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Have been working on this white paper for weeks, and have been having a very rough time with all the links and reference material i have found online, finally got them organized but this is a very manual procedure are there any software's that:

1) Organize , sort and bookmark your links and reference pages and give you one click access to them

2) Auto generate the bibliography, based on what you already linked

3) Give you templates of research paper layouts

4) Templates and examples of index's

P.S: Need software for Windows XP, and it can be a paid software

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closed as off-topic by fixer1234, DavidPostill, mdpc, nc4pk, random Jul 10 '15 at 18:30

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up vote 14 down vote accepted

Have you taken a look at Lyx?

LyX is a document processor that encourages an approach to writing based on the structure of your documents (WYSIWYM) and not simply their appearance (WYSIWYG).

If you combine it with a good bibtex frontend like JabRef you have a winning duo.

Let's take your requests one by one:

Organize , sort and bookmark your links and reference pages and give you one click access to them

JabRef does a wonderful job with letting you enter, categorise and organise your bibliography entries.

JabRef screen

Auto generate the bibliography, based on what you already linked

This is a snap with Lyx. Simply include your JabRef-managed bibliography file and start quoting from it. Add a bibliography entry and it will be auto-generated.

Lyx citation

Give you templates of research paper layouts

Lyx, being based on Latex, has a wealth of formats suitable for various journals and institutions.

Templates and examples of indexes

Indexes are automatically managed, once you add index entries.

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+1 for suggesting LaTeX – Scott Pack Aug 20 '09 at 19:53
+1. I think the real problem is that people are brought up learning to use a piece of software that focuses on presentation when the assignment focuses on semantics. – Travis Aug 20 '09 at 20:44

Endnote is very good for this.

If you use Firefox, Zotero is an extension that is also pretty good. I used it for Chicago/Turabian papers, though at the time, it didn't have bibliography generation for it. Check here to see if yours is supported.

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+1 I can recommend Endnote for your bibliography, note that you can often download/import references from the scientific search engines. But this will probably only work if the software uses standard formats – Ivo Flipse Aug 20 '09 at 21:55
+1 for Zotero (but not Endnote...). Zotero can also import papers/metadata from scientific search engines, as they appear in Firefox. It also works well with BibTex and Lyx/LaTeX. – sblair Oct 25 '09 at 12:51

I believe Mendeley fits quite a few of your requirements.

alt text

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Have you tried Microsoft Onenote for keeping track of all your links and snippits and screen clippings, etc? Highly recommend, it is awesome!

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Flamory offers distraction-free bookmarking. With a single hotkey press, it saves selection, screenshot, and position within the document.

I used OneNote for a long time, but for me, the hardest part was to find the needed bookmark, after I've made hundreds of them. With Flamory things got better, because I can quickly scroll through visual thumbnails and even search by the content of bookmarked document.

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