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I want to design a website that, in addition to the usual parts like blog, contact us, image gallery, etc., has another part for books and articles. The admin must be able to enter book and article details (title, author, reference, publisher, publish date, etc.) to these posts and users must have an advanced search to find the books and articles which they want.

Since I use WordPress for the whole site, should I write plugins for the books and articles parts? Or use WordPress for the usual parts and write a separate PHP page for books and articles?

If you advise WordPress, how can I create an advanced search?

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You can use WordPress for everything you've mentioned. But your Question is overly broad, you should to narrow it down to a specific problem (and explain how you've tried to solve it). – akTed Feb 4 '13 at 22:55

You will want to register custom post types for each of the sections (books, articles, etc).

Your post types should be registered as a custom plugin so that they can be kept in the case you decide to switch your theme.

Custom post types: http://codex.wordpress.org/Post_Types

WordPress plugin API: http://codex.wordpress.org/Plugin_API

The advanced search is a bit trickier, but I wrote a commercial plugin for exactly that: http://pippinsplugins.com/advanced-search-shortcode/

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