User:Jjmcd/Drafts/F11 Engineering and Scientific

Chemistry

gabedit

gabedit is a gui for a number of computational chemistry packages. Highlights of version 2.1.17 include:

• full undo/redo for geometry changes
• full control over displayed bonds
• support for reading connectivities from gabedit, hin, pdb, mol2 and mol files
• molecular dynamics conformational searches using MM potential (Amber 99) and Semi-Empirical method (from Open Mopac or PCGamess)
• migration from GDK drawing functions to Cairo
• geometry and plots can be exported to eps, ps, pdf or svg formats

For complete details see the upstream changelog at: http://sites.google.com/site/allouchear/Home/gabedit/download/changelog

gnome-chemistry-utils

A set of chemical utilities

 Old Version: 0.10.0 -> New Version: 0.10.3

Project site: (http://www.nongnu.org/gchemutils/)

gromacs

GROMACS binaries

 Old Version: 4.0 -> New Version: 4.0.4

Project site: (http://www.gromacs.org)

gromacs-mpi

GROMACS MPI binaries

 Old Version: 4.0 -> New Version: 4.0.4

Project site: (http://www.gromacs.org)

openbabel

Chemistry software file format converter

 Old Version: 2.2.0 -> New Version: 2.2.1

Project site: (http://openbabel.org/)

Mathematics

Macaulay2

System for algebraic geometry and commutative algebra

 Old Version: 1.1 -> New Version: 1.2

Project site: (http://www.math.uiuc.edu/Macaulay2/)

atlas

Automatically Tuned Linear Algebra Software

 Old Version: 3.6.0 -> New Version: 

Project site: (http://math-atlas.sourceforge.net/)

galculator

GTK 2 based scientific calculator

 Old Version: 1.3.1 -> New Version: 1.3.4

Project site: (http://galculator.sourceforge.net/)

ginac

C++ library for symbolic calculations

 Old Version: 1.4.3 -> New Version: 1.4.4

Project site: (http://www.ginac.de/)

maxima

Symbolic Computation Program

 Old Version: 5.16.3 -> New Version: 5.17.1

Project site: (http://maxima.sourceforge.net/)

maxima-gui

Tcl/Tk GUI interface for maxima

 Old Version: 5.16.3 -> New Version: 5.17.1

Project site: (http://maxima.sourceforge.net/)

octave

A high-level language for numerical computations

 Old Version: 3.0.2 -> New Version: 3.0.3

Project site: (http://www.octave.org)

numpy

A fast multidimensional array facility for Python

 Old Version: 1.2.0 -> New Version: 1.2.1

Project site: (http://numeric.scipy.org/)

seaview

Graphical multiple sequence alignment editor

 Old Version: 2.4 -> New Version: 4.0

Project site: (http://pbil.univ-lyon1.fr/software/seaview.html)

speedcrunch

A fast power user calculator for KDE

 Old Version: 0.9 -> New Version: 0.10

Project site: (http://speedcrunch.digitalfanatics.org)

wxMaxima

Graphical user interface for Maxima

 Old Version: 0.7.5 -> New Version: 0.7.6

Project site: (http://wxmaxima.sourceforge.net/)

Statistics

R

A language for data analysis and graphics

 Old Version: 2.8.0 -> New Version: 2.8.1

Project site: (http://www.r-project.org)

Plotting/Visualization

gnuplot

A program for plotting mathematical expressions and data

 Old Version: 4.2.3 -> New Version: 4.2.4

Project site: (http://www.gnuplot.info/)

GMT

Generic Mapping Tools

 Old Version: 4.3.1 -> New Version: 4.4.0

Project site: (http://gmt.soest.hawaii.edu/)

GMT-coastlines-all

All coastline data for GMT

 Old Version: 1.9 -> New Version: 1.10

Project site: (http://gmt.soest.hawaii.edu/)

GMT-coastlines-full

Full resolution coastline data for GMT

 Old Version: 1.9 -> New Version: 1.10

Project site: (http://gmt.soest.hawaii.edu/)

GMT-coastlines-high

High resolution coastline data for GMT

 Old Version: 1.9 -> New Version: 1.10

Project site: (http://gmt.soest.hawaii.edu/)

GMT-doc

Documentation for Generic Mapping Tools

 Old Version: 4.3.1 -> New Version: 4.4.0

Project site: (http://gmt.soest.hawaii.edu/)

gtkwave

Waveform Viewer

 Old Version: 3.1.13 -> New Version: 3.2.0

Project site: (http://home.nc.rr.com/gtkwave/)

veusz

GUI scientific plotting package

 Old Version: 1.1 -> New Version: 1.2.1

Project site: (http://home.gna.org/veusz/)

Scientific Publishing

TeXmacs

Structured wysiwyg scientific text editor

 Old Version: 1.0.7 -> New Version: 1.0.7.1

Project site: (http://www.texmacs.org)

stix-fonts-integrals

STIX scientific and engineering fonts, additional integral glyphs

 Old Version: 0.9 -> New Version: 

Project site: (http://www.stixfonts.org/)

stix-fonts-pua

STIX scientific and engineering fonts, PUA glyphs

 Old Version: 0.9 -> New Version: 

Project site: (http://www.stixfonts.org/)

stix-fonts-sizes

STIX scientific and engineering fonts, additional glyph sizes

 Old Version: 0.9 -> New Version: 

Project site: (http://www.stixfonts.org/)

stix-fonts-variants

STIX scientific and engineering fonts, additional glyph variants

 Old Version: 0.9 -> New Version: 

Project site: (http://www.stixfonts.org/)

Biology

perl-bioperl

Perl tools for computational molecular biology

 Old Version: 1.5.2_102 -> New Version: 1.6.0

Project site: (http://www.bioperl.org/)

python-biopython

Python tools for computational molecular biology

 Old Version: 1.48 -> New Version: 1.49

Project site: (http://www.biopython.org/)

Finite Element Analysis

freefem++

freefem++ is a finite element analysis package which has been updated to 3.0.

Highlights:

• complete change of the graphical interface (freefem++ replaced freefem++-nw)
• added medit (visualization software by P. Frey) inside freefem++ under the name ffmedit
• the IDE version is gone until Antoine Le Hyaric makes a good one see: http://www.ann.jussieu.fr/~lehyaric/ffcs
• introduced client-server architecture freefem++ <-> ffglut
• ffglut visualizer using glut library

Full upstream changelog is here: http://www.freefem.org/ff++/ftp/INNOVATION

Data Manipulation

hdf

A general purpose library and file format for storing scientific data

 Old Version: 4.2r3 -> New Version: 4.2r4

Project site: (http://hdfgroup.org/products/hdf4/index.html)

hdf5

A general purpose library and file format for storing scientific data

 Old Version: 1.8.1 -> New Version: 1.8.2

Project site: (http://www.hdfgroup.org/HDF5/)

rrdtool

Round Robin Database Tool to store and display time-series data

 Old Version: 1.3.4 -> New Version: 1.3.6

Project site: (http://oss.oetiker.ch/rrdtool/)

Earth Sciences

wgrib2

Manipulate, inventory and decode GRIB2 files

 Old Version: 1.7.2b -> New Version: 1.7.7.i

Project site: (http://www.cpc.ncep.noaa.gov/products/wesley/wgrib2/)

Distributed Computing

gridengine

Grid Engine - Distributed Computing Management software

 Old Version: 6.2 -> New Version: 6.2u1

Project site: (http://gridengine.sunsource.net/)

EDA

geda-docs

Documentation for gEDA

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org)

geda-examples

Circuit examples for gEDA

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org)

geda-gattrib

Attribute editor for gEDA

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org/tools/gattrib/index.html)

geda-gnetlist

Netlister for the gEDA project

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org/tools/gnetlist/index.html)

geda-gschem

Electronics schematics editor

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org/tools/gschem/index.html)

geda-gsymcheck

Symbol checker for electronics schematics editor

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org/tools/gsymcheck/index.html)

geda-symbols

Electronic symbols for gEDA

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org)

geda-utils

Several utilities for the gEDA project

 Old Version: 20080127 -> New Version: 20081231

Project site: (http://www.geda.seul.org/tools/utils/index.html)

pcb

An interactive printed circuit board editor

 Old Version: 0.20080202 -> New Version: 0.20081128

Project site: (http://pcb.sourceforge.net)

gerbv

Gerber file viewer from the gEDA toolkit

 Old Version: 2.0.0 -> New Version: 2.2.0

Project site: (http://gerbv.sourceforge.net/)

ngspice

A mixed level/signal circuit simulator

 Old Version: 17 -> New Version: 18

Project site: (http://ngspice.sourceforge.net/)

magic

A very capable VLSI layout tool

 Old Version: 7.5.147 -> New Version: 7.5.169

Project site: (http://opencircuitdesign.com/magic/index.html)

toped

VLSI IC Layout Editor

 Old Version: 0.9.0 -> New Version: 0.9.2

Project site: (http://www.toped.org.uk)

Misc

149 packages checked, 51 differences.