We had a workshop! On binder!
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Is mybinder 95% of the way to next-gen computational science publishing, or only 90%?
If you haven't seen mybinder.org, you should go check it out. It's a site that runs IPython/Jupyter Notebooks from GitHub for free, and I think it's a solution to publishing reproducible computational work.
For a really basic example, take a look at my demo Software Carpentry lesson. Clicking …
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Docker workshop at BIDS - post-workshop report
We just finished the second day of a workshop on Docker at the Berkeley Institute for Data Science. I was invited to organize the workshop after some Berkeley folk couldn't make our Davis workshop in November, and so I trundled on down for two days to give it a try …
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Transcriptomic analysis with Docker containers and data volumes
As part of our Docker hands-on workshop earlier this month, I learned a lot about building Dockerfiles, running Docker containers on remote hosts with docker-machine, and using data volumes to manage data in remotely hosted Docker containers.
During and after the workshop, I put together Docker images (and, more importantly …
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Adventures in replicable scientific papers: Docker
About a month ago, I took some time to try out Docker, a container technology that lets you bundle together, distribute, and execute applications in a lightweight Linux container. It seemed neat but I didn't apply it to any real problems. (Heng Li also tried it out, and came to …
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PyCon sprints - playing with Docker
I'm at the PyCon 2015 sprints (day 2), and I took the opportunity to play around with Docker a bit.
First, I created a local docker container that contained an installed version of khmer. I ran a blank docker container:
docker run -it ubuntu
and then installed the khmer prereqs …
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