Free carolina biological software for linux

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq.

SYNOPSIS

# Bio::PrimarySeqI is the interface class for sequences.

# If you are a newcomer to bioperl, you should
# start with Bio::Seq documentation. This
# documentation is mainly for developers using
# Bioperl.

# to test this is a seq object

$obj->isa("Bio::PrimarySeqI") ||
$obj->throw("$obj does not implement the Bio::PrimarySeqI interface");

# accessors

$string = $obj->seq();
$substring = $obj->subseq(12,50);
$display = $obj->display_id(); # for human display
$id = $obj->primary_id(); # unique id for this object,
# implementation defined
$unique_key= $obj->accession_number();
# unique biological id

# object manipulation

eval {
$rev = $obj->revcom();
};
if( $@ ) {
$obj->throw(-class => Bio::Root::Exception,
-text => "Could not reverse complement. ".
"Probably not DNA. Actual exceptionn$@n",
-value => $@);
}

$trunc = $obj->trunc(12,50);

# $rev and $trunc are Bio::PrimarySeqI compliant objects

This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers only class which defines what methods have to be implmented by other Perl objects to comply to the Bio::PrimarySeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information on the main class for sequences.

PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the larger object complete with features. There is a pure perl implementation of this in Bio::PrimarySeq. If you just want to use Bio::PrimarySeq objects, then please read that module first. This module defines the interface, and is of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl sequence objects, even though it is not using Perl to store the sequence etc.

This interface defines what bioperl consideres necessary to "be" a sequence, without providing an implementation of this. (An implementation is provided in Bio::PrimarySeq). If you want to provide a Bio::PrimarySeq compliant object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap, generally by providing a wrapper class which would inheriet from your object and this Bio::PrimarySeqI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object.

Aeromys is a webmail application designed for extremely fast access to email through the web. An interesting feature of the aplication is that it caches the messages from the server before user requested it.
I had the idea for Aeromys several years ago when I was thinking about how PHP was essentially an inappropriate technology for writing a web application. I like to make the distinction between a web site, and a web application. A web site is what you are looking at right now, it displays information and can be navigated. It is by nature in page-form. However, an application is different. It takes much more processing and more overhead. This is the problem I saw with most web applications written in PHP. They were slow, not because of a flaw in their design or poor implementation, but simply because of the nature of HTTP and PHP.
As I got to thinking about it, I realized that the application server model is much more appropriate. Application servers have been in use for quite a while, they are not a new or novel concept. However, as Ill show later, some of the things Im trying to do with Aeromys are new to the webmail domain, and are pretty exciting.
Another inherent problem with using PHP for web applications is that there is a lot of down time. PHP can only run after a user has requested a page. That is, Apache will spawn the PHP process, parse the PHP script, and execute it. All this time, the user is waiting on the other end. Delays of even a second are noticed. In a webmail application, these kind of delays are common because the PHP process must connect out to the IMAP server, which takes time.
Enter Aeromys. Aeromys has a webmail daemon (webmaild) that is constantly running in the background. This daemon keeps track of the users who have logged into the system and keeps their IMAP connections alive between page loads. Also, while the user is reading his or her email, this daemon takes advantage of the down time and pre-fetches information that it thinks will be requested for the next page load. This is what I call "predictive caching." When the user makes the next page request, hopefully the information required for building that page will have already been cached and can be displayed instantly.
This semester (Spring 2005), I am working on Aeromys as an independant study project under Dr. Peter Wurman at North Carolina State University in Raleigh, NC. It is my hope to continue this work on through as my masters thesis and possibly a doctoral dissertation. So I have a personal vested interest in this project.
Enhancements:
- Added basic sorting method
- Switched back-end libraries from c-client to libEtPan
- Improved interactive mode
- Improved logging and debugging capabilities
- Fixed several crash bugs

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools.
Enhancements:
Documentation updates
- Addition of an extensive discussion of the leastsquares_superposition and RMSD-calculation methods, including a description of the mathematical theory behind their operation.
- Fully documented the rotation/translation methods
- Addition of a documented example program ("gyration_radius.cpp")
Bug fixes
- Fixed copy construction bug in PDBAtomDecorator that caused compilation errors in rare situations.
- Fixed a bug in PDBFileParser that caused a compilation error in the PDBSystem copy constructor.
- Fixed a const-conversion bug in GroupedElementIterator which prevented proper interoperation of const and non-const iterator types.
- Fixed a crash-producing bug in stream output for the TypeID class.
- Fixed a math error in RMSD and superposition methods that would corrupt molecule coordinates.
- Fixed a bug that caused all default-constructed PDBAtom objects to be treated as HETATMs.
Feature additions
- Added operator[] to AtomicStructure and PolymerStructure-derived classes.
- Added protected increment() and decrement() operators to TypeID class.
- PDBFileParser can now handle PDB files with ill-formed residue numbering (i.e. Files where residue numbers are repeated in successive chains).

Xholon runtime framework executes applications that are event-driven or that have highly dynamic structure or behavior. Specify your models using XML and Java, or using third-party UML2 tools and MDA transformations.
To get started, read or actively work through the basic HelloWorld tutorial. Its a very simple application, but it demonstrates many of the main concepts.
For more detail on the concepts behind Xholon, you might want to read one of the papers thats been published. These describe how to model cells and other complex biological entities using tools designed for developing real-time and embedded systems.
This earlier work used Rational Rose RealTime and C++, rather than the current Java. Xholon is intended to be a runtime framework that can execute the same types of systems described in those papers, plus many more traditional non-biological event-driven systems.
The goal of the Cellontro sister project is to develop complex biological simulations using the Xholon framework. Most of the features described in the published papers have been re-implemented as Cellontro applications using Xholon.
Also have a look at the sample applications that are included with the Xholon software. These give an idea of the range of applications that can be supported by the Xholon runtime framework.
These have been employed as use cases to determine what functionality is most important in Xholon. The digital watch simulation is a good example of a Xholon application with a hierarchical state machine, developed using a UML modeling tool.
A Xholon is essentially a holon. A holon is an entity that lives within a hierarchical structure, and is both a whole and a part at the same time.
In mainstream computer science terms, a Xholon is a node in a tree. The node has a single parent, possibly one or more children, and possibly one or more siblings. A Xholon may also be an active agent able to interact in real-time with other Xholons in the tree.
In UML2 terminology, a Xholon is a structured classifier that may exist as a part within other structured classifiers, and that may in turn contain other structured classifiers as parts of itself. The result is a hierarchical containment structure, nested to an arbitrary number of levels.
As a part, a Xholon plays a specific role within another structured classifier. Xholons are UML classes that are subsequently refined using UML2 composite structure diagrams. Structured classifiers interact with each other through ports, by passing messages or by making function calls.
Using the more philosophical terminology used to describe holons, a Xholon is something that is simultaneously both a whole and a part. Since everything in the universe is a holon, then everything running within a computer application should be a Xholon. The term holon was invented by Arthur Koestler in 1967.
The Xholon Project is inspired by biological concepts. A major incentive behind the project is to build a run-time environment that is equally adapted to running simulations of biological systems, and to running more traditional real-time, embedded and other event-driven reactive systems.
Xholon applications may contain structures that are highly mutable. A Xholon is an active agent that can modify the tree structure in which it lives. It can navigate the tree to interact with any other node, it can add, delete or modify other nodes, it can exchange messages with other nodes, and it can move itself to another position within the tree.
The Xholon Project incorporates many concepts of the Real-time Object-Oriented Modeling (ROOM) methodology, much of which has been incorporated into UML2. At the same time, Xholon removes some of the limitations of ROOM to allow for greater flexibility, mutability and mobility of active objects.
The Xholon run-time can serve as a target for a Model Driven Architecture (MDA) transformation pipeline. MDA stresses the importance of models, and the ability to transform those models, through a series of steps, into an executing target system.
You can create your model using a UML tool such as Gentlewares Poseidon or NoMagics MagicDraw, save the model as an XMI file, transform it using XSLT (or by some other MDA means) into a Xholon model and application, and then execute the model.
Enhancements:
- UML state machine simulation capabilities have been extended, including animation, and fork, join, junction.
- Additional Agent-Based Modeling functionality is available.
- The NetLogo-like syntax has been enhanced.
- The architecture is more flexible and is ready to more fully support integration of multiple domains.
- Histograms and probability distributions are now available. Line charts update in real-time.
- Numerous other modeling, simulation, transformation, and execution features have been added.

HASAS is a HydroAcoustic Signal Analysis System. Is a modular system for passive sonar signal analysis.

It can be used for biological research or surveillance, for example. The soundcard is used as input device, and it currently includes all the very basic functionality; beamformed audio, direction finding, level histogram, LOFAR/DEMON (narrowband spectrogram), wideband spectrogram, and raw audio.

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.