I’m happy to announce that if you live in the Greater Boston area that our book, Python For The Life Sciences is now on a book shelf near you. You can pick up a copy at Harvard Book Store in Harvard Square, Cambridge, Porter Square Books in, you guessed it, Porter Square, Cambridge or The Book Rack in Arlington. We hope to continue to add more bookstores.
The book has ended up somewhat larger than originally planned, clocking in at over 300 pages, and covers a wide range of life science research topics from biochemistry and gene sequencing, to molecular mechanics and agent-based models of complex systems. We hope that there’s something in it for anybody who’s a life scientist with little or no computer programming experience, but who would love to learn to code.
You can download the complete first chapter for free at Leanpub and everybody who buys this first edition will have complete access to book updates to this particular edition. Help us improve the book by emailing us feedback or if you spot any errors to: email@example.com
Our Amber Biology book Python For The Life Sciences is now nearing publication – we anticipate sometime in the early summer of 2016 for the publication date. As requested by many folks we are releasing the first draft of the table of contents. If you’re interested in updates you can sign up for our book mailing list. You can also checkout a preview chapter on Leanpub.
Python at the bench:
In which we introduce some Python fundamentals and show you how to ditch those calculators and spreadsheets and let Python relieve the drudgery of basic lab calculations (freeing up more valuable time to drink coffee and play Minecraft)
Building biological sequences:
In which we introduce basic Python string and character handling and demonstrate Python’s innate awesomeness for handling nucleic acid and protein sequences.
Of biomarkers and Bayes:
In which we discuss Bayes’ Theorem and implement it in Python, illustrating in the…
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My Amber Biology colleague, Gordon Webster, and I are working on an accessible introduction for biologists interested in getting into programming. Python for the Life Scientists will cover an array of topics to introduce Python and also serve as inspiration for your own research projects.
But we’d also like to hear from you.
What are the life science research problems that you would tackle computationally, if you were able to use code?
You can contact us here in the comments, on firstname.lastname@example.org or on the more detailed post:
Innovation. It’s as American as apple pie. From the US President on down, everybody is talking about innovation. From university presidents and corporate leaders to Silicon Valley tycoons, all agree that we need more of it. Airport bookstores have walls of books on innovation: a quick search on Amazon resulted in 70,140 titles containing the word “innovation”, 711 of which were published in the last 90 days alone. Many of them are little more than generic business advice books with the word “innovation” shoehorned into the title, including gems such as Creating Innovation Leaders (earning bonus points for including buzzwords “leadership” and “creativity”). So it was with some trepidation that I recently picked up Scott Berkun’s The Myths of Innovation – first published in 2007 – and found it had a refreshing and unpretentious take on the subject. Since it has become such an overused buzzword, Berkun argues that…
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We are in the era of Big Data in human genomics: a vast treasure-trove of information on human genetic variation either is or will soon be available. This includes older projects such as the HapMap, and 1000 Genomes to the in-progress 100,000 Genomes UK. Two technologies have made this possible: the advent of massively parallel “next generation” sequencing where each individuals’ DNA is fragmented and amplified into billions of pieces; and powerful computational algorithms that use these fragments (or “reads”) to identify all the “variants” – any changes that are different to the “reference genome” – in each individual.
With existing tools this has become a relatively straightforward task. Identification of single nucleotide polymorphisms or variants (SNVs) – single base differences between the individual and the reference genome – especially medically relevant ones – is beginning to become routine. A project I worked on with…
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Author Peter Carey, one of Australia’s best known literary exports (he has lived in New York City for the past 20 years) is probably most identified with novels such as The True History of the Kelly Gang, Illywhacker, and Oscar and Lucinda which all draw heavily on Australian history and mythology of the late 19th and early 20th centuries. Oscar and Lucinda was also made into 1997 film film of the same name featuring Ralph Fiennes and Cate Blanchette. Despite this reputation, Carey has written novels that deal with more contemporary life, including the darkly comic Bliss, in which bored advertising executive, Harry Joy, is briefly clinically dead, but upon returning to life, finds himself in a reality that may, or may not, be a version of hell. (Bliss was also made into a highly underrated film, with the peerless Barry Otto as Joy). Carey’s most recent effort, Amnesia, delves into the very present day concerns of technology and surveillance. Largely split between a present-day “thriller” narrative and a slightly disheveled and cut-up history of both 1950s and 1980s Melbourne life as seen through the lens of politically active family, Amnesia fuses Carey’s brilliant use of language, with more overt political undertones.
Aaron Sorkin’s cable news drama The Newsroom wrapped up it’s third, and final season at the end of last year on HBO. As pure piece of entertainment it’s fun to watch, especially with a great cast and the pyrotechnic dialog for which Sorkin is a specialist, but as a commentary on the current state of news, it has some serious flaws, that bothered me enough to write them down. What’s that, you’ve never heard of The Newsroom? Well, allow me a brief recap: Jeff Daniels plays Will McAvoy, a cable news anchor of the Dan Rather/Tom Brokaw/Peter Jennings vintage on the fictional Atlantis Cable News (ACN) network (a sly dig at Atlanta-based CNN, no doubt). The series opens in the Q&A portion of a panel discussion on a university campus featuring McAvoy, when a college student asks a particularly naive question: “Can you say why America is the greatest country in the world?”. After a few attempts to avoid answering this directly (clearly he disagrees with the premise of the question), McAvoy decides enough is enough and starts channelling his inner Howard Beale (the fictional TV newscaster from the 1976 film Network who extorted his audience to open their windows and yell: “I’m as mad as hell, and I’m not taking it anymore”). McAvoy’s response is worth reading in detail, it’s pure Sorkin, the kind of thing that we all wish important people would say, but never do.Read More »
I have a new post on the Biosystems Analytics blog:
The sad passing of evolutionary computation and genetic algorithm pioneer John H. Holland earlier this week prompted me to think more about how his approach to complex adaptive systems research fits into the biological and biomedical landscape of research of today.