Free entity relationship diagram software for linux

Bio::Ontology::Relationship is a relationship for an ontology.

SYNOPSIS

$rel = Bio::Ontology::Relationship->new( -identifier => "16847",
-subject_term => $subj,
-object_term => $obj,
-predicate_term => $pred );

This is a basic implementation of Bio::Ontology::RelationshipI.

The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (ontology). It is called triple because it is a tuple of three ontology terms.

There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of (child, relationship type, parent) would be equivalent to the terminology chosen here, disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. Especially in the case of ontologies with a wide variety of predicates the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds B), or even conflicting (e.g., A is-parent-of B), and are therefore strongly discouraged.

Ghost Diagrams is a project that takes sets of tiles and tries to find patterns into which they may be formed. The patterns it finds when given randomly chosen tiles are often surprising.

It turns out that tiling patterns are a form of computation of equal power to Turing machines, lambda calculus, and cellular automata. For example, here is a tileset implementing "Rule 110", a cellular automaton known to be capable of universal computation.

Considerations similar to the halting problem and Godels theorem apply. There is no upper limit to their capacity to surprise us. Furthermore, tiles have an intuitive quality that other forms of computation lack. You can see how they fit together.

An organism is more than the sum of its organs. When the organs are fitted together, the organism becomes something more. This surprising something more we call "spirit" or "ghost". Ghost Diagrams finds the ghosts implicit in simple sets of tiles.

Term::Animation is a Perl module that provides a framework to produce sprite animations using ASCII art. Each ASCII sprite is given one or more frames, and placed into the animation as an animation entity.

An animation entity can have a callback routine that controls the position and frame of the entity. The module can also do collision detection between entities.

INSTALLATION

To install this module type the following:

perl Makefile.PL
make
make test
make install

Myco::Entity is a common base class for all Myco entity classes.

SYNOPSIS

### Entity class definition

package Myco::Foo;
use base qw(Myco::Entity);

# Start building metadata
my $metadata = Myco::Entity::Meta->new
( name => __PACKAGE__,
tangram => { table => Foo }
);

$metadata->add_attribute(name => attr1, type => string);
$metadata->add_attribute(name => attr2, type => string);

# class-specific methods defined ...
#

# Fill in $schema with all added_attributes and discover other metadata
$metadata->activate_class;



### Entity class usage

use Myco::Foo;

# Constructor
$obj = Myco::Foo->new;
$obj = Myco::Foo->new(attr1 => value, attr2 => value);

# Access class metadata (see Myco::Entity::Meta)
$meta = Myco::Foo->introspect;
$meta = $obj->introspect;

# Accessors
$obj->get_attr1; # get attribute value
$obj->set_attr1(value); # set attribute value

# Instance methods
$id = $obj->save; # update objects state in persistent
# storage, create new record if needed;
# returns objects Tangram id
$obj->destroy;
$obj->modify(attr1 => val, attr2 => val);
$object_id = $obj->id;
$obj->is_transient; # returns true if object is in Tangram
# transient storage

## object retrieval (see class Myco documentation
# for full detail)

$obj = Myco->load($object_id);

# fetch all objects of given type
@objects = Myco->select(ref $obj);

Provides, via inheritence, common interface in support of basic lifecycle needs for myco entity objects.

This is accomplished through the encapsulation of the CPAN module Class::Tangram which provides a basis for "in-memory" object behavior. Consult its documentation for details on schema definition syntax, getter/setter behavior, check functions, etc.

The common interface for object persistence behavior (referred within myco as "transaction" behavior) is provided through defintion of a handful of related instance methods. This is done with reliance on the services of the class Myco, which encapsulates the functionality of Tangram::Storage and provides system-wide connection handling.

Unit Circle project shows the relationship between trigonometric and angles functions like sine and cosine. To do this, the program implements an interactive "unit circle" (radius = 1) diagram, where the user can click or drag to set angles and see how the values of trigonometric functions change accordingly.

The unit circle (where the radius equals 1) provides a very clear demonstration of how various trigonometric functions relate to angles and one another. Draw an angle line from the origin to a point on the circumphrence of the circle; the (x,y) coordinates of that point will will be the cosine and sine of the angle.

In Unit Circle, use the mouse to set the angle line by either clicking or dragging the pointer inside the diagram. Or, change the trigonmetric values in the fields, and the angle will automatically adjust.

The inspiration for this program was provided by my home-schooled daughters, who had difficulty understanding the nature of trigonometry. As an educational tool, Unit Circle has been a success, and it may evolve into a larger application for exploring other aspects of trigonometry and geometry.

Elixir is a declarative layer on top of SQLAlchemy. The project is a fairly thin wrapper, which provides the ability to define model objects following the Active Record design pattern, and using a DSL syntax similar to that of the Ruby on Rails ActiveRecord system.

Elixir does not intend to replace SQLAlchemys core features, but instead focuses on providing a simpler syntax for defining model objects when you do not need the full expressiveness of SQLAlchemys manual mapper definitions.

Examples:

The Elixir source distribution includes a sample web application that uses the TurboGears web application framework. The application builds upon the tutorials Movie model to create a simple store for buying movies.

The Video Store sample application also includes an example of how to use Elixir with the TurboGears "identity" framework for security and authorization. If you are planning to use Elixir with your TurboGears application, and need to support authorization using identity, you can use this model as a basis:

from turbogears.database import metadata, session
from elixir import Unicode, DateTime, String, Integer
from elixir import Entity, has_field, using_options
from elixir import has_many, belongs_to, has_and_belongs_to_many
from sqlalchemy import ForeignKey
from datetime import datetime

class Visit(Entity):
has_field(visit_key, String(40), primary_key=True)
has_field(created, DateTime, nullable=False, default=datetime.now)
has_field(expiry, DateTime)
using_options(tablename=visit)

@classmethod
def lookup_visit(cls, visit_key):
return Visit.get(visit_key)

class VisitIdentity(Entity):
has_field(visit_key, String(40), primary_key=True)
has_field(user_id, Integer, ForeignKey(tg_user.user_id, name=user_id_fk, use_alter=True), index=True)
using_options(tablename=visit_identity)

class Group(Entity):
has_field(group_id, Integer, primary_key=True)
has_field(group_name, Unicode(16), unique=True)
has_field(display_name, Unicode(255)),
has_field(created, DateTime, default=datetime.now)
has_and_belongs_to_many(users, of_kind=User, inverse=groups)
has_and_belongs_to_many(permissions, of_kind=Permission, inverse=groups)
using_options(tablename=tg_group)

class User(Entity):
has_field(user_id, Integer, primary_key=True)
has_field(user_name, Unicode(16), unique=True)
has_field(email_address, Unicode(255), unique=True)
has_field(display_name, Unicode(255))
has_field(password, Unicode(40))
has_field(created, DateTime, default=datetime.now)
has_and_belongs_to_many(groups, of_kind=Group, inverse=users)
using_options(tablename=tg_user)

@property
def permissions(self):
perms = set()
for g in self.groups:
perms = perms | set(g.permissions)
return perms

class Permission(Entity):
has_field(permission_id, Integer, primary_key=True)
has_field(permission_name, Unicode(16), unique=True)
has_field(description, Unicode(255))
has_and_belongs_to_many(groups, of_kind=Group, inverse=permissions)
using_options(tablename=permission)

More Elixir examples are coming soon, and we would appreciate any additional sample applications that you could provide to illustrate more complex mappings.