 years, 2 months ago) by sem
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Slave port to science/libsvm PR: ports/73981 Submitted by: Rong-En Fan <rafan(at)infor.org>
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Sat Nov 27 21:38:03 2004 UTC (7 years, 2 months ago) by pav
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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
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Mon Nov 15 22:53:44 2004 UTC (7 years, 2 months ago) by pav
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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>
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Mon Nov 15 22:18:08 2004 UTC (7 years, 2 months ago) by thierry
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Add getdp 1.0.0, a rather general finite element solver using mixed finite elements. Suggested by: Pedro F. Giffuni.
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Tue Oct 19 01:36:11 2004 UTC (7 years, 3 months ago) by maho
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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>
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Thu Aug 26 08:37:09 2004 UTC (7 years, 5 months ago) by ijliao
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add py-scipy 0.3 Scientific tools for Python
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Sat Aug 21 16:34:56 2004 UTC (7 years, 5 months ago) by pav
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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>
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Sat Aug 14 08:45:41 2004 UTC (7 years, 5 months ago) by maho
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Add abinit, calculates total energy, charge density and electronic structure of systems.
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Fri Apr 30 15:44:32 2004 UTC (7 years, 9 months ago) by markus
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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
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Fri Apr 2 07:29:38 2004 UTC (7 years, 10 months ago) by kris
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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
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Tue Mar 23 23:34:29 2004 UTC (7 years, 10 months ago) by thierry
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Add ovt 2.3, the Orbit Visualization Tool. PR: 57860 Submitted by: Mykola Khotyaintsev <ko@nest.irfu.se>
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Sat Mar 20 04:50:45 2004 UTC (7 years, 10 months ago) by maho
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A Density functional software. This software has a unique design based upon the DFT++ algebraic framework introduced in Computer Physics Communications 128, 1-45 (June 2000). This framework allows us to transparently separate the computational guts (cache optimization, parallelization, etc.) from the introduction of new representations (plane waves, wavelets) and new physics (new density functionals, linear response theory, dielectric solutions). The software is fully cache and register optimized, and runs in serial, threaded, MPI and mixed threaded-MPI parallel environments.
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Fri Mar 19 09:32:49 2004 UTC (7 years, 10 months ago) by maho
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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.
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Sun Mar 14 16:52:34 2004 UTC (7 years, 10 months ago) by pav
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Add gave, a gtk+ based grid data analyser and viewer written in Ruby. PR: ports/64249 Submitted by: Shin'ya Murakami <murakami@ahs.scitec.kobe-u.ac.jp>
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Sun Mar 14 16:34:51 2004 UTC (7 years, 10 months ago) by pav
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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>
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Fri Feb 27 23:54:13 2004 UTC (7 years, 11 months ago) by pav
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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>
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Fri Feb 27 22:44:17 2004 UTC (7 years, 11 months ago) by pav
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Add cdcl-gtk, a slave port for science/cdcl with enabled Gtk support. PR: ports/62872 Submitted by: Shin'ya Murakami <murashin@edamame.summing.com>
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Fri Feb 27 22:35:22 2004 UTC (7 years, 11 months ago) by pav
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Add cdcl, a scientific graphic library for geoscience PR: ports/62871 Submitted by: Shin'ya Murakami <murashin@edamame.summing.com>
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Wed Feb 25 22:55:01 2004 UTC (7 years, 11 months ago) by pav
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Unhook hdf* ports in graphics, hook them in science.
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Sun Feb 1 03:09:51 2004 UTC (8 years ago) by pav
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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>
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Sat Nov 8 09:08:52 2003 UTC (8 years, 3 months ago) by glewis
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. Welcome felt to the science category. PR: 58178 Submitted by: Pedro F. Giffuni <giffunip@yahoo.com>
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Fri Oct 24 04:19:28 2003 UTC (8 years, 3 months ago) by ijliao
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add kmovisto 0.5.1 A real 3-D molecule viewer
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Sat Oct 4 02:30:06 2003 UTC (8 years, 4 months ago) by maho
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Remove # chemtool-devel is now real developer version of chemtool.
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Mon Sep 8 12:45:59 2003 UTC (8 years, 5 months ago) by edwin
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New port: science/at Acoustic ToolBox The Acoustic ToolBox includes four acoustic models: BELLHOP: A beam/ray trace code KRAKEN: A normal mode code SCOOTER: A finite element FFP code SPARC: A time domain FFP code A common input structure has been used throughout so that only minor modifications are needed to switch from one program to another. All the models produce shade files which can be processed using a common set of plotting routines to plot transmission loss vs. range or vs. range and depth. These plotting routines are contained in the GLOBAL directory. PR: ports/42378 Submitted by: Heiner Strauss <heiner@bilch.com>
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Thu Jul 24 09:50:24 2003 UTC (8 years, 6 months ago) by maho
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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).
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Tue Jul 22 21:34:51 2003 UTC (8 years, 6 months ago) by kris
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Comment out chemtool-devel, which provides a duplicate chemtool-1.6 version since the upgrade of chemtool. Pointy hat to: maho
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Sat May 10 01:29:10 2003 UTC (8 years, 9 months ago) by maho
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Added new port chemtool-devel. Chemtool is a nice drawing tool for chemist, however, it has not been released almost 1 year. So I added developer version as -devel. Have fun!
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Sun May 4 02:33:51 2003 UTC (8 years, 9 months ago) by maho
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Add new port science/ghemical a computational chemistry software package
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Tue Apr 8 00:09:55 2003 UTC (8 years, 10 months ago) by marcus
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Add gchempaint, a 2D chemical structure editor for GNOME 2. PR: 50539 Submitted by: Pav Lucistnik <pav@oook.cz>
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Tue Apr 8 00:04:57 2003 UTC (8 years, 10 months ago) by marcus
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Add gchemutils a set of C++ class and GTK+-2 widgets related to chemistry. PR: 50538 Submitted by: Pav Lucistnik <pav@oook.cz>
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Fri Apr 4 10:22:54 2003 UTC (8 years, 10 months ago) by ijliao
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add mpb 1.4.2 MIT Photonic-Bands
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Fri Apr 4 07:28:22 2003 UTC (8 years, 10 months ago) by ijliao
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add libctl 2.2 Control Language Library
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Sun Jan 5 17:04:59 2003 UTC (9 years, 1 month ago) by ijliao
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add openbabel 1.100.0 Chemistry file translation program
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Tue Oct 15 10:02:15 2002 UTC (9 years, 3 months ago) by ijliao
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add xloops-ginac 0.1.3 A program calculating Feynman diagrams
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Mon Oct 14 20:11:16 2002 UTC (9 years, 3 months ago) by ijliao
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add flounder 0.32a A quick way to visualize regularly spaced 4D data
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Mon Sep 16 09:26:18 2002 UTC (9 years, 4 months ago) by ijliao
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add mmtk 2.2 An Open Source program library for molecular simulation applications PR: 42332 Submitted by: Glenn Johnson <glennpj@charter.net>
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Thu Aug 8 08:39:29 2002 UTC (9 years, 6 months ago) by ijliao
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add glens 0.3 OpenGL gravitational lens simulator
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Mon Jul 22 06:52:23 2002 UTC (9 years, 6 months ago) by ijliao
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add bblimage 0.66 A set of software tools for medical image processing
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Tue Jul 16 06:53:47 2002 UTC (9 years, 6 months ago) by ijliao
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add mpqc-mpich PR: 40631 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
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Tue May 28 03:31:27 2002 UTC (9 years, 8 months ago) by ijliao
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add oases 2.2 Ocean Acoustics and Seismic Exploration Synthesis PR: 38548 Submitted by: Heiner Strau? <heiner@bilch.com>
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Tue May 14 03:59:00 2002 UTC (9 years, 9 months ago) by ijliao
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add euler 1.60.4 A program computes with real and complex numbers and matrices
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Sat Mar 9 10:58:52 2002 UTC (9 years, 11 months ago) by ijliao
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add mayavi 1.1 The MayaVi Data Visualizer
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Tue Mar 5 03:36:06 2002 UTC (9 years, 11 months ago) by ijliao
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add gdis 0.73.3 Display and manipulation of isolated molecules and periodic systems
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Fri Feb 8 06:15:14 2002 UTC (10 years ago) by petef
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Add p5-Chemistry-Elements 0.91, perl extension for working with Chemical Elements. PR: 33412 Submitted by: Seamus Venasse <svenasse@polaris.ca>
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Wed Jan 9 14:50:51 2002 UTC (10 years, 1 month ago) by ijliao
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add vis5d+ 1.2.1 An OpenGL-based volumetric visualization program for scientific datasets
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Wed Dec 19 03:44:59 2001 UTC (10 years, 1 month ago) by petef
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Add libsvm 2.33, a library for Support Vector Machines. PR: 32997 Submitted by: Chia-Hsing Yu <davidyu@oio.cx>
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Fri Sep 21 05:56:36 2001 UTC (10 years, 4 months ago) by knu
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Sort entries.
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Wed Sep 12 16:36:24 2001 UTC (10 years, 5 months ago) by sada
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New port: xmakemol - a motif molecule viewer program PR: ports/27981 Submitted by: Chi Zhang <chizhang@midway.uchicago.edu>
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Mon Jun 11 03:27:00 2001 UTC (10 years, 8 months ago) by will
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Add mpqc 1.2.5, the massively parallel quantum computing library and program. PR: 26908 Submitted by: batman <batman@udel.edu>
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Tue May 8 00:03:05 2001 UTC (10 years, 9 months ago) by will
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Fix broken ordering and remove sample directory.
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Tue May 8 00:02:21 2001 UTC (10 years, 9 months ago) by will
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Add clhep 1.6.0.0, an object-oriented toolkit for particle physics applications by CERN.
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Fri Mar 30 19:22:54 2001 UTC (10 years, 10 months ago) by ijliao
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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 ?
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Sat Mar 24 21:40:17 2001 UTC (10 years, 10 months ago) by asami
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Add new categories science and ukrainian.