Documentation Scientific and Technical Beat

Fedora continues to add to its strong complement of scientific and technical packages with a host of new offerings for Fedora 15. In addition to the new packages shown here, many other packages have been updated for this release. Refer to the Fedora Technical Notes at http://docs.fedoraproject.org for more complete details.

BEDtools

BEDTools is a set of utilities allow to one to address common genomics tasks such as finding feature overlaps and computing coverage. BEDtools is new to Fedora.

R

R is a popular statistics package with many add on packages to address specific needs. Fedora 15 brings a few new add-on packages to R.

• R-GenomicRanges provides general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

• • http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html

• R-ROC - The ROC library is a collection of R classes and functions related to receiver

operating characteristic (ROC) curves. These functions are targeted at the use of ROC analysis with DNA microarrays The R-ROC package provides a set of utilities for ROC.

• • http://bioconductor.org/packages/release/bioc/html/ROC.html

• R-affydata is a set of example affymetrix datasets. These datasets are somewhat larger than the examples included in the affy package, and are intended to better represent "real-world" datasets.

• • http://www.bioconductor.org/packages/2.6/data/experiment/html/affydata.html

APE

ape (Atomic Pseudopotential Engine) is a tool for generating atomic pseudopotentials within a Density-Functional Theory framework. It is distributed under the GPL and it produces pseudopotential files suitable for use with

• SIESTA
• OCTOPUS
• ABINIT
• PWscf

http://www.tddft.org/programs/APE/node/9

coot

coot (Crystallographic Object-Oriented Toolkit) is a set of tools for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. coot 0.6.2 is included in Fedora 15.

http://www.biop.ox.ac.uk/coot/

cp2k

cp2k is a program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

Fedora 15 includes cp2k version 2.1. For details refer to http://cp2k.berlios.de/

dia-optics

dia-optics is a shape library for the popular dia drawing package. The included shapes may be reviewed at http://dia-installer.de/shapes/optics/index_en.html

gpsbabel-gui

gpsbabel is a package for manipulating GPS data from a variety of devices and manipulating that data. Fedora 15 now includes a GUI for that data. Refer to http://www.gpsbabel.org/ for additional information.

gretl

gretl is a cross-platform software package for econometric analysis. It includes links to R, octave and ox for more detailed analysis. A full list of features may be found at http://gretl.sourceforge.net/

libxc

libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. The project maintains a wiki at http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

ltl2ba

ltl2ba provides fast translation from LTL formulae to Büchi automata. Fedora 15 includes version 1.1.

openeuclide

Also new to Fedora 15 is openeuclide. OpenEuclide is a 2D geometry software: figures are defined dynamically by describing formal geometrical constraints.

openscada

openscada system is open implementation SCADA (Supervisory Control And Data Acquisition) systems.

Fedora 15 ships the stable release version 0.7.0 with implementations of the database ODBC module, PostgresSQL and transport module of the DB and the new mechanism/module of OpenSCADA system's test; there were found and corrected many errors in order to better optimization, increase stability, sustainability and system's performance. Notable optimization was made in the Visual Control Area (VCA) and its visualizers; changes were made in the VCA engine (UI.VCAEngine) modules: UI.Vision and UI.WebVision visualizers, aimed at stabilizing, optimization of memory consumption and improvement of user's properties of VCA. It has been made a new object API of the user's programming, which provides the integration of user's functions in the objects' tree of OpenSCADA, in addition, to a number of changes to the existing library of functions of the user's API. For all details please refer to the Changelog in your package or to the News section on the project website at http://oscada.org/ .

plotdrop

plotdrop is a frontend to GNU plot. Data files are added to plotdrop by simply dragging them from nautilus. The project maintains a website at http://plotdrop.sourceforge.net/

psfex

PSFEx (“PSF Extractor”) extracts models of the Point Spread Function (PSF) from FITS images processed with SExtractor, and measures the quality of images. The generated PSF models can be used for model-fitting photometry or morphological analyses.

http://www.astromatic.net/software/psfex

root

root is a package for analyzing large amounts of data. Fedora 15 incldes several new add-ons for root:

• root-genetic
• root-graf-fitsio
• root-hist-factory
• root-io
• root-proof-pq2

Project site: http://root.cern.ch/