And there is a similar question on stackoverflow, but this time the inquirer doesn't have a name similar to yours :-)

I think that any good bioinformatician should read at least once the Software Carpentry for Biologist tutorial, or at least be familiar with all the subjects explained there. Titus Brown, author of pygr and python core developer, wrote a similar manual called Advanced Software Carpentry, which is also worth reading.

I am not aware of free books on bioinformatics that available online. Looking forward for other members on BioStar to share their thoughts.

Alternate resources:

• Bioinformatics at Wikipedia
• EBI 2Can: a bioinformatics education portal maintained by EBI

You can search for "bioinformatics" at NCBI book shelf. An interesting example is NCBI hand book: it is a tutorial style handbook that explains various analysis workflows in bioinformatics with good overview. See Genome Assembly and Annotation process

If you are particularly interested in Bio-* libraries check the cook book style how-to's at BioPerl, BioPython, BioJava and BioRuby

Other potential free resource will be online course material like MIT Open Course ware. Results from a quick search using bioinformatics is here

I like the online book "Producing Open Source Software: How to Run a Successful Free Software Project".

Lots of other books are free when you raid friend's bookshelves, libraries (print and ebooks), and http://www.swaptree.com :)

ETA: Just found some more free books at the "NCBI Bookshelf" (now searchable via PubMed)

Specifically bioinformatics related:

• "Bioinf in Tropical Disease Research"
• "NCBI C++ Toolkit"
• "UMLS Ref Manual"
• And presumably more to come?

I had answered a similar question here, to a similarly-named colleague :)