Free finescale modeler software for mac

The CONSIDEO MODELER combines the leading methods for systems thinking. The MODELER allows to visualize, explore, evaluate, communicate and foresee intuitively the complex connections in any field. As easy to use as mindmapping though more powerful you will be able to model you everydays decisions.

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.
Note: In order to use the program you need to register first.
Enhancements:
- Removal of limits on the number of pseudo atoms, segments, the length of file names and most other strings, and the number of parameters in parameter files.
- Removal of the read_restyp() command. To read a user-defined residue type file, set restyp_lib_file when creating an environ object.
- Bug fix: the correct VDW radii (as selected by topology.submodel) are now used for PSA calculations (previously the all-hydrogen radii were used in all cases).
- Improved error handling: almost all errors should be recoverable now (using the standard Python exception handling mechanism) and incorrect input should trigger an error rather than causing Modeller to crash (please report any crashes as bugs to the developers).
- SALIGN bug fixes, improved binning of access classes.
- Modeller scripts are now more like real Python scripts; the PYTHONPATH environment variable is honored, and additional command line arguments can be given to your scripts (accessible as sys.argv).
- Bug fix for alignment.segment_matching(): correct alignment scores are now written.
- Support for AMD64 and EM64T (Opteron/Xeon64) Linux machines.
- DOPE model assessment now returns only the DOPE energy itself by default, ignoring other energy terms.
- Bug fix for model.restraints.pick() when used with absolute position restraints; always allow 1-atom restraints to pass the residue_span_range check.

Requirements:
Mac OS X 10.2 or later. For best performance, a Quartz Extreme compatible AGP video card is required.

Enhancements:
Version 0.9.5: Updated to shell version 1.6. See "About the Shell" for changes.

SDE for Oracle JDeveloper (Modeler Edition) 1.1 is regarded as a full featured and advanced UML CASE tool/plug-in tightly integrated with JDeveloper. This UML CASE tool supports full software development lifecycle - analysis, design, implementation, testing and deployment. This UML tool helps you build quality applications faster, better and cheaper. You can draw all types of UML diagrams in JDeveloper, generate Java code, reverse engineer Java code to class diagrams and generate documentation.

Other UML Modeling Tools / UML Plug-ins: Java Platform (Windows/Linux/Mac OS X):

• SDE for Oracle JDeveloper
• SDE for IBM WebSphere (WSAD)
• SDE for Borland JBuilder
• SDE for IntelliJ IDEA
• SDE for Eclipse
• SDE for NetBeans
• SDE for Sun ONE

Major Features:

1. The latest UML support (use case diagram, sequence diagram, collaboration diagram, object diagram, class diagram, statechart/state diagram, activity diagram, component diagram, deployment diagram)
2. Use case modeling (use case description, scheduling...)
3. Textual analysis for identifying candidate classes, use cases, actors, flow of events...
4. Business Workflow diagram
5. CRC Card diagram
6. Reverse engineering - code to model, code to diagram (Java to UML models, Java to UML diagram)
7. Instant Reverse for XML, XML Schema, Dot NET dll/exe, C++, CORBA IDL
8. Code Generation - generate code, model to code, diagram to code (UML to code, UML model to Java)
9. Incremental round-trip engineering
10. Automatic synchronization between source code and diagrams
11. Plug-in and template
12. Automatic diagram layout - rearrange classes and connectors in UML diagrams in different styles
13. Import/export XMI
14. Import Rational Rose
15. Export diagrams to SVG, PNG, JPG
16. Microsoft Visio Integration - draw UML diagrams with MS Visio shapes
17. Report generator for generating UML documentation to HTML or PDF
18. Version control
19. Multilingual support

White_dune is a low level VRML97 tool for Unix/Linux/MacOSX and M$Windows.
It can read VRML97 files, display and let the user change the scenegraph/fields.
Unlike most highlevel tools, it uses a light model based on the VRML97 standard.

White_dune is not finished yet, especially in the 3D preview window. But even if you do not see the node/field in 3D, you can graphically change the values.

White_dune is a simple NURBS/SuperFormula 3D Modeller, but it do not have tools to change polygon meshes (VRML IndexedFaceSet nodes) that can be taken seriously (yet).

IndexedFaceSet nodes can be created via conversion from NurbsSurface nodes oder SuperFormula PROTOs or by "pure VRML97" export, but for some tasks you may prefer to work with a polygon mesh 3D modeller with VRML97 export and rework the results (e.g. color, texture, lightning, animation, interaction....) in white_dune.

BaseTen is a freeware, open source database framework created in Cocoa for working with PostgreSQL databases. BaseTen has been designed with familiar, Core Data -like semantics and APIs.

Main features:
- BaseTen Assistant imports Core Data / Xcode data models.
- Discovers the database schema automatically at runtime, including 1-1, 1-many and many-many relationships.
- Database changes are propagated to clients automatically, without polling.
- In-memory database objects are uniqued, and objects fetched via relationships are faults by default.
- Support for RDBMS features like database-driven data validation, multi-column primary keys and updateable views.
- Autocommit and manual save/rollback modes, both with NSUndoManager integration.
- A BaseTen-aware NSArrayController subclass automates locking and change propagation.
- Fetches are specified with NSPredicates (the relevant portions of which are evaluated on the database).

System requirements:
-
- AppKit for the optional BXSynchronizedArrayController.
-

Enhancements
BaseTen:
- BaseTens date and time type handling has been significantly overhauled.
- Timestamp and datetime types are now always returned as NSDates.
- NSDates are stored into the database in UTC. When fetching, database values are assigned the UTC time zone, or, if they are qualified with some other time zone on the database, converted to UTC.
- NSCalendar is now used instead of NSCalendarDate when converting NSDates to date strings.
- PostgreSQL "time" types are now handled. On the Cocoa side, they are converted to NSDates with the appropriate time offset from the reference date.
- New and changed data type support
- The XML data type can now be fetched as NSXMLDocument. This happens if the database schema is enforcing document-only values with a constraint such as CHECK(column IS DOCUMENT).
- "bit" and "varbit" fields are now fully supported. They are fetched as NSStrings because they cant easily be represented as octets.
- In additiong to fetching "point" fields as NSPoints, NSPoint values can now be saved into the database.
- Changes to the way BaseTen supports database relationships
- The default key names for to-many relationships have changed to the format "Set". The previous form, "", is now deprecated. Add a symbolic breakpoint to BXDeprecationWarning to find uses of these deprecated keys.
- BaseTen can now extract direction-specific relationship names from a foreign key constraints name. The combined length of these two names can be a maximum of 61 bytes of UTF-8. This facility is used by the updated BaseTen Assistant to import the direction-specific names from Xcode Data Modeler schemas.
- When creating new objects with a field values dictionary, to-one related objects (or their object IDs) can now be specified as an alternative to specifying the values of the foreign key fields. The relationship name is used as the key.
Other changes:
- All text transferred between the database and BaseTen will now be normalized to Unicode normal form D, ie. the format produced by -[NSString decomposedStringWithCanonicalMapping].
- Most locking queries sent by BaseTen can now be disabled, and documentation has been added to describe the locking functionality.
- More of BaseTens internals have now been documented in the reference manual.
- When inserting, updating or deleting rows, BaseTen now notices (and posts notifications of) changes that occur as a result of database triggers or rules firing. The only requirement is that said changes are to entities other than the one being changed by BaseTen; changes to the same entity will still be ignored.
- BXDatabaseObjectID is now documented as thread-safe since it only uses NSURL.
- BXSetProxies are now declared as deriving from NSMutableSet, as the NSCountedSets countability property isnt currently used by BaseTen.
- BaseTen will no longer try to unescape non-"bytea" columns.
- More SSL status codes are now available for determining when SSL is unavailable, automatic SSL certificate verification fails, user clicks Cancel in the certificate trust panel or some other SSL error occurs.
- Worked around potential issues with garbage collection where BaseTen used pointers to objects internal structures.
- KVO willChange notifications sent from -setPrimitiveValue:forKey: are now always called before the update. In certain cases with earlier BaseTen versions, observers might receive the notification after the change had been made.
- Some connection error messages are now more accurate.
BaseTenAppKit:
- BXSynchronizedArrayController can now remove objects even if the content set is bound to another array controller.
- BXSynchronizedArrayControllers property fetchesOnConnect is now called fetchesAutomatically. If its set, a fetch will also be performed when an already-connected database context is assigned to the array controller.
- BaseTenAppKit now embeds the Interface Builder plug-in. Interface Builder loads the plug-in if the framework has been added to a project.
- Fixed a crasher which occurred when connecting to a server with SSL capability in asynchronous mode.
- Fixed awkward user interaction when clicking Cancel in the certificate trust panel.
- Fixed a bug which caused object creation to fail if BXSynchronizedArrayController was instantiated in a nib and hadnt performed a fetch.
BaseTen Assistant:
- BaseTen Assistant can now name both sides of one-to-many and one-to-one relationships with the names entered in the Xcode Data Modeler.
- Optional relationships are now be created as optional and required relationships as required.
- Columns will no longer be created for transient attributes in data models.
- Relationships are now listed in the Inspector and info windows.
- A graphical representation of the database schema can now be created for use with Graphviz or OmniGraffle.
- Temporary information can now be deleted from BaseTen schema.
- Help is now more comprehensive.

GEMS is designed to allow developers to rapidly create a graphical modeling tool with no coding and immediately begin addressing the challenging aspects of these types of complex domains.
GEMS provides extensive support for integrating intelligent mechanisms into a modeling tool to provide visual modeling queues, simulation, constraint-compliant batch processing, and analysis.
The goal of the Generic Eclipse Modeling System (GEMS) is to bridge the gap between the communities experienced with visual metamodeling tools, such as the Generic Modeling Environment (GME), and those built around the Eclipse modeling technologies, such as the Eclipse Modeling Framework (EMF) and Graphical Modeling Framework (GMF).
GEMS is an open project and encourages developers to extend, enhance, and use its tools. GEMS has been developed in conjunction with research work done in collaboration with Siemens, IBM, and PrismTech. GEMS is an open source project, based on the Eclipse License.
Main features:
- A graphical language for metamodel specification that can capture
- domain entities
- attributes of entities
- inheritance relationships
- connection and containment relationships between entities
- distinct modeling views
- graphical information, such as connection styles, colors, and fonts
- constraints
- GEMS provides extensive support for intelligent modeling guidance including
- automatic solving of inference-based constraints for connection and containment
- applying batch changes to a model that are guided by a set of global constraints
- visually suggesting connection endpoints and element parents that conform to the specified constraints
- support for simulations
- mechanisms for integrating constraint solvers
- mechanisms for creating re-usable templatized constraint solvers
- mechanisms for discovering why a model cannot meet a set of global domain constraints
- graphical mechanisms for suggesting optimal modeling decisions derived from a constraint solver
- A code generation framework, which does not require any coding or XML editing, for transforming a GEMS metamodel into a working Draw2D/GEF Eclipse plug-in for editing instances of the language
- Ecore Model
- EMF Classes
- GEF/Draw2D Figures
- GEF/Draw2D Edit Parts
- other GEF/Draw2D Infrastructure for creating the palette, etc.
- plugin descriptor for the tool
- build descriptor for the project
- classpath descriptor for the project
- The visual appearance of the generated modeling tool can be customized by creating CSS stylesheets to modify the icons, colors, fonts, connection styles, and other visual attributes of the modeling entities
- The views available to a modeler can be customized through a mechanism similar to CSS stylesheets
- The generated graphical modeling plug-ins, created by GEMS, support extensive external customization through extension points for
- adding code generators and transformation, such as Open Architecture Ware, Java Emitter Templates, and Atlas Transformation Language
- model pre and post processing
- model event listeners
- triggers for invoking actions (similar to database triggers)
- constraint languages
- menus
- palette customizers
- intelligent modeling guides
- model serializers
- GEMS provides built-in support for constraints written in Java, OCL, and Prolog
- constraints can also be used as triggers for invoking actions
- Models and constraint solvers can be accessed remotely using a built-in CORBA server
System requirements:
- Java 1.5 (or higher), the Eclipse Modeling Framework, and the Graphical Editor Framework.