Free bio index blast software for linux

Domino Blast project is a physics-based driving/demolition game with a childrens toys theme.

Domino Blast is a hybrid driving and destruction game with a childrens toys theme. Its environments consist of buildings constructed from domino tiles and a player-controllable toy car. The objective of the game is to wreak as much havoc as possible, within a time limit.

Its game-play is simplistic yet satisfying; similar to the satisfaction gained from watching a tumbling Jenga tower, except the objective is to tumble the tower, rather than slowly deconstruct it. As the game progresses, levels become more dense and the buildings that inhabit them become larger and more complex.

Bio::NEXUS is a Perl module providing an object-oriented, Perl-based applications programming interface (API).

NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. It is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data).

The NEXPL library of Perl software (copyright 2004 Liang, Qiu and Yang) is distributed under an open source license (see LICENSE). If you use this software, please acknowledge:
Bio::NEXUS. An Object-oriented NEXUS API in Perl. T.J. Hladish, C.L. Liang, W.-G. Qiu, P. Yang, V. Gopalan and A. Stoltzfus. Available at http://www.molevol.org/camel/software.

INSTALLATION AND TESTING

This software has been tested under Linux as well as MaxOS X 10.2 and higher, and even a few Windows installations. The package installs using the standard procedure, and runs several hundred tests:

perl Makefile.PL
make
make test
make install

For more information, or to customize, see doc/Installation.pod.

Bio::Tree::NodeNHX is a Simple Tree Node with support for NHX tags.

SYNOPSIS

use Bio::Tree::NodeNHX;
my $nodeA = new Bio::Tree::NodeNHX();
my $nodeL = new Bio::Tree::NodeNHX();
my $nodeR = new Bio::Tree::NodeNHX();

my $node = new Bio::Tree::NodeNHX();
$node->add_Descendents($nodeL);
$node->add_Descendents($nodeR);

print "node is not a leaf n" if( $node->is_leaf);

Makes a Tree Node with NHX tags, suitable for building a Tree. See Bio::Tree::Node for a full list of functionality.

ruby index/search is a general indexing framework for ruby. With it, you can create collections of documents, then index and search them. Currently, both inverted indexing and LSA indexing are supported, with rudimentary result clustering in the works.

The indices may be marshalled out (with Marshal.dump()), then pulled back in with Marshal.load(), to allow for relatively quick search operations in both LSA and inverted indices.

Bio::Das::Lite is a Perl extension for the DAS (HTTP+XML) Protocol.

SYNOPSIS

use Bio::Das::Lite;
my $bdl = Bio::Das::Lite->new_from_registry({category => Chromosome});
my $results = $bdl->features(22);

SUBROUTINES/METHODS

new : Constructor
my $das = Bio::Das::Lite->new(http://das.ensembl.org/das/ensembl1834);

my $das = Bio::Das::Lite->new({
timeout => 60,
dsn => http://user:pass@das.ensembl.org/das/ensembl1834,
http_proxy => http://user:pass@webcache.local.com:3128/,
});

Options can be: dsn (optional scalar or array ref, URLs of DAS services)
timeout (optional int, HTTP fetch timeout in seconds)
http_proxy (optional scalar, web cache or proxy if not set in %ENV)
caching (optional bool, primitive caching on/off)
callback (optional code ref, callback for processed XML blocks)
registry (optional array ref containing DAS registry service URLs
defaults to http://das.sanger.ac.uk/registry/services/das)
proxy_user (optional scalar, username for authenticating forward-proxy)
proxy_pass (optional scalar, password for authenticating forward-proxy)
user_agent (optional scalar, User-Agent HTTP request header value)

new_from_registry : Constructor
Similar to new above but supports capabilities and category
in the given hashref, using them to query the DAS registry and
configuring the DSNs accordingly.

my $das = Bio::Das::Lite->new_from_registry({
capabilities => [features],
category => [Protein Sequence],
});

Options are as above, plus
capability (optional arrayref of capabilities)
category (optional arrayref of categories)

SVN::Log::Index is a Perl module that can index and search over Subversion commit logs.

SYNOPSIS

my $index = SVN::Log::Index->new({ index_path => /path/to/index });

if($creating) { # Create from scratch if necessary
$index->create({ repo_url => url://for/repo });
}

$index->open(); # And then open it

# Now add revisions from the repo to the index
$index->add({ start_rev => $start_rev,
end_rev => $end_rev);

# And query the index
my $results = $index->search(query);

SVN::Log::Index builds a KinoSearch index of commit logs from a Subversion repository and allows you to do arbitrary full text searches over.

Bio::Biblio is a Bibliographic Query Service module.

SYNOPSIS

use Bio::Biblio;
my $biblio = new Bio::Biblio;

print $biblio->find (perl)->get_count . "n";

my $collection = $biblio->find (brazma, authors);
while ( $collection->has_next ) {
print $collection->get_next;
}

#The new() method can get parameters, for example:

$biblio = Bio::Biblio
(-access => soap,
-location => http://industry.ebi.ac.uk/soap/openBQS,
-destroy_on_exit => 0);

# See below for some one-liners

This is a class whose instances can access bibliographic repositories. It allows to query a bibliographic database (such as MEDLINE) and then to retrieve resulting citations from it. The citations are returned in an XML format which is native to the repository but there are also supporting modules for converting them into Perl objects.

The detailed descriptions of all query and retrieval methods are in Bio::DB::BiblioI (an interface). All those methods should be called on instances of this (Bio::Biblio) module.

The module complies (with some simplifications) with the specification described in the OpenBQS project. Its home page is at http://industry.ebi.ac.uk/openBQS. There are also links to available servers providing access to the bibliographic repositories (namely to MEDLINE).
The module also gives an access to a set of controlled vocabularies and their values. It allows to introspect bibliographic repositories and to find what citation resource types (such as journal and book articles, patents or technical reports) are provided, and what attributes they have, eventually what attribute values are allowed.

Here are some one-liners:

perl -MBio::Biblio -e print new Bio::Biblio->get_by_id ("94033980")
perl -MBio::Biblio
-e print join ("n", @{ new Bio::Biblio->find ("brazma")->get_all_ids })
perl -MBio::Biblio
-e print new Bio::Biblio->find ("Java")->find ("perl")->get_count