Debian Med Biology development packages

The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl.

The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian.

The suggested package enhances the manual pages.

Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

SQUID -- библиотека функций языка C для анализа ДНК-последовательностей. В неё включены маленькие утилиты для преобразования, отображения статистики и другие функции для работы с ДНК-последовательностями.

Настоящее имя пакета - "squid", но так как в архиве пакетов уже есть squid (кэширующий прокси), пакет переименован в "biosquid".

AcePerl is an object-oriented Perl interface for the AceDB database. It provides functionality for connecting to remote AceDB databases, performing queries, fetching ACE objects, and updating databases. The programmer's API is compatible with the JADE Java API, and interoperable with the API used by BoulderIO.

AceDB is a genome database system developed since 1989 primarily by Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger Institute). It was originally developed for the C.elegans genome project , from which its name was derived (A C. elegans DataBase).

This module provides a Perl wrapper for the FANN library (http://leenissen.dk/fann/wp/).

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.

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

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.

Bio::PrimerDesigner предоставляет низкоуровневый интерфейс для двоичных исполняемых файлов primer3 и epcr, а также поддерживает методы для возвращения результатов. В дополнение к доступу к локальным установкам primer3 или e-PCR, он также предлагает возможность доступа к двоичным файлам primer3 через удаленный сервер.

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.

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.

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.

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.

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.

libGenome is a freely available toolkit for developing bioinformatic related software in C++. It is intended to take the hassle out of performing common tasks on genetic sequence and annotation data.

Among other things, libGenome can help you:

• Read and write Multi-FastA format files
• Read and write GenBank flat file database entries
• Append, chop, truncate, reverse, complement, translate, and otherwise mangle sequence data
• Access annotation in GenBank flat files

This is the development package containing the statically linked library and the header files.

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.

This package contains the GenomeTools static library and necessary header files.

Besides basic bioinformatics data structures, the library contains components for sequence and annotation handling, sequence compression, index structure generation and access, efficient matching, annotation visualization and much more.

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.

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.

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.

This package supplies development versions of NCBI's non-graphical C libraries, along with the corresponding header files.

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

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.

qsearch is a library for universal hierarchical clustering using an arbitrary distance matrix as input. It searches through the space of all possible unrooted trees of a given size and finds the closest match based on a weighted quartet cost function determined by the distance matrix. When used in combination with other feature extraction libraries such as libcomplearn this system can be used for fast and accurate phylogenetic reconstruction, linguistic analysis, or stemmatology.

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.

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.

'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.

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.

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.

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.

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.

LibSBML is a library designed to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with many example programs), but rather a library you can embed in your own applications. This package contains files necessary for development with libsbml.

The functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.

SRF (sort for Sequence Read Format) is a generic format capable of storing data generated by any DNA sequencing technology. This library is an implementation of SRF and provides basic input-output functions.

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.

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".

Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic biological applications.

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.

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.

The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments.

MCL is currently being used in sciences like biology (protein family detection, genomics), computer science (node clustering in Peer-to-Peer networks), and linguistics (text analysis).

This package provides functions to do work in bioinformatics in Octave, a numerical computation software. It contains functions to convert amino acid characters into integers (aa2int), convert between amino acid representations (aminolookup), cleave peptides (cleave), convert integers into amino acid characters (int2aa) and reverse a nucleotide sequence (seqreverse).

This Octave add-on package is part of the Octave-Forge project.

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.

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.

The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project.

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.

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.

Biobase is part of the Bioconductor project, and is used by many other packages. Biobase contains standardized data structures to represent genomic data, and functions that are needed by many other packages or which replace R functions.

Bioconductor is a project to develop innovative software tools for use in computational biology. It is based on the R language. You should already be quite familiar with R before using Bioconductor. Bioconductor packages provide flexible interactive tools for carrying out a number of different computational tasks.

Most other Bioconductor packages are not packaged for Debian, but this packages provides in its Debian documentation instructions on how to install unofficial auto-generated Bioconductor packages for Debian and Ubuntu systems, that are prepared by members of the Debian Med team.

Classes and methods for handling genetic data. Includes The package provides a library for the statistics environment R that contains classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, and more.

NOTE: THIS PACKAGE IS NOW OBSOLETE.

The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for information.

The package provides routines for the GNU R statistics environment for statistical Analysis of indirectly measured Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap.

BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.

SeqAn is a C++ template library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

This package contains the developer files, documentation and examples.

S4 generic functions needed by many other Bioconductor packages.

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

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.

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.

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

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

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.

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,...

OpenMM is a library which provides tools for modern molecular modeling simulation. This package provides C++ header files for the development with that library.

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.

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API.

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.

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.

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.

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.

 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.