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Bio-Data, Bioinformatics and the Gears that Make Biological Machines Tick

MOVED TO SUNDAY 28th July because of conflict on the CCL Calendar.

The intersection of biology and computer science is showing tremendous potential. Literally thousands of data sources great and small are publicly available now. Come and enjoy a low key introduction to all the 'omes' - genomes, transcriptomes, proteomes, methylomes, metabolomes, etc. We'll play with some of the more useful data sources, tools and biological pathways.

No biology training is necessary - the talk will be accessible to anyone. Programming skills are useful, but not necessary.

If you have a laptop, please bring it. We will try to look at data in the class and preview a couple of tools.

Cygwin on windows machines, OsX or linux are useful here, but we can go over these at the time if needed.

We will be designing a project for anyone who wants to go deeper and get more experience with Bioinformatics.

Ron Shigeta PhD has been doing bioinformatics for 12 years in biotech in the east bay, before that he made biological information as a protein crystallographer.

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  • ron s.

    Hey everyone, Sorry i've been so quiet here. Just to let you know, for the next installment, we're shooting for Sunday August 11 at 7 p.m. but the reservation of the room is still hanging up. hopefully will post in a day or so. The evening will be devoted to parsing genome data and using it with biopython.

    August 3, 2013

  • Ryan B

    Hi All, here's the video from earlier video from the Bioinformatics intro class!

    July 29, 2013

  • ron s.

    Anyone who couldn't come and wants an update can email me directly. And it looks like Ryan B made a video of this so I'll post that in a day or two.

    July 28, 2013

  • ron s.

    Had a great time -thanks to everyone for coming! The consensus was good that we should try to start the glowing plants project - we start in ~2 weeks. I'll be sending a resource page and posting papers to Mendeley perhaps next week. I'll be posting a followup meetup in about a week. If Sunday is not good for you, can you let me know? We'll also be having evening focused on protein folding and synthetic biology in the next month or so.

    July 28, 2013

  • Urvish P.

    Cant make it this time. Last minute work thing.

    July 28, 2013

    • Urvish P.

      Haha I hauled ass to make it 7 minutes late. Great meetup ron. You did a fantastic job explaining things.

      1 · July 28, 2013

    • ron s.

      thanks for coming it was good to meet you!

      July 28, 2013

  • Carl G

    great meetup!

    1 · July 28, 2013

  • A former member
    A former member

    Injured myself today. Not gonna make it :(

    July 28, 2013

    • ron s.

      take it easy Dange - hope you are feeling better in the morning!

      July 28, 2013

  • Willow

    After August 1 I have a fully open and/or unknown schedule. Here's to finding a job! I hope...

    1 · July 23, 2013

    • ron s.

      we'll try for the next in about 2 weeks from the current one- stay tuned.

      July 23, 2013

  • ron s.

    Hi Willow - sure thing - will be looking for biweekly ongoing class/presentation... lmk what days work for you and I'll also take a poll at the class.

    July 23, 2013

  • Willow

    Gah!!!! I wish SO BAD to go to this...My parents are coming west and we're booked in Yosemite.
    Please PLEASE can we do it again????

    July 23, 2013

  • Ben L.

    At a conference, sorry

    July 18, 2013

    • ron s.

      next time, ben!

      July 18, 2013

  • ron s.

    Ken sorry about the change up - see you next time :)

    July 17, 2013

  • Ken O.

    next time

    1 · July 17, 2013

  • ron s.

    As far as reading or resources to look over before we get together... I don't think there's much reading that will help - there's a task oriented website that would be relevant, we're going to be doing similar things:

    http://rosalind.info/problems/locations/

    We're going to be approaching bioinformatics as more of an engineering/hacker practice, so more focused on what we want to do rather than trying to cover theory for problems which might happen, so the usual text books will not be as relevant. i'll post a resources list after the meetup - i've just started building the slides :)

    July 17, 2013

  • ron s.

    Hey everyone, there's a conflict with the CCL general meeting this month, so we have to find a new time for the event :/ I'm sending a doodle poll your way about this. I'll move this time by the end of the day, so please put in your opinion asap so we can find the best time.

    July 17, 2013

  • Tony H.

    I invited two really smart people who will try to attend.

    1 · July 17, 2013

  • ron s.

    Hi Niranjana,

    I've found that this sort of thing doesn't work so well on skype or google hangout - there will probably be a series of these - do you think you might be able to come later?

    July 16, 2013

    • Niranjana N.

      Yes, in a few weeks. Hope you plan to do it again!

      1 · July 16, 2013

  • Niranjana N.

    This sounds wonderful! Any chance of skyping in, or a webcast? Am confined to the house for a bit, unfortunately.

    July 16, 2013

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