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Does anyone know if there exist a Latex manual with focuses on chemistry and perhaps also system biology?

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I'm not sure exactly what you'd want in such a text. The basics of LaTeX stay much the same, and at least in chemistry most of the 'specialism' consists of diagrams which I'd suggest may well be best created using an external tool. –  Joseph Wright Sep 16 '12 at 15:22
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All the manuals of all the packages listed here: mychemistry.eu/known-packages. Although -- that's probably overkill. But you should be able to find some useful information there :) –  cgnieder Sep 16 '12 at 15:22
    
Basically, concerning some "typography issue" like "chemical equations and molecule structures", the best thing to do is to go through a few manuals of a few packages, choose the one you like the most and become a master in using this one package step-by-step. –  tohecz Sep 16 '12 at 17:36
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I suggest follow the tohecz's comment. In www.ctan.org/keyword/physics there are a easy index of packages associated with the keywords of Chemistry, Biology (and Physics, obviously). Browsing in the directory of each package usually you can find a pdf manual (probably also in your hard disk).

Alternatively, go to texcatalogue.sarovar.org and then to Topical index and search for Biology or Chemistry

May be is also worth to mention the article LaTeX Tools for Life Scientists (BioTEXniques?).

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