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Open Bioinformatics: Exploring the Genome

This is the first installment in 'hackathons' where we will design parts for the glowingplant project.  [See the East Bay Express Article on glowingplant this weekend!]

We'll have a 45 minute talk about Arabidopsis thaliana - perhaps the most common plant model in biology - and look at the genome data.  We're not going to talk about how the glowing plant will work tonight.  Sorry there's not enough time!  

Then we'll break into teams and work for the rest of the evening exploring the data and making steps toward making some parts for glowing plants and iGEM!

Last time some folks asked for some pre-reading.  If you can install python on your laptop that would be great - we'll find a way to get people started if they aren't ready to do this themselves.  

If you are looking for a biopython introduction This YouTube video (http://www.youtube.com/watch?v=Tl_b-qcBXR4) will be a good deal of what we want to do during the meetup.  (thanks Felicia!)

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  • Urvish P.

    Damn I just saw this, I had been looking forward to it since the last meeting. Can I still come?

    1 · August 9, 2013

    • Urvish P.

      Yes! I'll come early this Sunday!

      August 16, 2013

    • ron s.

      great!

      August 16, 2013

  • Shriram

    Great session! I'm happy to try help with installs next week...

    August 12, 2013

    • ron s.

      Can anyone else come to help people set up? We have 3 now.. I'm betting we could use more.

      August 15, 2013

    • Urvish P.

      I'll come as well... pip install biopython. Oh that didn't work? Sudo !!

      August 16, 2013

  • ron s.

    Hey all Just want to let you all know that even though its taking longer than I thought to get the reservation, that there will be a meetup for Bioinformatics this sunday. We'll start at 7 and anyone who wants to come at 6 can get help install biopython. Anyone who can come to help do the installs please do so!

    August 14, 2013

    • A former member
      A former member

      Damn! Gonna be in Portland for a (much needed) vacation then.

      August 14, 2013

    • ron s.

      no problem Dange see you next time..

      August 14, 2013

  • A former member
    A former member

    Ron, I, and the people I was working with, had a hard time trying to even get to the Biopython program. It was very frustrating and time-consuming for me and I didn't even get to the genome part.
    Not everybody knows Linux or programming or whatever intricacies are needed just to get to the task. I found this very cumbersome and intimidating. This is the kind of thing that makes science inaccessible to many. I felt that was glossed over and a foregone conclusion that everyone is a computer whiz. This is an issue that needs to be addressed unless this is going to be a very exclusive club that is antithetical of what it proposes to be- putting science in the hands of many. Just my thoughts. -Dange

    August 12, 2013

    • ron s.

      Hey Dange - so we have an hour beforehand for people to come and set up biopython on their machines. I announced it on the meetup, but I think its hard to tell people what to expect, so we'll have to feel out what we can do to help get people going.

      August 12, 2013

    • A former member
      A former member

      Thank you, Ron. There is always one guy never afraid to ask the dumb questions they say there are none of. I am he. As a matter of fact, for my personal edification and learning, I would like to come an hour early and maybe be able to assist others once I'm up to speed.

      1 · August 12, 2013

  • ron s.

    Hey all - thanks for coming tonight! We had a lot of good energy in the room. I hope you'll all feel like coming - the next two will be sunday the 18th and Sunday Sept 2nd at 7 p.m. I'll try to show up early and help with BioPython installs next week (can any successful installers come and help with that?). If you pledge to come and stick it out through the whole project, you can show up even if you are on the waitlist. We want consistent team to see the project through!

    August 11, 2013

    • Ken O.

      Ron - how do I access the bitbucket.org/rondo downloads? when I access the link I get the msg "Nothing to see here." I created an account, but that did not provide access to Glowing Plants Parts. Is it rondo or something else? - Ken

      August 12, 2013

    • ron s.

      I fixed the link on the web page: http://boundarycondit...­

      August 12, 2013

  • Niranjana N.

    Really enjoyed the session. Thank you Ron!

    August 12, 2013

    • ron s.

      Great meeting you both! See you next time! :)

      August 12, 2013

  • Bee W.

    Unfortunate and last minute schedule change - unable to go! Please give my spot to someone on the waiting list, and if you're able to post materials post-meeting, I would love to see them.

    August 11, 2013

    • ron s.

      the link at the bottom of the page here is where all the materials are - take a look :)

      August 11, 2013

  • Ken O.

    it put me back in the classroom - as a student

    1 · August 11, 2013

  • ron s.

    Hey guys - three days to go. For those of you who want to come prepared... Here are some topics I want to cover very lightly or not at all. We'll try to get groups of people where questions can be answered. The Genetic Code
    Python (installing software and basic grammar)
    Git (you don't have to learn this at all to do the hackathon). Please let me know if these are tragic omissions :)

    August 8, 2013

  • A former member
    A former member

    "Bio Hackers" article in East Bay Express, worth checking out to get a taste of one flavor of public opinion: http://bit.ly/18RZjA1

    1 · August 5, 2013

  • Willow

    Gah!!! I'm going to be gone AGAIN.
    Poop.

    Can i request video again, with clear view of the slides? Maybe you could even post the .ppt? :)
    pleeeaasee

    August 4, 2013

    • ron s.

      The materials from last time are posted at www.boundaryconditions.o­rg/biology.html can't guarantee video, but we'll try some ...

      August 4, 2013

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