Episode 02 – Systems Biology with Pedro Beltrao

After a long wait episode 02 is now done. It includes some musings on Systems Biology and an interview with Pedro Beltrao (starting at 7:10). The full collection of links (articles, clips, tracks etc.) is here and brief show notes bellow. The gap between episodes has admittedly been long but I’m giving myself a pass just this once. During that time there were funding issues at my current company; as a result I’ve negotiated a new job (more on that soon), and took a holiday. I don’t want to make any claims about release frequency, although ideally once per month, but for now let’s just say that each episode will be done when it’s done. Finally, thanks to Pedro for doing the interview and leave a comment if there any problems with the feeds, iTunes or audio quality.

Introduction

  • Why Systems Biology?

Biological Complexity

Interview: Pedro Beltrao

Scale, complexity, synthetic biology

Wrap-up

Episode 01 – Neil Saunders

Welcome to nodalpoint rebooted as a podcast (if you don’t care about the ‘why’, just scroll to the end and hit play).  I started nodalpoint when I was a graduate student about 10 years ago and it evolved into one of the early bioinformatics/science blogging networks. For a bit more on  the history of nodalpoint, please see this post. The site was active until at least last year, but as I moved on in my science career (mainly in industry), I found less and less time to maintain nodalpoint. There were some great contributions by Duncan Hull towards then end, however without a driver people ended up drifting off to do independent blogs. Although I had less time for nodalpoint, I was still following the conversation on blogs, Friendfeed, and now Twitter. I still wanted a way to contribute, but something a little more low-key and independent; with less requirement for frequent updates.

I have always been fascinated with radio, and the natural extension of radio for the Internet is of course podcasting. At the moment I have a train journey to work, which is the perfect time to listen to podcasts. With the notable exceptions of Deepak and Hari’s Coast to Coast Bio Podcast, I could not find any science podcasts relevant to me as a computational biologist. Of course there are plenty of podcasts in the style of what-kind-of-wacky-stuff-has-science-discovered-this-week, and some slightly better general science podcasts from Nature, Science and Futures in Biotech. And so it finally came together: a niche, the desire to reboot nodalpoint, and the expectation for updates on most podcasts not as frequent as blogs, delusions of radio grandeur etc.

I grabbed a mic, fired-up an audio editor, and then proceed to fall straight into a technology rabbit hole; of course I had to do it all on Linux which added an extra level of difficulty. I won’t cover the nuances of professional sound editing and broadcasting, suffice it to say that it is easy to podcast, very hard to do it well. Surprisingly hard. Of course that rich radio sound is only a small part of the equation: content, delivery, and a suitable guest are what really matter. I managed to convince Neil Saunders to be part of this amateur broadcasting indulgence of mine. Neil was a significant early contributor to nodalpoint and now has his own blog: What You’re Doing is Rather Desperate. So with a deep breath and production values be damned, I give you Nodalpoint Conversations Episode 01.

Part 1

Interlued 1

Part 2

  • What technologies interest you: metagenomics
  • Pipelines and workflow tools
  • Exploratory data analysis vs. workflow environments
  • Bio* tool kits
  • Your day-to-day work tools: ubuntu, ruby
  • Programing language discussion, why ruby ?
  • Monitoring the conversation: Blogs, Twitter and Friendfeed, a distraction ?

Interlude 2

  • Reflections on how we work as computational biologists

Part 3

  • Can open science work in the same way open source does
  • Ratio of users to contributors to open source projects is large
  • Why contribute ? Outreach is just a good thing.
  • The mad sci-network
  • Awareness, of open source, open science in the workplace.
  • Awareness, but no uptake. Reference management apears to be the issue.
  • Being cautious when making scientific claims

Wrap-up

  • Thoughts on the future of nodalpoint conversations