Debian Med Project
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Summary
Biology development
pacchetti Debian Med per lo sviluppo di applicazioni per la microbiologia

Questo metapacchetto installa pacchetti Debian che possono essere utili per lo sviluppo di applicazioni per la ricerca microbiologica.

The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Pure Blend.

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Biology development packages

Official Debian packages with high relevance

Bioperl
strumenti Perl per biologia molecolare computazionale
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Il progetto Bioperl è uno sforzo coordinato per raccogliere metodi computazionali comunemente utilizzati in bioinformatica in un insieme di moduli Perl standard in stile CPAN ben documentati e liberamente disponibili. È ben accettato dalla comunità ed è usato da molti progetti di alto profilo, ad esempio Ensembl.

I pacchetti raccomandati sono necessari per eseguire alcuni dei binari inclusi; per una spiegazione dettagliata che include gli specifici moduli Perl inclusi, vedere README.Debian.

Il pacchetto suggerito migliora le pagine del manuale.

Please cite: Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson and Ewan Birney: The Bioperl toolkit: Perl modules for the life sciences.. (PubMed,eprint) Genome Res. 12(10):1611-1618 (2002)
Bioperl-run
wrapper BioPerl: script
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Contiene script dal pacchetto BioPerl-Run. Questo pacchetto installa anche tutte le applicazioni pacchettizzate in Debian per cui possono essere creati wrapper; quelle che non sono Libere sono "Consigliate" da questo pacchetto.

The package is enhanced by the following packages: kalign phyml mcl exonerate clustalw
Biosquid
utilità per l'analisi di sequenze biologiche
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SQUID è una libreria di funzioni in C per l'analisi delle sequenze. Include molti piccoli programmi di utilità per convertire, mostrare statistiche, manipolare e fare altre operazioni sui file di sequenza.

Il nome originale del pacchetto è "squid" ma, visto che già era presente un pacchetto squid nell'archivio (il server proxy), è stato rinominato in "biosquid".

Questo pacchetto contiene alcuni strumenti per dimostrare le funzionalità della libreria SQUID.

Libace-perl
accesso orientato agli oggetti per i database ACEDB
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AcePerl è un'interfaccia Perl orientata agli oggetti per il database AceDB. Fornisce funzionalità per connettersi ai database AceDB remoti, eseguire query, caricare oggetti ACE e aggiornare database. La API di programmazione è compatibile con la API Java JADE ed è interoperabile con le API usate da BoulderIO.

AceDB è un sistema di database genomico sviluppato a partire dal 1989 principalmente da Jean Thierry-Mieg (CNRS, Montpellier) e Richard Durbin (Istituto Sanger). È stato originariamente sviluppato per il progetto del genoma C.elegans, dal quale è stato derivato il suo nome (A C. elegans DataBase).

Please cite: Lincoln D. Stein and Jean Thierry-Mieg: Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases. (PubMed,eprint) Genome Research 8(12):1308-1315 (1998)
Libai-fann-perl
wrapper Perl per la libreria FANN
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Questo modulo fornisce un wrapper Perl per la libreria FANN (Fast Artificial Neural Network) (http://leenissen.dk/fann/wp/).

L'interfaccia orientata agli oggetti AI::FANN fornisce una mappatura quasi diretta all'API della libreria C.

Libbambamc-dev
Development files for reading and writing BAM (genome alignment) files
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The BAM Format is a binary format for storing sequence data. This is a lightweight C implementation of the read name collation code from the larger bambam C++ project to handle BAM file input and BAM file output.

This package contains the static library and header files.

Libbamtools-dev
C++ API for manipulating BAM (genome alignment) files
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BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.

This is the developers API package

Please cite: Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Stromberg and Gabor T. Marth: BamTools: a C++ API and toolkit for analyzing and managing BAM files. (PubMed,eprint) Bioinformatics 27(12):1691-2 (2011)
Libbio-graphics-perl
Generate GD images of Bio::Seq objects
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The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature, Das::Segment::Feature and Bio::DB::Graphics objects. It can be used to draw sequence annotations, physical (contig) maps, protein domains, or any other type of map in which a set of discrete ranges need to be laid out on the number line.

Libbio-mage-perl
Container module for classes in the MAGE package: MAGE
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MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the Microarray Gene Expression Data Society (MGED). This package contains Perl modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum Information About a Microarray Experiment) records of microarray ("DNA chips") experiments.

The Bio::MAGE module contains the following Bio::MAGE classes:

  • NameValueType
  • Extendable
  • Identifiable
  • Describable
Libbio-mage-utils-perl
Extra modules for classes in the MAGE package: MAGE
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MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the Microarray Gene Expression Data Society (MGED). This package contains Perl modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum Information About a Microarray Experiment) records of microarray ("DNA chips") experiments.

Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology, as well as SQL utilities.

Libbio-primerdesigner-perl
modulo Perl per progettare primer per PCR usando primer3 ed epcr
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Bio::PrimerDesigner fornisce un'interfaccia di basso livello agli eseguibili binari primer3 ed epcr, e metodi per restituire i risultati. In aggiunta ad accedere alle installazioni locali di primer3 ed e-PCR, offre anche la possibilità di accedere al binario primer3 attraverso un server remoto.

Libbiococoa-dev
Bioinformatics framework for GNUstep and Cocoa (development files)
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BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications.

This package contains the development files, documentation and examples for developing GNUstep applications using the BioCocoa framework.

Libbiojava-java
Java API to biological data and applications (default version)
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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is provided by a vibrant community which meets annually at the Bioinformatics Open Source Conference (BOSC) that traditionally accompanies the Intelligent Systems in Molecular Biology (ISMB) meeting. Much like BioPerl, the employment of this library is valuable for everybody active in the field because of the many tricks of the trade one learns just by communicating on the mailing list.

This is a wrapper package which should enable smooth upgrades to new versions.

Please cite: R. C. G. Holland, T. Down, M. Pocock, A. Prlićand D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer and M. J. Schreiber: BioJava: an Open-Source Framework for Bioinformatics. (PubMed,eprint) Bioinformatics 24(18):2096-2097 (2008)
Libbiojava3-java
Java API to biological data and applications (default version)
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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is provided by a vibrant community which meets annually at the Bioinformatics Open Source Conference (BOSC) that traditionally accompanies the Intelligent Systems in Molecular Biology (ISMB) meeting. Much like BioPerl, the employment of this library is valuable for everybody active in the field because of the many tricks of the trade one learns just by communicating on the mailing list.

This is a wrapper package which should enable smooth upgrades to new versions.

Libchado-perl
database schema and tools for genomic data
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Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

Libffindex0-dev
library for simple index/database for huge amounts of small files (development)
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FFindex is a very simple index/database for huge amounts of small files. The files are stored concatenated in one big data file, separated by '\0'. A second file contains a plain text index, giving name, offset and length of the small files. The lookup is currently done with a binary search on an array made from the index file.

This package contains the header files and documentation needed to develop applications with libffindex.

Libfreecontact-perl
fast protein contact predictor - binding for Perl
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the Perl binding.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Libfreecontact0-dev
fast protein contact predictor library - development files
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains files necessary for developing applications with libfreecontact.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Libgenome-model-tools-music-perl
module for finding mutations of significance in cancer
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The MuSiC suite is a set of tools aimed at discovering the significance of somatic mutations found within a given cohort of cancer samples, and with respect to a variety of external data sources.

Libgenome-perl
pipelines, tools, and data management for genomics
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This is the base namespace module for the Genome software tree.

That tree has several primary components:

Genome::Model: a data modeling pipeline management system for genomics

Genome::Model::Tools a tree of >1000 tools and tool wrappers for genomics

Genome::* a variety of sample tracking classes with an RDBMS back-end

Only the tools system is currently released.

See genome for a complete inventory of all tool packages, and for command-line access to those tools.

Libgenometools0-dev
file di sviluppo per GenomeTools
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Questo pacchetto contiene i file header necessari e la libreria statica di GenomeTools.

Oltre alle strutture dati di base relative alla bioinformatica, questa libreria contiene componenti per gestione di sequenze e annotazioni, compressione di sequenze, generazione e accesso a strutture con indici, ricerca efficiente di corrispondenze, visualizzazione delle annotazioni e molto altro.

Libgo-perl
perl modules for GO and other OBO ontologies
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This is a collection of perl code for dealing with Gene Ontologies (GO) and Open Biomedical Ontologies (OBO) style ontologies. It is part of the ‘go-dev’ distribution, but this Debian package is made from the CPAN archive. This package contains both scripts (which can be used with no knowledge of perl), and libraries which will be of use to perl programmers using GO or OBO.

Libhmsbeagle-dev
High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
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BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.

The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution.

The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units.

This package contains development files needed to build against Beagle library.

Please cite: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. (PubMed,eprint) Systematic Biology 61(1):170-3 (2012)
Libjebl2-java
Java Evolutionary Biology Library
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.

This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library.

Remark of Debian Med team: Fork from jebl

This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library.

Libncbi6-dev
NCBI libraries for biology applications (development files)
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This package supplies development versions of NCBI's non-graphical C libraries, along with the corresponding header files.

Libnhgri-blastall-perl
Perl extension for running and parsing NCBI's BLAST 2.x
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NHGRI::Blastall will enable usage of BLAST out of a Perl script, if BLAST2 or WU-BLAST are installed locally. Main features are:

  • run BLAST (also via network, which requires blastcl3)
  • BLAST single sequences against each other or against a given library
  • format databases
  • mask out repetitive DNA
  • read, parse and filter existing BLAST reports
Libopenms-dev
libreria per gestione ed analisi di dati LC/MS - file di sviluppo
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OpenMS è una libreria per gestione ed analisi di dati LC/MS. OpenMS offre un'infrastruttura per lo sviluppo di software relativo alla spettrometria di massa e potenti soluzioni per la visualizzazione 2D e 3D.

OpenMS offre analisi per vari protocolli di quantificazione, inclusa quantificazione label-free, SILAC, iTRAQ, SRM, SWATH…

Fornisce algoritmi incorporati per identificazione de-novo e ricerche in database, così come adattatori per altri strumenti all'avanguardia come X!Tandem, Mascot, OMSSA…

OpenMS gestisce i formati PSI (Proteomics Standard Initiative) per i dati MS e permette una facile integrazione degli strumenti nei motori per flussi di lavoro come Knime, Galaxy, WS-Pgrade e TOPPAS attraverso il concetto TOPPtools e una gestione unificata dei parametri.

Questo pacchetto fornisce i file di sviluppo della libreria.

Please cite: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher: OpenMS – an Open-Source Software Framework for Mass Spectrometry. (PubMed,eprint) BMC Bioinformatics 9(163) (2008)
Libpal-java
Phylogenetic Analysis Library
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The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. At present PAL consists of approximately 200 public classes/interfaces in 16 packages Please refer to the API documentation for a detailed description of all classes and methods available, and to the release history for an overview of the development history of PAL.

Librcsb-core-wrapper0-dev
development files for librcsb-core-wrapper0
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The RCSB Core Wrapper library was developed to provide an object-oriented application interface to information in mmCIF format. It includes several classes for accessing data dictionaries and mmCIF format data files.

This package contains files necessary for developing applications with the library.

The package is enhanced by the following packages: librcsb-core-wrapper0-dbg
Librg-blast-parser-perl
very fast NCBI BLAST parser - binding for Perl
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This package contains Perl binding for a very fast C++ library that parses the default output of NCBI BLAST programs. BLAST results are returned in a convenient hash structure.

Evaluated on a very small test set, this parser is considerably faster than Zerg::Report from libzerg-perl.

Librg-reprof-bundle-perl
protein secondary structure and accessibility predictor
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'reprof' is an improved implementation of 'prof', a popular protein secondary structure and accessibility predictor. Prediction is either done from protein sequence alone or from an alignment - the latter should be used for optimal performance.

This package provides the perl modules implementing 'reprof' along with the necessary data files.

Librostlab-blast0-dev
very fast C++ library for parsing the output of NCBI BLAST programs
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This package provides a very fast library for parsing the default output of NCBI BLAST programs into a C++ structure.

libzerg is faster, but it provides only lexing (i.e. it only returns pairs of token identifiers and token string values). librostlab-blast uses a parser generated with bison on top of a flex-generated lexer very similar to that of libzerg.

This package contains files necessary for developing applications with librostlab-blast.

Librostlab3-dev
C++ library for computational biology (development)
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This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products.

The library provides the following facilities:

  • current working directory resource
  • exception with stack backtrace
  • file lock resource
  • passwd and group structures for C++
  • effective uid and gid resource
  • rostlab::bio::seq class with stream input operator for FASTA format
  • umask resource

This package contains files necessary for developing applications with librostlab.

Libsbml5-dev
libreria System Biology Markup Language - file di sviluppo
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LibSBML è una libreria progettata per assistere nella lettura, scrittura, manipolazione, traduzione e convalida di file e flussi di dati SBML. Non è essa stessa un'applicazione (benché venga fornita con molti programmi d'esempio), ma piuttosto una libreria che si può incorporare nelle proprie applicazioni. Questo pacchetto contiene i file necessari sviluppare con libsbml.

Please cite: Benjamin J Bornstein, Sarah M Keating, Akiya Jouraku and Michael Hucka: LibSBML: An API Library for SBML. (PubMed,eprint) Bioinformatics 24(6):880-881 (2008)
Libsort-key-top-perl
Perl module to select and sort top n elements of a list
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The functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.

They are all variations around 'keytopsort { CALC_KEY($_) } $n => @data;'.

In array context, this function calculates the ordering key for every element in @data using the expression inside the block. Then it selects and orders the $n elements with the lower keys when compared lexicographically.

In scalar context, the value returned by the functions on this module is the cutoff value allowing to select nth element from the array.

Libsrf-dev
implementazione C++ del formato SRF per dati di sequenze di DNA
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SRF (acronimo di Sequence Read Format, formato per lettura di sequenza) è un formato generico capace di memorizzare dati generati da qualsiasi tecnologia di sequenziamento del DNA. Questa libreria è un'implementazione di SRF e fornisce funzioni di input/output di base.

Libstaden-read-dev
development files for libstaden-read
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This package contains the header and development files needed to build programs and packages using the Staden io_lib.

The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.

Libtfbs-perl
scanning DNA sequence with a position weight matrix
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The TFBS perl modules comprise a set of routines to interact with the Transfac and Jaspar databases that describe a special family of proteins, the transcription factors. These bind to genomic DNA to initiate (or prevent) the readout of a gene. Once multiple binding sites are known for a transcription factor, these are gathered in a single file and are aligned in order to find position-specific characteristica that might be used to predict such binding events in novel DNA sequences.

If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18:1135-1136".

Please cite: Boris Lenhard and Wyeth W. Wasserman: TFBS: Computational framework for transcription factor binding site analysis. (PubMed) Bioinformatics 18(8):1135-1136 (2002)
Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
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Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic biological applications.

Libzerg-perl
fast perl module for parsing the output of NCBI BLAST programs
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The Zerg library contains a C/flex lexical scanner for BLAST reports and a set of supporting functions. It is centered on a "get_token" function that scans the input for specified lexical elements and, when one is found, returns its code and value to the user.

It is intended to be fast: for that the authors used flex, which provides simple regular expression matching and input buffering in the generated C scanner. And it is intended to be simple in the sense of providing just a lexical scanner, with no features whose support could slow down its main function.

Please cite: Apuã C M Paquola, Abimael A Machado, Eduardo M Reis, Aline M Da Silva and Sergio Verjovski-Almeida: Zerg: a very fast BLAST parser library. (PubMed,eprint) Bioinformatics 19(8):1035-6 (2003)
Libzerg0-dev
development libraries and header files for libzerg
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Zerg is a C library for lexing - lexically scanning - the output of NCBI BLAST programs.

Based on a GNU Flex-generated lexical scanner, it runs extremely fast, being especially useful for processing large volumes of data. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers.

If you need a parser and not only a lexer, check out librostlab-blast.

This package contains the header files and documentation needed to develop applications with libzerg.

Please cite: Apuã C M Paquola, Abimael A Machado, Eduardo M Reis, Aline M Da Silva and Sergio Verjovski-Almeida: Zerg: a very fast BLAST parser library. (PubMed,eprint) Bioinformatics 19(8):1035-6 (2003)
Mcl
algoritmo Cluster di Markov
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Il pacchetto MCL è un'implementazione dell'algoritmo MCL, fornisce strumenti per manipolare matrici sparse (le strutture dati essenziali dell'algoritmo MCL) e per eseguire esperimenti su cluster.

MCL viene attualmente utilizzato nelle scienze come la biologia (rilevamento di famiglie proteiche, genomica), informatica (cluster dei nodi in reti peer-to-peer) e linguistica (analisi del testo).

The package is enhanced by the following packages: zoem
Pyfai
python library for Fast Azimuthal Integration
Maintainer: Jerome Kieffer
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PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

Python-biom-format
formato BIOM (Biological Observation Matrix)
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Il formato di file BIOM (Biological Observation Matrix, matrice di osservazioni biologiche) è progettato per essere un formato di uso generico per rappresentare campioni biologici con tabelle di contingenza delle osservazioni. BIOM è uno standard riconosciuto per l'Earth Microbiome Project ed è un progetto candidato del Genomics Standards Consortium.

Il formato BIOM è progettato per l'uso generico in vaste aree delle scienze -omiche comparative. Per esempio, in indagini su geni marker, l'uso principale di questo formato è quello di rappresentare tabelle OTU: in questo caso le osservazioni sono OTU e la matrice contiene i conteggi corrispondenti al numero di volte che ogni singola OTU è stata osservata in ciascun campione. Nel caso di dati di metagenomi, questo formato può essere usato per rapresentare tabelle metagenomiche: le osservazioni in questo caso potrebbero corrispondere ai sottosistemi SEED e la matrice conterrebbe i conteggi corrispondenti al numero di volte che ogni sottosistema è stato osservato in ciascun metagenoma. Analogamente, nel caso di dati genomici, questo formato può essere usato per rappresentare un insieme di genomi: le osservazioni in questo caso corrisponderebbero ancora una volta ai sottosistemi SEED e i conteggi corrisponderebbero al numero di volte che ogni sottosistema è stato osservato in ciascun genoma.

Please cite: Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai R. Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight and J. G. Caporaso: The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. (eprint) GigaScience 1:7 (2012)
Python-biopython
libreria Python per bioinformatica (implementata in Python 2)
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Il progetto Biopython è un'associazione internazionale di sviluppatori di strumenti Python disponibili liberamente per i calcoli biologici molecolari.

È uno sforzo collaborativo distribuito per sviluppare librerie e applicazioni Python che si rivolgono verso i bisogni dei lavori in bioinformatica attuali e futuri. Il codice sorgente è reso disponibile sotto la licenza Biopython, che è estremamente liberale e compatibile con pressoché qualsiasi licenza esistente. Il progetto lavora accanto alla Open Bioinformatics Foundation, che generosamente fornisce lo spazio web e CVS per il progetto.

Questo pacchetto è per la versione 2 di Python.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
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Python-cogent
framework for genomic biology
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PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for:

  • controlling third-party applications,
  • devising workflows; querying databases,
  • conducting novel probabilistic analyses of biological sequence evolution, and
  • generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.
Please cite: Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying and Gavin A Huttley: PyCogent: a toolkit for making sense from sequence. (PubMed,eprint) Genome Biology 8(8):R171 (2007)
Python-corepywrap
library that exports C++ mmCIF accessors to Python
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The RCSB Core Wrapper library was developed to provide an object-oriented application interface to information in mmCIF format. It includes several classes for accessing data dictionaries and mmCIF format data files.

This library provides Python bindings for librcsb-core-wrapper.

The package is enhanced by the following packages: librcsb-core-wrapper0-dbg
Python-csb
infrastruttura Python per bioinformatica strutturale
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L'insieme di strumenti CSB (Computational Structural Biology, biologia strutturale computazionale) è una libreria di classi Python per leggere, archiviare e analizzare strutture biomolecolari in una varietà di formati, con un ricco supporto per le analisi statistiche.

CSB è progettato per la riusabilità e l'estensibilità e viene fornito con un'API pulita e ben documentata che segue le buone prassi di progettazione orientata agli oggetti.

Python-freecontact
fast protein contact predictor - binding for Python
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the Python binding.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Python-htseq
high-throughput genome sequencing read analysis utilities
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HTSeq can be used to performing a number of common analysis tasks when working with high-throughput genome sequencing reads:

  • Getting statistical summaries about the base-call quality scores to study the data quality.
  • Calculating a coverage vector and exporting it for visualization in a genome browser.
  • Reading in annotation data from a GFF file.
  • Assigning aligned reads from an RNA-Seq experiments to exons and genes.
Python-mmtk
molecular modeling toolkit
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The Molecular Modeling Toolkit (MMTK) is a library for molecular simulation applications. It provides the most common methods in molecular simulations (molecular dynamics, energy minimization, normal mode analysis) and several force fields used for biomolecules (Amber 94, Amber 99, several elastic network models). MMTK also serves as a code basis that can be easily extended and modified to deal with non-standard situations in molecular simulations.

Python-pysam
interface for the SAM/BAM sequence alignment and mapping format
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Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API.

The package is enhanced by the following packages: python-pysam-tests
Python-rdkit
raccolta di software per chemioinformatica e apprendimento automatico
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RDKit è un ambiente software per chemioinformatica e apprendimento automatico basato su Python/C++. Le funzionalità includono:

  • gestione e trasformazione di reazioni chimiche,
  • ricerca di sottostrutture con SMARTS,
  • SMILES canonico,
  • allineamento molecola-molecola,
  • un vasto numero di descrittori,
  • frammentazione usando le regole RECAP,
  • generazione e descrizione di coordinate 2D,
  • generazione di coordinate 3D usando l'incorporazione di geometria,
  • campi di forza UFF,
  • calcolo di codici (R/S) stereochimici,
  • ricerca di farmacofori,
  • calcolo di similarità di forma,
  • impronte digitali di coppie di atomi e torsioni topologiche,
  • mappe delle caratteristiche e vettori di mappe di caratteristiche,
  • algoritmi di apprendimento automatico,
  • calcolo della carica parziale di Gasteiger-Marsili.

I formati di file gestiti da RDKit includono MDL Mol, SDF, TDT, SMILES e il formato binario di RDKit.

Python3-biopython
libreria Python per bioinformatica (implementata in Python 3)
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Il progetto Biopython è un'associazione internazionale di sviluppatori di strumenti Python disponibili liberamente per i calcoli biologici molecolari.

È uno sforzo collaborativo distribuito per sviluppare librerie e applicazioni Python che si rivolgono verso i bisogni dei lavori in bioinformatica attuali e futuri. Il codice sorgente è reso disponibile sotto la licenza Biopython, che è estremamente liberale e compatibile con pressoché qualsiasi licenza esistente. Il progetto lavora accanto alla Open Bioinformatics Foundation, che generosamente fornisce lo spazio web e CVS per il progetto.

Questo pacchetto è per la versione 3 di Python.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python3-csb
infrastruttura Python per bioinformatica strutturale (versione Python3)
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L'insieme di strumenti CSB (Computational Structural Biology, biologia strutturale computazionale) è una libreria di classi Python per leggere, archiviare e analizzare strutture biomolecolari in una varietà di formati, con un ricco supporto per le analisi statistiche.

CSB è progettato per la riusabilità e l'estensibilità e viene fornito con un'API pulita e ben documentata che segue le buone prassi di progettazione orientata agli oggetti.

Questa è la versione per Python 3 del pacchetto.

R-bioc-biobase
funzioni base per Bioconductor
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Biobase fa parte del progetto Bioconductor ed è usato da molti altri pacchetti. Biobase contiene strutture dati standardizzate per rappresentare dati genomici e funzioni che sono necessarie per molti altri pacchetti o che rimpiazzano funzioni R.

Bioconductor è un progetto per sviluppare strumenti software innovativi da usare nella biologia computazionale. È basato sul linguaggio R. Prima di usare Bioconductor si dovrebbe avere una certa familiarità con R. I pacchetti Bioconductor forniscono strumenti interattivi flessibili per effettuare svariati compiti computazionali diversi.

La maggior parte degli altri pacchetti Bioconductor non sono pacchettizzati per Debian, ma questo pacchetto fornisce nella sua documentazione Debian le istruzioni su come installare pacchetti Bioconductor autogenerati non ufficiali per sistemi Debian e Ubuntu, che sono preparati dai membri del team Debian Med.

Please cite: Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean Y H Yang and Jianhua Zhang: Bioconductor: Open software development for computational biology and bioinformatics. (PubMed,eprint) Genome Biology 5(10):R80 (2004)
Remark of Debian Med team: This is a part of Bioconductor project

A nice overview about all modules of BioDonductor is given at http://www.bioconductor.org/packages/release/bioc/

R-cran-genetics
pacchetto GNU R per genetica di popolazione
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Classi e metodi per gestire dati genetici. Il pacchetto fornisce una libreria per l'ambiente statistico R che contiene classi per rappresentare genotipi e aplotipi dal marcatore singolo fino a marcatori multipli su più cromosomi. Le funzioni comprendono le frequenze degli alleli, marcatura di omo/eterozigoti, marcatura dei portatori di determinati alleli, stima e test per disequilibrium di Hardy-Weinberg, stima e test per linkage disequilibrium, e altro.

NOTA: QUESTO PACCHETTO È ATTUALMENTE OBSOLETO.

Il progetto R-Genetics ha sviluppato un insieme di pacchetti genetici avanzati per sostituire "genetics". Per maggiori informazioni visitare la pagina principale del progetto all'indirizzo: http://rgenetics.org.

R-cran-haplo.stats
pacchetto GNU R per l'analisi degli aplotipi
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Questo pacchetto fornisce le routine per l'ambiente statistico GNU R per l'analisi statistica degli aplotipi misurati indirettamente con i caratteri e le covariate quando la fase di associazione è ambigua. I metodi statistici assumono che tutti i soggetti siano non correlati e che gli aplotipi siano ambigui (a causa di una fase di associazione dei marcatori genetici sconosciuta). Le principali funzioni sono: haplo.em, haplo.glm, haplo.score, haplo.power e seqhap.

Ruby-bio
strumenti Ruby per la biologia molecolare computazionale
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Il progetto BioRuby mira ad implementare con il linguaggio Ruby un ambiente integrato per la bioinformatica. La filosofia di progettazione della libreria BioRuby è KISS (Keep It Simple, Stupid; mantieni le cose semplici, stupido) per massimizzare l'usabilità e l'efficienza come strumento quotidiano per i biologi. Il progetto è nato in Giappone ed è supportato dalla Università di Tokyo (Human Genome Center), dalla Università di Kyoto (Bioinformatics Center) e dalla Open Bio Foundation.

Please cite: Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama: BioRuby: bioinformatics software for the Ruby programming language. (PubMed,eprint) Bioinformatics 26(20):2617-9 (2010)
Sbmltoolbox
toolbox libsbml per Octave e MATLAB
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SBMLToolbox fornisce un insieme di funzioni di base per leggere, scrivere, manipolare e simulare modelli SBML (System Biology Meta Language). È un pacchetto libero e Open Source sulla base di libSBML con piena compatibilità per il funzionamento con MATLAB così come con Octave e per condividere modelli tra i due sistemi.

L'insieme di strumenti non è una soluzione completa pronta all'uso per la biologia dei sistemi. Si focalizza sul facilitare la gestione dei dati SBML e serve da punto di partenza per gli utenti e gli sviluppatori per stabilire i propri metodi.

Seqan-dev
libreria C++ per l'analisi di sequenze biologiche (sviluppo)
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SeqAn è una libreria di template C++ di algoritmi e strutture dati efficienti per l'analisi di sequenze, pensata principalmente per i dati biologici. Questa libreria applica un modello progettuale generico unico che garantisce alte prestazioni, generalità, estensibilità e integrazione con le altre librerie. SeqAn è facile da usare e semplifica lo sviluppo di nuovi strumenti software con minime perdite in termini di prestazioni.

Questo pacchetto contiene i file di sviluppo, la documentazione ed esempi.

Please cite: Andreas Doring, David Weese, Tobias Rausch and Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. (PubMed,eprint) BMC Bioinformatics 9(1):11 (2008)

Official Debian packages with lower relevance

Libfreecontact-doc
documentation for libfreecontact
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains HTML documentation for libfreecontact.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Libgtextutils-dev
libreria Gordon Text_utils (file di sviluppo)
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File di sviluppo per la libreria Gordon Text_utils (gtextutils).

Librostlab-blast-doc
very fast C++ library for parsing the output of NCBI BLAST programs
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This package provides a very fast library for parsing the default output of NCBI BLAST programs into a C++ structure.

libzerg is faster, but it provides only lexing (i.e. it only returns pairs of token identifiers and token string values). librostlab-blast uses a parser generated with bison on top of a flex-generated lexer very similar to that of libzerg.

This package contains html and pdf documentation.

Librostlab-doc
C++ library for computational biology (documentation)
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This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products.

The library provides the following facilities:

  • current working directory resource
  • exception with stack backtrace
  • file lock resource
  • passwd and group structures for C++
  • effective uid and gid resource
  • rostlab::bio::seq class with stream input operator for FASTA format
  • umask resource

This package contains html documentation.

Python-biopython-doc
documentazione per la libreria Biopython
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Documentazione ed esempi su come usare la libreria Biopython.

Questo pacchetto contiene anche i test di unità della suite di test, per permettere la riproduzione dei risultati dei test.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python-biopython-sql
gestione dello schema di database BioSQL per Biopython (Python 2)
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Questa è l'interfaccia di Biopython al database BioSQL (vedere www.biosql.org per i dettagli). Anche BioPerl, BioJava e BioRuby forniscono le loro interfacce nello stesso schema SQL condiviso.

Questo pacchetto è per la versione 2 di Python.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python3-biopython-sql
gestione dello schema di database BioSQL per Biopython (Python 3)
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Questa è l'interfaccia di Biopython al database BioSQL (vedere www.biosql.org per i dettagli). Anche BioPerl, BioJava e BioRuby forniscono le loro interfacce nello stesso schema SQL condiviso.

Questo pacchetto è per la versione 3 di Python.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
R-bioc-affy
metodi BioConductor per array di oligonucleotidi dell'Affymetrix
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Questo pacchetto fa parte della suite GNU R BioConductor. Contiene funzioni per analisi esplorativa di array di oligonucleotidi.

Please cite: Laurent Gautier, Leslie Cope, Benjamin M. Bolstad and Rafael A. Irizarry: affy - analysis of Affymetrix GeneChip data at the probe level. (PubMed,eprint) Bioinformatics (3):307-315 (2004)
R-bioc-affyio
BioConductor tools for parsing Affymetrix data files
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This BioConductor package provides routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.

R-bioc-altcdfenvs
ambienti CDF alternativi per BioConductor
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Questo modulo BioConductor fornisce ambienti CDF alternativi (alias mappature probeset) che sono strutture dati di comodo e funzioni per gestire cdfenvs.

Please cite: Laurent Gautier, Morten Mooller, Lennart Friis-Hansen and Steen Knudsen: Alternative mapping of probes to genes for Affymetrix chips. (PubMed,eprint) BMC Bioinformatics (5):111 (2004)
R-bioc-annotationdbi
GNU R Annotation Database Interface per BioConductor
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Questo modulo di BioConductor fornisce codice per l'interfaccia utente e la connessione al database per i pacchetti con dati di annotazioni che usano l'archiviazione dati SQLite.

R-bioc-biocgenerics
funzioni generiche per Bioconductor
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Funzioni S4 generiche necessarie per molti altri pacchetti Bioconductor.

Bioconductor fornisce strumenti per l'analisi e la comprensione di dati genomici di grandi dimensioni. Bioconductor usa il linguaggio di programmazione statistico R ed è open source e a sviluppo aperto.

R-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
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The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

R-bioc-graph
gestisce strutture di dati di grafi per BioConductor
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Questo modulo per BioConductor implementa alcune semplici funzionalità di gestione dei grafi. Sono per esempio usate nel modulo hypergraph che a sua volta è utilizzato da diversi altri pacchetti BioConductor.

R-bioc-hypergraph
strutture di dati di ipergrafi per Bioconductor
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Questo pacchetto di Bioconductor implementa alcune funzionalità semplici per rappresentare e manipolare ipergrafi.

R-bioc-iranges
GNU R low-level containers for storing sets of integer ranges
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The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions.

R-bioc-makecdfenv
BioConductor CDF Environment Maker
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Questo pacchetto ha due funzioni. La prima legge il file di descrizione di un chip (CDF) Affymetrix e crea un ambiente con una tabella hash contenente la mappatura posizioni/insiemi di sonde. L'altra crea un pacchetto che carica automaticamente questo ambiente.

R-bioc-preprocesscore
BioConductor collection of pre-processing functions
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This BioConductor module contains a library of pre-processing functions. It is imported by several other BioConductor modules.

R-cran-rocr
GNU R package to prepare and display ROC curves
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ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parametrized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parametrization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.

ROCR features: ROC curves, precision/recall plots, lift charts, cost curves, custom curves by freely selecting one performance measure for the x axis and one for the y axis, handling of data from cross-validation or bootstrapping, curve averaging (vertically, horizontally, or by threshold), standard error bars, box plots, curves that are color-coded by cutoff, printing threshold values on the curve, tight integration with Rs plotting facilities (making it easy to adjust plots or to combine multiple plots), fully customizable, easy to use (only 3 commands).

Performance measures that ROCR knows: Accuracy, error rate, true positive rate, false positive rate, true negative rate, false negative rate, sensitivity, specificity, recall, positive predictive value, negative predictive value, precision, fallout, miss, phi correlation coefficient, Matthews correlation coefficient, mutual information, chi square statistic, odds ratio, lift value, precision/recall F measure, ROC convex hull, area under the ROC curve, precision/recall break-even point, calibration error, mean cross-entropy, root mean squared error, SAR measure, expected cost, explicit cost.

Please cite: Tobias Sing, Oliver Sander, Niko Beerenwinkel and Thomas Lengauer: ROCR: visualizing classifier performance in R. (PubMed,eprint) Bioinformatics 21(20):3940-3941 (2005)

Packaging has started and developers might try the packaging code in VCS

Libbio-das-perl
interface to Distributed Annotation System (DAS)
Responsible: Steffen Moeller (DMPT)
License: Artistic
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Version: 0.94-1

Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. Both unencrypted (http:) and SSL-encrypted (https:) DAS servers are supported.

Libforester-java - wnpp
Libraries for evolutionary biology and comparative genomics research
License: LGPL 2.1+
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Version: 0.971-1

Forester is a library of Java software for phylogenomics and evolutionary biology research. It can be used to read or write phylogenetic trees, export trees to graphics file,...

Libswarm2-dev - wnpp
agent-based modeling to education, biomedical research and others
License: GPL-2+
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Version: 2.4.1-1

The Swarm conceptual framework for agent-based model (ABMs) and provides many tools for implementing, observing and conducting experiments on ABMs. Users write their own software but (a) follow Swarm's conceptual framework and conventions to design the software, and (b) use the Swarm libraries to do much of the work. The library is written in Objective-C.

This package contains the development files and documentation for developing agent-based models using Swarm.

Unofficial packages built by somebody else

Libmems-1.5-1
library to support DNA string matching and comparative genomics
Responsible: Andreas Tille
License: GPL

libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements.

No known packages available but some record of interest (WNPP bug)

Libgbfp-dev - wnpp
GBParsy is a GenBank flatfile parser library
Responsible: Scott Christley
License: GPL
Debian package not available
Language: C

GBParsy is a library of functions that parses the GenBank flatfile, which is a representative and popular sequence format. The library is optimized for speed and efficient use of memory so it can rapidly parse large sequence such as Arabidopsis chromosome for genomic analysis.

Libgff-perl - wnpp
Perl bindings for GFF Annotation Protocol
Responsible: David Paleino
License: GPL-1+
Debian package not available

GFF (Gene Finding Feature) is a format for describing genes and other features associated with DNA, RNA and Protein sequences.

This package provides a Perl module to use GFF objects.

No known packages available

Bioclipse
platform for chemo- and bioinformatics based on Eclipse
License: Eclipse Public License (EPL) + exception
Debian package not available

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

Bioclipse will provide functionality for chemo- and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin. To stay updated on upcoming features, releases, new plugins etc, please register for the mailing list bioclipse-announce. The development is best followed on the Bioclipse Wiki where we document the progress and ideas of the development on a daily basis.

Octace-bioinfo
Bioinformatics manipulation for Octave
License: GPL-2+
Debian package not available
 aa2int:
   Convert amino acid characters into integers.
 aminolookup:
   Convert between amino acid representations.
 cleave:
   Cleave a peptide SEQUENCE using the PATTERN at the POSITION relative to the pattern.
 int2aa
   Convert amino acid integers into characters.
 seqreverse
   Reverse a nucleotide sequence.
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 167387