Software for writing scientific papers?

[earlycj5]

What do you mean? Lyx is just a WYSIWYG editor built on latex. I would stick to your template. WYSIWYG is not optimal for writing, nor typesetting. I actually don't know what they're good for besides eyecandy.

I'd hesitate to call Lyx a WYSIWYG, it's somewhere in-between a WSYWIG (MS Word, OOwriter) and Latex. More of a front-end for Latex for the uninitiated.

I do prefer just using Latex but for the boss who wants to track changes, Lyx offers that so I use it.

[XCan]

Ah, indeed you are right. It's more one of those WYSIWYM editor iirc.

[earlycj5]

Ah, indeed you are right. It's more one of those WYSIWYM editor iirc.

Yeah, I couldn't remember the term that they used, but that was it.

[Campitor]

If you just open the generated html file in Firefox and save as a text file, does that tidy it up at all? You might need to put it all in one column maybe.

Yes. you're right. The multicolumn, although really neat, is not good for exporting. I will try and do separate pages for each section: Introduction, Methods, Results, Discussion. Although using the 4 columns is nice because you can get a good idea of the hole paper. I thinks this software is going to be very useful. Thanks.

Allow me to suggest Zotero, particularly the very stable beta version which enables the collaboration you're seeking.

I love Zotero...but I only use it as a reference manager. My notes are limited to papers. I don't think is a good tool for my writing style. But it is an invaluable tool for research. I'm also developing a bunch of citation-styles for the biological sciences. CSL is still a bit limited though.

OO does support master documents where sections are in separate odt files and you can re-order them easily. And if you use the styles for you formating Image and table numbers are taken care off automatically.

Thanks for the suggestion. Most of the time I don't do that much writing to warrant a full article. Sometimes my notes are something like "Variation of inbreeding coefficients discussion goes here". So a hole document for that sentence would be overkill. Basket seems to be exactly what I needed.

Have you tried using restructured text or markdown? Their idea is a bit similar to latex, but both offer conversion to odt and latex.

No. Never heard of it. After some googling, it seems like a markup language similar (simplified) to HTML coding. Is that right? I thought about this for a while and I think it would be really nice if one could develop a markup system (maybe based on xml) where you could just write a single document and markup sections (a section may be a line or a paragraph or multiple paragraphs) based on a structure like: <idea>, <intro>, <methods>, <discussion>, <important>, <bogus>, etc. But these can be placed anywhere in the document, as ideas or paragraphs flow down randomly from the ether. Later on a compiler can put all these sections in a specific order: Introduction, Objectives, Methods, Ideas, etc. and export into html, text, or latex. I don't know... maybe my ADD is just beyond help. Thanks for the suggestion.

I think Mek & Tosj today released Papers, a new application designed to revolutionize the way scientists deal with scientific papers.

Isn't this a Mac Application?

Thank you all for your comments and suggestions.

[ahmatti]

No. Never heard of it. After some googling, it seems like a markup language similar (simplified) to HTML coding. Is that right? I thought about this for a while and I think it would be really nice if one could develop a markup system (maybe based on xml) where you could just write a single document and markup sections (a section may be a line or a paragraph or multiple paragraphs) based on a structure like: <idea>, <intro>, <methods>, <discussion>, <important>, <bogus>, etc. But these can be placed anywhere in the document, as ideas or paragraphs flow down randomly from the ether. Later on a compiler can put all these sections in a specific order: Introduction, Objectives, Methods, Ideas, etc. and export into html, text, or latex. I don't know... maybe my ADD is just beyond help. Thanks for the suggestion.

I haven't actually used either, but from what I have read they seem intresting. From what I read reStructuredText can be used to write a whole book with bibliography, tables and images and you can convert it to HTML, Latex or odt. Markup I guess is more for producing HTML documents. Stackoverflow has some anwers about the differences the http://stackoverflow.com/questions/3...structuredtext.

reStructuredText is a part of the Python docutils and is has been used to write the new Python documentation. I think the quickstart guide makes it seem simple enough. http://docutils.sourceforge.net/docs...uickstart.html and intend to give it a try.

I don't think a program for reordering papers based on the section headers exists, but it should brr possible to create a parser to reorder e.g restructredtext or Latex document based on primary headings. EDIT: It looks like you might get what you want with docutils: http://docutils.sourceforge.net/docs...-it-is-written

[Stan_1936]

....reStructuredText can be used to write a whole book with bibliography, tables and images and you can convert it to HTML, Latex or odt. ...

Have you tried using restructured text or markdown? Their idea is a bit similar to latex, but both offer conversion to odt and latex.

I experienced odt to latex and it doesn't work very well (I mean: a lot of cleaning and adjusting is needed......

None of the so-called "converters" to LaTeX offer a solution that does not require extensive cleaning and adjusting. Not even LyX. And certainly not OpenOffice/MS Word.

For journals, as was what the OP was interested in, forget about LyX....it'll butcher things! For other written material, LyX will do the job.