DIYbioinformatics

What: DIYbioinformatics 

When: Wed April 20th 7-9 PM 

Where: The Institute for the Future, 124 University Ave, Palo Alto, CA, 94301 

Bring: Wi-Fi connected laptop if you wish to follow along the demos 

Cost: Free!

For this special meetup, BioCurious will be joining forces with the Bay Area Bioinformatics Forum to focus on DIYbioinformatics!

Unlike may other scientific pursuits which require at least some unusual equipment, most bioinformatics research can be done on a standard computer  which most people already have in their home. We want to encourage people to take advantage of this fact and pursue answers to real scientific questions using bioinformatics.

This meeting will have a series of talks focused on Bioinformatics techniques which budding DIY Bioinformaticians will be able to take back home with them and apply to their own bioinformatics research. The talks will require only very basic biological and computer knowledge to follow. Participants are encouraged to bring wifi connected laptops so that they can follow along some of the workshops and gain hands on experience.

In addition to 2 half hour talks, we are soliciting folks to prepare lightning talks (10 minute short talks). Keep in mind the focus of the meeting and the audience. Lightning talk slots will be given on a first requested basis. Let me know if you're interested in presenting. Powerpoint slides on a thumb drive to accompany your talk are optional.

We will be updating this invitation with more information on the specific topics as we get closer to the event.


Topics:

  • Basic BLAST workshop (30min) - Doug Hershberger (LS9)
  • Next Generation Sequencing workflow and analysis (30min) - Darryl Leon (Life Technologies)
  • PROSITE and Pfam protein family database (10min) - Jon Rodriguez (Stanford)
  • Bioconductor for next-gen sequence analysis (10min) - Cory Barr (Genentech)
  • Creating Diverse Interfaces for the BIOFAB's Electronic Datasheets (10min) - Cesar Rodriguez (BIOFAB)
  • Metagenomics of Microbial Communities (10min) - Patrik D'haeseleer (Lawrence Livermore National Laboratory)

Abstracts:

Basic BLAST workshop - Doug Hershberger

Follow along on your wifi computer as we explore BLAST, the number one tool for predicting the function of unknown genes by homology. We will discuss, the basic theory behind predicting function based on homology. Tackle a real world example. Discuss the different databases available for searching and the impacts they can have on your results. We will finish up with an example of determining the difference between two proteins with similar but distinct structures and functions.

Next Generation Sequencing workflow and analysis - Darryl Leon

A single NGS workflow will be reviewed, and you can follow along with your laptop. You will learn about how to use Galaxy (NGS tool box) for mapping reads to a reference genome, and you will be able to see your mapped reads in IGV ( a genome viewer).  This tutorial is ideal for beginners to the NGS world.

PROSITE and Pfam protein family databases - Jon Rodriguez

Have the sequence of a protein that you've discovered or designed, and want to predict its function? The PROSITE and Pfam databases let you take any amino acid or DNA sequence and find out which "family" of proteins it codes for. Thus you can look up which well-studied proteins are related to yours, providing a starting point for your investigation!

Bioconductor for next-gen sequence analysis - Cory Barr

Biotech corporations are relying heavily on open-source software for bioinformatics and computational biology. In this presentation, we'll explore a major open-source project for next-gen sequencing analysis: the Bioconductor project.  We'll see how major research centers are using and investing in it. We'll also see how you can begin using it yourself.

Creating Diverse Interfaces for the BIOFAB's Electronic Datasheets - Cesar Rodriguez

At the International Open Facility for the Advancement of Biotechnology (BIOFAB), we are creating open-source libraries of standard biological parts.  We are providing design information and performance data for the parts via the Internet in the form of "electronic datasheets".  The electronic datasheets are presently implemented as a client-web service application composed of the Data Access Client (DAC) and the Data Access Web Service (DAWS).  Due to the client-web services architecture, other client applications can consume and display the data and information provided by the DAWS. I'm encouraging the emergence of a diverse ecosystem of client applications that provide creative interfaces for the DAWS.  For example, I'd like to see the development of an iPad and/or Android tablet -based client application. It'll be a treat to see what novel creations emerge!

Metagenomics of Microbial Communities - Patrik D'haeseleer

Most of the biomass on Earth is microbial, yet we are able to culture and sequence less than 1% of those microbes. New sequencing methods allow us to sequence microbial communities directly, without having to grow isolates first, giving us an unprecedented view of the complexity of the world around us. I'll show you some of the methods used to analyze this meta-genomic information, and how we're using these to help turn plant biomass into biofuels.   

 

 

 

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  • Paul M.

    Large gathering, Great information! Can't wait till the next one.

    April 21, 2011

  • Luke

    Very informative. Love the lightning talks. Covers more ground in less time.

    April 21, 2011

  • A former member
    A former member

    I really enjoyed it. How can we get the slides for the last (Patrik D'haeseleer) presentation?

    April 21, 2011

  • Doug H.

    Awesome lightning talks! Thanks to all who spoke and attended.

    April 21, 2011

  • Tracy N.

    Tracy Nguyen
    Singularity University
    Academic Coordinator

    We are actively searching for a teaching fellow for our Biotechnology and Bioinformatics Track. Please let me know if you are interested.

    April 20, 2011

  • Julie B.

    Director, Bioinformatics ? full time position (San Francisco Bay Area)
    Were working to fill the position below. Pls contact me if you are interesed.
    Lead Bioinformatics program & development
    EXPERIENCE:
    PhD in bioinformatics or equivalent
    10+ years industry experience in bioinformatics required
    Experience in analyzing information on genome-wide scale required
    Experience writing procedures in a GLP environment required
    Experience developing diagnostic analysis software desired

    April 17, 2011

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