Revisiting the gig economy: a Labor Day post

Biosystems Analytics

Reposted from my Ronin Institute blog post

The Ronin Institute’s Research Scholars are drawn from many different career stages, levels of experience and backgrounds, and given that we don’t advocate a single model of a career in scholarship (in contrast to the traditional academic pipeline), it isn’t surprising that Research Scholars explore many different means to support their scholarship (we are still analyzing the results of the independent scholarship survey we did last year, but this much is clear). For many Research Scholars who are also freelancers, especially those in the sciences, one common means of support is being hired for short or long-term projects by academic institutions, private companies or non-profit organizations. This may be in in full-time or part-time capacity as an independent contractor or consultant. Ideally these projects utilise the scholars’ unique research background and skills and the experience and skills gained during consulting activities will…

View original post 1,196 more words

Advertisements

Listen to a podcast interview with Alex Lancaster discussing new book

Biosystems Analytics

Listen to, or read a transcript of, a podcast interviewwith Biosystems Analytics’ and Python for the Life Sciences co-author, Alex Lancaster. The interview was recorded for our digital publisher Leanpub’s author podcast series, by Leanpub co-founder Len Epp. In a wide-ranging discussing Len discussed Alex’s career, funding in science, evolutionary biology, the state of the book publishing industry and many other things. The podcast was recorded back in November 2016.

View original post

Python for the Life Sciences now available in select book stores

Biosystems Analytics

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.

View original post

Python for the Life Sciences is now available on Leanpub

Biosystems Analytics

I’m very proud to announce that, together with my Amber Biology colleague Gordon Webster, that our book Python For The Life Sciences, is now available for purchase via Leanpub:

leanpubThe 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.

python-for-the-life-newYou 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: info@amberbiology.com

View original post

The limitations of Big Data in life science R&D

Biosystems Analytics

Big Data has become an increasingly large presence in the life science R&D world, but as I have blogged about previously, increasingly larger datasets and better machine algorithms alone, will not leverage that data into bankable knowledge and can lead to erroneous inferences.  My Amber Biology colleague, Gordon Webster has a great post over on LinkedIn leavening the hype around Big Data, pointing out that analytics and visualizations alone are insufficient for making progress in extracting knowledge from biological datasets:

Applying the standard pantheon of data analytics and data visualization techniques to large biological datasets, and expecting to draw some meaningful biological insight from this approach, is like expecting to learn about the life of an Egyptian pharaoh by excavating his tomb with a bulldozer

“-omics” such as those produced by transcriptomic and proteomic analyses are ultimately generated by dynamic processes consisting of individual genes, proteins and other molecules…

View original post 130 more words

Table of contents preview for Python for the Life Sciences

Biosystems Analytics

book-coverOur 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…

View original post 524 more words

Life scientists: what are you looking to code?

Biosystems Analytics

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 info@amberbiology.com  or on the more detailed post:

“Are you still using calculators and spreadsheets for research projects that would be much better tackled with computer code?” on the Digital Biologist.

View original post