What are the good study material for learning the application of mathematics for biology?
ITunes university is a great place to start. Although many of the free sources that are available from ITunes are available elsewhere (e.g., YouTube), such as the calculus material offered by MIT's OpenCourseWare, ITunesU offers you a way to search through free courses/lectures and other material better than perhaps any other source.
As for free textbooks in calculus, download the free texts from this site: http://classicalrealanalysis.info/Free-Downloads.php
Despite being free, the focus on calculus as the first step of analysis and the fact that they don't teach the ridiculous Riemann integral approach to integration all the mainstream calculus textbooks do make them free calculus textbooks superior to ones you'd pay $100 or more for. However, they aren't exactly "simplified" the way that e.g., The Calculus Direct, The Hitchhiker's Guide to Calculus, etc., are. There is one text I know of (Funny Little Calculus Text) which is simplified, but not well (in my opinion).
For discrete mathematics, I haven't been shown much or happened upon much, but do recommend this source: http://www.cims.nyu.edu/~regev/teaching/discrete_math_fall_2005/dmbook.pdf
For number theory and related topics (including elementary topics) see:
Online number theory lecture notes and teaching materials
(http://www.numbertheory.org/ntw/lecture_notes.html)
I can't vouch for the material, but I was made aware of a thorough free treatment of trig here: https://orion.math.iastate.edu/butler/PDF/trig_notes.pdf
While not simple (as this topic really can't be) for complex analysis I know of two free book-length treatments:
http://www.wisdom.weizmann.ac.il/~oded/PS/CC/all.pdf
&
http://rutherglen.science.mq.edu.au/wchen/lnicafolder/lnica.html
Sorry I can't offer more texts, but I would recommend searching through material ITunes University has brought together.
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