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'non-free/science' section (3/1)

/non-free/abyss/abyss

de novo, parallel, sequence assembler for short reads

ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread.

/non-free/arb/arb-common

phylogenetic sequence analysis suite - common files

ARB is a graphical suite of tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the sequence entries is structured according to phylogeny or other user-defined criteria. . The ARB project (from the Latin "arbor", a tree) is a joint initiative of the Lehrstuhl fuer Mikrobiologie http://www.mikro.biologie.tu-muenchen.de/ and the Lehrstuhl fuer Rechnertechnik und Rechnerorganisation http://wwwbode.informatik.tu-muenchen.de/ of the Technical University of Munich. . This package provides the architecture independent scripts of ARB.

/non-free/arb/arb

phylogenetic sequence analysis suite - main program

ARB is a graphical suite of tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the sequence entries is structured according to phylogeny or other user-defined criteria. . The ARB project (from the Latin "arbor", a tree) is a joint initiative of the Lehrstuhl fuer Mikrobiologie http://www.mikro.biologie.tu-muenchen.de/ and the Lehrstuhl fuer Rechnertechnik und Rechnerorganisation http://wwwbode.informatik.tu-muenchen.de/ of the Technical University of Munich.

/non-free/arb/libarb

phylogenetic sequence analysis suite - libraries

ARB is a graphical suite of tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the sequence entries is structured according to phylogeny or other user-defined criteria. . The ARB project (from the Latin "arbor", a tree) is a joint initiative of the Lehrstuhl fuer Mikrobiologie http://www.mikro.biologie.tu-muenchen.de/ and the Lehrstuhl fuer Rechnertechnik und Rechnerorganisation http://wwwbode.informatik.tu-muenchen.de/ of the Technical University of Munich. . This package provides the dynamic libraries which are used by ARB.


GUI to help set up, launch and analyze AutoDock dockings

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . AutoDock is a well established package for the automated screening of libraries of formal representation of chemical compounds that putatively bind to a particular protein at hand. This package provides a graphical user interface that is helping with the preparation of the protein for such analyses. . The tool AutoLigand, which may help to constrain the location of the binding pocket for yet undescribed proteins, is accompanying the main executable 'runAdt'.

/non-free/blimps/blimps-utils

blocks database improved searcher

BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a protein sequence against blocks or a block against sequences. . This package contains the binaries.

/non-free/caftools/caftools

maintenance of DNA sequence assemblies

This package contains code from different authors that allow sequence assemblies to be converted into formats such as CAF (Common Assembly Format) or GAP4. . CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data. CAF was designed during the Sanger sequencing era. Its modern-day successor is the SAM format, or its binary equivalents BAM and CRAM.


Parsers and algorithms for computational chemistry (data files)

A Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner. . This package contains unittests and example log files that could not be included in the main cclib package.


Non-free datafiles for Celestia, a real-time visual space simulation

Celestia is a free 3D astronomy program. Based on the Hipparcos Catalogue, it allows users to display objects ranging in scale from artificial satellites to entire galaxies in three dimensions using OpenGL. Unlike most planetarium software, the user is free to travel about the Universe. . This package contains the data files for Celestia that have no DFSG compatible license or an unclear license.


MPI-distributed global sequence alignment with ClustalW

ClustalW is a popular tool for multiple sequence alignment. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is an MPI implementation of ClustalW. Based on version 1.82 of the original ClustalW, both the pairwise and progressive alignments are parallelized with MPI, a popular message passing programming standard. The pairwise alignments can be easily parallelized since the many alignments are time independent on each other. However the progressive alignments are essentially not parallelizable because of the time dependencies between each alignment. . Here the recursive parallelism paradigm is applied to the linear space profile-profile alignment algorithm. This approach is more time efficient on computers with distributed memory architecture. Traditional approach that relies on precomputing the profile-profile score matrix has also been implemented. Results shown the latter is indeed more appropriate for shared memory multiprocessor computer. . ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments. . The original ClustalW/ClustalX can be found at URL: http://www.clustal.org/download/pre-2/

/non-free/cluster3/cluster3

Reimplementation of the Eisen-clustering software

The open source clustering software available here contains clustering routines that can be used to analyze gene expression data. Routines for hierarchical (pairwise simple, complete, average, and centroid linkage) clustering, k-means and k-medians clustering, and 2D self-organizing maps are included. The routines are available in the form of a C clustering library, an extension module to Python, a module to Perl, as well as an enhanced version of Cluster, which was originally developed by Michael Eisen of Berkeley Lab. The C clustering library and the associated extension module for Python was released under the Python license. The Perl module was released under the Artistic License. Cluster 3.0 is covered by the original Cluster/TreeView license. . This package only contains the command line and motif gui versions of Cluster 3.0.

/non-free/cufflinks/cufflinks

Transcript assembly, differential expression and regulation for RNA-Seq

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.


EMBOSS conversions of the programs in the phylip package

This package is the adaptation of the PHYLIP package in which its programs can operate with the biological sequence formats and databases of the European Molecular Biology Open Software Suite (EMBOSS). The software packages adapted for EMBOSS are called EMBASSY. . PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. . The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them from the original programs and avoid namespace conflict.

/non-free/fasta3/fasta3-doc

user guide for FASTA tools

The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. . The use of the package's many binaries and the equally representated conceptual approaches towards sequence analyses are summarised in this PDF.

/non-free/fasta3/fasta3

tools for searching collections of biological sequences

The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. . * Protein . - Protein-protein FASTA - Protein-protein Smith-Waterman (ssearch) - Global Protein-protein (Needleman-Wunsch) (ggsearch) - Global/Local protein-protein (glsearch) - Protein-protein with unordered peptides (fasts) - Protein-protein with mixed peptide sequences (fastf) . * Nucleotide . - Nucleotide-Nucleotide (DNA/RNA fasta) - Ordered Nucleotides vs Nucleotide (fastm) - Un-ordered Nucleotides vs Nucleotide (fasts) . * Translated . - Translated DNA (with frameshifts, e.g. ESTs) vs Proteins (fastx/fasty) - Protein vs Translated DNA (with frameshifts) (tfastx/tfasty) - Peptides vs Translated DNA (tfasts) . * Statistical Significance . - Protein vs Protein shuffle (prss) - DNA vs DNA shuffle (prss) - Translated DNA vs Protein shuffle (prfx) . * Local Duplications . - Local Protein alignments (lalign) - Plot Protein alignment "dot-plot" (plalign) - Local DNA alignments (lalign) - Plot DNA alignment "dot-plot" (plalign)

/non-free/fsl/fsl-5.0-core

analysis tools for FMRI, MRI and DTI brain imaging

FSL is a comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The suite consists of various command line tools, as well as simple GUIs for its core analysis pipelines. Among others, FSL offers implementations of standard GLM analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis. . Some FSL components require additional data packages (fsl-atlases, fsl-first-data, fsl-possum-data) that are currently available from the NeuroDebian repository only. For more information on how to obtain these data packages visit http://neuro.debian.net. . Users aiming to perform a complete FSL 5.0 installation (including all data components) are advised to install the 'fsl-5.0-complete' package from NeuroDebian. . FSL interoperates well with other brain imaging related software. This includes Caret, FreeSurfer (cortical flattening and modelling). All FSL tools support the NIfTI format.

/non-free/fsl/fsl-core

metapackage for the latest version of FSL

FSL is a comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The suite consists of various command line tools, as well as simple GUIs for its core analysis pipelines. Among others, FSL offers implementations of standard GLM analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis. . Some FSL components require additional data packages (fsl-atlases, fsl-first-data, fsl-possum-data) that are currently available from the NeuroDebian repository only. For more information on how to obtain these data packages visit http://neuro.debian.net. . Users aiming to perform a complete FSL installation (including all data components) are advised to install the 'fsl-complete' package from NeuroDebian.

/non-free/gliese/gliese

stellar data set from the Third Catalogue of Nearby Stars

This package provides a star catalog which contains approximately 3800 star records including the known stars nearer to Earth than approximately 80 light-years, taken from the Third Catalogue of Nearby Stars (preliminary edition), Gliese and Jahreiss, 1991. . This stellar data set may be viewed with the StarPlot program available from Debian, but can also be used with other astronomical software.

/non-free/gmap/gmap

spliced and SNP-tolerant alignment for mRNA and short reads

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.

/non-free/igv/igv

Integrative Genomics Viewer

The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems.


Tycho-2 star catalog for KStars

This package contains the data of the Tycho-2 star catalog for KStars, the desktop planetarium for KDE. It allows users to share a single centralized installation of the data instead of each needing to download their own personal copy of the whole catalog. It can also configure KStars to disable these user downloads.


GeoTIFF library -- EPSG Geodetic Parameter Dataset

This C library supports TIFF 6.0 based interchange format for georeferenced raster imagery. The GeoTIFF standard has been developed for reading, and writing geographic meta-information tags on top of TIFF raster. . This package contains EPSG Geodetic Paramenters data files which can be used with standard projections. These data are useful to better dump geo-contents of many GeoTIFF files.


Bhtree library extension module

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . Python binding for looking Barnes-Hut tree code used for finding neighboring points (e.g. when building bonds by distance).


Computer Aided Drug Discovery (CADD) Pipeline

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . The Computer Aided Drug Discovery (CADD) Pipeline is a workflow environment designed to support molecular dyanmics simulations and virtual screening experiments for in silico drug discovery, with a special focus on supporting the use of the Relaxed Complex Scheme. It includes web based access to applications such as NAMD, AutoDock, PDB2PQR, APBS, MGLToos and couples them in a flexible and scalable fashion through cloud computing. It is developed as a standalone application, using Vision (https://www.nbcr.net/pub/wiki/index.php?title=MGLTools#Vision) as the backend engine for visual programming and workflow execution. The scientific applications are made accessible through CADD using Opal Web services (https://www.nbcr.net/pub/wiki/index.php?title=Opal) for scalable and distributed computation. . The workflow components of the CADD pipeline are currently released as Vision networks packaged for specific processes in a modular fashion. These modules may be coupled at ease for more complex processes. In the future, they may also be accessible from workflow repositories such as MyExperiment.org, and from AutoDockTools. The Opal services used in the CADD workflow may be accessed using programmatic access, the Opal Server Dashboard or other workflow clients such as Kepler, VisTrails or Taverna through Opal plugins available at Opal Sourceforge website (http://opal.nbcr.net). . Features . * Automatic launching of NAMD simulation on TeraGrid and NBCR resources, including experimental support for migration of simulation between resources. * Selection of representative snapshots/conformations from MD simulations using clustering tools such as QR factorization from VMD and Ptraj from Amber. * Support of Virtual Screening using AutoDock, AutoDock Vina * Support of Relaxed Complex Scheme based Virtual Screening and Rescoring * Visualization and analysis of Virtual Screening hits


Python classes to interpret trajectories of Gromacs

This package is an optional part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . It allows one to read and analyse the trajectories of molecular dynamics simulations performed with Gromacs.


visualization of 3D geometry using the OpenGL with Python

The library is needed by mgltools-autodocktools at runtime. It provides the viewer of three-dimensional objects that used for the interactive display of protein structures. . The Viewer class is a fully functional visualization application providing control over a number of rendering parameters. This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds.


Python library for geometric analyses

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . The library implements a series of functions for geometric analyses, e.g., for calculating distances or intersections.


Molecular Graphics Laboratory utility collection

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . It is needed by mgltools-autodocktools at runtime, providing a series of utility functions on from parallel programming to statistics.


Python classes to read and manipulate molecules

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . It provides a series of functions to calculate properties of protein structures and allows performing local modifications.


Python GUI library for the editing of networks

This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . It provides a graphics user interface to edit networks and is used by the Vision packages that formulates workflows.