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/)
High Energy Physics
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
Astronomy
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.
