As I said I would do, I am now in the progress of setting up and seeding the biology in python community site, which can be found at bio.scipy.org. Part of the goal, as set at the SciPy 2007 Biology Birds of a Feather (BoF) meeting (organized by Titus Brown), is to establish a community site where anyone using Python in the field of Biology can come together, communicate, share ideas, and share code.

As part of the programming guide, I posted my “Preparing to learn python guide“, in which, I mention the things about Python I wish I had known when I started learning Python. I am guessing it will be most useful to those who have programmed before in another language and are trying to learn Python.

Also, I posted a link to Software Carpentry in the programming guide. Thanks Greg for starting that project!

During the Biology birds of a feather meeting at SciPy 2007, which was organized by Titus Brown, we meet to discuss were those of us using Python for biology/bioinformatics should work together as a community. Two interesting thoughts came up:

1. Need to establish python/biology community, via website, biology-in-python mailing list, rss, blogs, etc.
2. Having a core set of “interfaces” for handling basic bioinformatics objects would allow independent projects to share these basic objects. I am sure others will describe this better and in more detail in the near future.

I personally believe that even if we only accomplish the first item, it would significantly help the bioinformatics community. I do hope the 2nd is accomplished as well.

What I see is that most people who are new to the python bioinformatics community end up finding BioPython. The only problem is that many people doing bioinformatics with Python who choose not to use BioPython end up doing there own thing an not communicating with the community. The idea here is to make a new python/biology community site were we can communicate, share code, share ideas, etc. In other words support the community as a whole rather than just having communities for individual projects.

I agreed to setup this initial site and seed it information, bioinformatics python packages by category, a place holder for cookbooks, advice for testing and software engineering (referencing Greg Wilsion’s Software Carpentry material, etc.). I would like to thank Enthought as they have agreed to host the website. I will add the more information on the community site as it is being setup. We’ll see how it goes.

Also, check out Titus Brown’s Birds of a Feather post.

I made the previous two posts on “Global Warming” from videos (and descriptions) I found on Google Video. I have been interested in the effects of “Global Warming” for some time now. The movie An Inconvenient Truth sparked my attention again. I highly recommend seeing the movie especially if you haven’t paid much attention to the “Global Warming” topic.

For those of you who don’t believe that “Global Warming” is happening, I have this question for you:

Are you willing to bet life on this planet as we know it, because you don’t believe Global Warming is happening? Maybe the outcome of Global Warming isn’t as extreme as some may believe it to, but maybe it will be worse. If Global Warming is real and we treat it has a scientific hoax, and don’t take action. Isn’t that worse than the scientists being wrong about the how extreme the changes will be on our planet? Isn’t it work taking action now “just in case”?