Anyone have any favorite programming books ... perhaps on advanced perl, or anything that might be useful to comp bio? Looking for a good book to go through a little every day that wouldn't feel so much like homework...Any recommendations? Thanks for your time!
Building bioinformatics solutions with Perl, R and MySQL.
extremely readable with some good code. not solely programming focused (considerable conceptual descriptions of problems/solutions and also, as you would expect from the title, some statistics/numerical data manipulation in R).
When I got started I found a copy of David Cross's Data Munging with Perl helpful. Contains several good command line solutions to common problems.
Not a book, but the online tutorials for database programming at Perlmonks are also pretty good.
I also liked the Building Bioinformatics Solutions book (mentioned by @occam) -- at the time it came out it was one of the few books that demonstrated concisely how various open-source tools can be put together into a workflow.
More specific answers will depend on what you want to use Perl for -- data handling, algorithm development for some task, web-based development, etc..
I like Data Mining: Practical Machine Learning Tools and Techniques by Witten, Frank and Hall. From the Amazon description, Data Mining "offers a thorough grounding in machine learning concepts as well as practical advice on applying machine learning tools and techniques in real-world data mining situations". And, it works together with the excellent (Java based) Weka machine learning software. Good for beginners and advanced users alike.