The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns. The nice thing is, most experienced OOP designers will find out they've known about patterns all along. It's just that they've never considered them as such, or tried to centralize the idea behind a given pattern so that it will be easily reusable.

Design Patterns: Elements of Reusable Object-Oriented Software

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Almost every expert in Object-Oriented Development stresses the importance of iterative development. As you proceed with the iterative development, you need to add function to the existing code base. If you are really lucky that code base is structured just right to support the new function while still preserving its design integrity. Of course most of the time we are not lucky, the code does not quite fit what we want to do. You could just add the function on top of the code base. But soon this leads to applying patch upon patch making your system more complex than it needs to be. This complexity leads to bugs, and cripples your productivity.

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Refactoring: Improving the Design of Existing Code

The performance of relational database applications often suffers. The reason is that query optimizers require accurate statistics about data in the database in order to provide optimal query execution plans. Unfortunately, the computation of these statistics must be initiated explicitly (e.g., within application code), and computing statistics takes some time. Moreover, it is not easy to decide when to update statistics of what tables in an application. A well-engineered solution requires adding source code usually in many places of an application. The issue of updating the statistics for database optimization is a crosscutting concern. Thus we propose to use aspect-orientation to automate the calculation. We show how nicely the update functionality can be modularized in an aspect and how easy it is to specify the exact places and the time when statistics updates should be performed to speed up complex queries. Due to the automatic nature, computation takes place on time for complex queries, only when necessary, and only for stale tables. The implementation language for the automated aspect-oriented statistics update concern is AspectJ, a well known and mature aspect-oriented programming language. The approach can however be implemented in any other aspect-oriented language. Unlike in traditional object-oriented pattern solutions, e.g. using the interceptor pattern, we do not have to modify existing code.

Aspect-oriented programming

物件導向軟體之架構(Object-Oriented Software Construction)探討

Jinsight is a tool that lets you visualize and explore many aspects of your Java program’s run-time behavior. It is helpful for performance analysis, debugging, and any task in which you need to better understand what your code is really doing. Jinsight was developed at IBM’s Research Division, and is available free as a technology preview.

Visualizing Object-Oriented Programs with Jinsight

The invention broadly and generally provides, in a computer-controlled display, a method of simplifying a graphical representation of a set of connected nodes comprising the steps of: (a) selecting a subset of the aforesaid set; and (b) under computer program control, hiding representations of all nodes except (i) nodes within the aforesaid subset and (ii) at least one node having a defined relationship to the aforesaid subset.

Method and system for automatically hiding irrelevant parts of hierarchical structures in computer user interfaces

A method and system are disclosed for manipulating a model, where that model represents some or all of a design. The design includes a multitude of design elements, the model includes a multitude of model elements, and each of the design elements is represented by a single model element. The method comprises the steps of generating a suite of documents from the model, each of the documents describing a view of the model; and displaying the documents to a user as a series of forms. The user provides information to the forms to change the documents, and changes to the documents result in both changes to the model and consistent changes across the suite of documents. In the preferred embodiment, the model identifies specific relationships between the elements of the model, and each of the model elements has defined properties.

Manipulating design models by editing generated reports

Design Patterns: Abstraction and Reuse of Object-Oriented Design (Reprint).

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John Vlissides

Papers

Visualizing Object-Oriented Programs with Jinsight

Method and system for automatically hiding irrelevant parts of hierarchical structures in computer user interfaces

Manipulating design models by editing generated reports

Design Patterns: Abstraction and Reuse of Object-Oriented Design (Reprint).

Composing Interfaces with Interviews