Free biological species concept software for linux

Biogenesis project is a unicellular organism evolution simulator.
Biogenesis simulates in a visual fashion the processes involved in the evolution of unicellular organisms in nature.
It tries to be a didactic approximation to the ideas of mutation or evolution, and can be enjoyed also as an entertainment.
Its intended to serve as a support to show students some basic biological facts. The idea of Biogenesis is taken from Primordial Life, but its an independent project.
Main features:
- The application should be multiplatform.
- There should exist translations in many languages. At the moment, there are only Catalan, English and Spanish translations.
- The representation should be abstract and simplified, but still scientifically accurate.
- It should be actively maintained.
- A good documentation should be enclosed with the application.
- It should be amusing.

GnuConcept is a colaborative mindmap tool for complex document creation. GnuConcept lets you draw the document concept map, edit all the concepts content and export it to several formats, like openoffice, xml or html.

The GnuConcept Interfaz is divided in two frames: the drawarea frame, where you can draw the concept tree; and the textarea where you can write and edit the concept content.

GnuConcept is free software released under the GPL license.

Invasores project was first designed as a proof of concept of which language would be faster to develop games.

Bio::ClusterI module is a cluster Perl interface.

SYNOPSIS

# see the implementations of this interface for details but # basically
my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
-members =>[$seq1,$seq2]);
my @members = $cluster->get_members();
my @sub_members = $cluster->get_members(-species=>"homo sapiens");

This interface is the basic structure for a cluster of bioperl objects. In this case it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for.

Bio::Seq is a sequence object, with features.

SYNOPSIS

# This is the main sequence object in Bioperl

# gets a sequence from a file
$seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat);
$seqobj = $seqio->next_seq();

# SeqIO can both read and write sequences; see Bio::SeqIO
# for more information and examples

# get from database
$db = Bio::DB::GenBank->new();
$seqobj = $db->get_Seq_by_acc(X78121);

# make from strings in script
$seqobj = Bio::Seq->new( -display_id => my_id,
-seq => $sequence_as_string);

# gets sequence as a string from sequence object
$seqstr = $seqobj->seq(); # actual sequence as a string
$seqstr = $seqobj->subseq(10,50); # slice in biological coordinates

# retrieves information from the sequence
# features must implement Bio::SeqFeatureI interface

@features = $seqobj->get_SeqFeatures(); # just top level
foreach my $feat ( @features ) {
print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
$feat->end," strand ",$feat->strand,"n";

# features retain link to underlying sequence object
print "Feature sequence is ",$feat->seq->seq(),"n"
}

# sequences may have a species

if( defined $seq->species ) {
print "Sequence is from ",$species->binomial_name," [",$species->common_name,"]n";
}

# annotation objects are Bio::AnnotationCollectionIs
$ann = $seqobj->annotation(); # annotation object

# references is one type of annotations to get. Also get
# comment and dblink. Look at Bio::AnnotationCollection for
# more information

foreach my $ref ( $ann->get_Annotations(reference) ) {
print "Reference ",$ref->title,"n";
}

# you can get truncations, translations and reverse complements, these
# all give back Bio::Seq objects themselves, though currently with no
# features transfered

my $trunc = $seqobj->trunc(100,200);
my $rev = $seqobj->revcom();

# there are many options to translate - check out the docs
my $trans = $seqobj->translate();

# these functions can be chained together

my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate();

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface.

In Bioperl we have 3 main players that people are going to use frequently

Bio::PrimarySeq - just the sequence and its names, nothing else.
Bio::SeqFeatureI - a location on a sequence, potentially with a sequence
and annotation.
Bio::Seq - A sequence and a collection of sequence features
(an aggregate) with its own annotation.

Although Bioperl is not tied heavily to file formats these distinctions do map to file formats sensibly and for some bioinformaticians this might help

Bio::PrimarySeq - Fasta file of a sequence
Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table
Bio::Seq - A single EMBL/GenBank/DDBJ entry

By having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See Bio::PrimarySeq and Bio::SeqFeatureI for more information.

Ian Korf really helped in the design of the Seq and SeqFeature system.

Bioperl project is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS).
On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
In order to take advantage of bioperl, the user needs a basic understanding of the perl programming language including an understanding of how to use perl references, modules, objects and methods. If these concepts are unfamiliar the user is referred to any of the various introductory or intermediate books on perl.
Weve liked S. Holzmers Perl Core Language, Coriolis Technology Press, for example. This tutorial is not intended to teach the fundamentals of perl to those with little or no experience in the perl language. On the other hand, advanced knowledge of perl - such as how to write a object-oriented perl module - is not required for successfully using bioperl.
Bioperl is open source software that is still under active development. The advantages of open source software are well known. They include the ability to freely examine and modify source code and exemption from software licensing fees.
However, since open source software is typically developed by a large number of volunteer programmers, the resulting code is often not as clearly organized and its user interface not as standardized as in a mature commercial product.
In addition, in any project under active development, documentation may not keep up with the development of new features. Consequently the learning curve for actively developed, open source source software is sometimes steep.
Enhancements:
- Many bugfixes and enhancements were made, including support for parsing the latest NCBI BLAST text format changes, PAML 3.15 support, a Taxonomy (Bio::Species) overhaul, a Bio::Map overhaul, a Bio::SearchIO speedup, the introduction of a Build.PL installation system, and fixes for some memory leaks in Bio::Tree.
- This version requires Perl 5.6.1 or later.

Bio::Map::CytoMap is a Bio::MapI compliant map implementation handling cytogenic bands.

SYNOPSIS

use Bio::Map::CytoMap;
my $map = new Bio::Map::CytoMap(-name => human1,
-species => $human);
foreach my $marker ( @markers ) { # get a list of markers somewhere
$map->add_element($marker);
}

This is the simple implementation of cytogenetic maps based on Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map.

For CytoMaps type is hard coded to be cytogeneticmap and units are set to but can be set to something else.

Bio::GMOD::Admin::Monitor::blat is a Perl module that can monitor a BLAT server.

SYNOPSIS

Check the installed version of a MOD
use Bio::GMOD::Util::CheckVersions.pm
my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase);
my $version = $gmod->live_version;
Update a MOD installation
use Bio::GMOD::Update;
my $gmod = Bio::GMOD::Update->new(-mod=>WormBase);
$gmod->update();
Build archives of MOD releases (coming soon...)
Do some common datamining tasks (coming soon...)

Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.

MODs are highly curated resources of biological knowledge. MODs typically incorporate the typical information found at common community sites such as NCBI. However, they greatly extend this information, placing it within a framework of experimental and published observations of biological function gleaned from experiments in model organisms.

Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.

Bio::GMOD aims to solve these problems by:

1. Making MODs easy to install
2. Making MODs easy to upgrade
3. Enabling cross-MOD data mining through a unified API
4. Insulating programmatic end users from model changes

NOTES FOR DEVELOPERS

Bio::GMOD.pm uses a generically subclass-able architecture that lets MOD developers support various features as needed or desired. For example, a developer may wish to override the default methods for Update.pm by building a Bio::GMOD::Update::FlyBase package that provides an update() method, as well as various supporting methods.

Currently, the only participating MOD is WormBase. The authors hope that this will change in the future!