20161031_134740

Michigan Biological Software Team to compete at iGEM with MICDE support

By | Educational, General Interest, News, SC2 | No Comments

MICDE is pleased to announce its support of the Michigan Biological Software Team (MiBioSoft), for its attendance at the 2017 International Genetically Engineered Machine (iGEM) competition in Boston.

Founded in 2014, MiBioSoft is a student-run organization at the University of Michigan that develops software for use in scientific research, with a focus on synthetic biology. It seeks to provide its members with opportunities to not only improve their skills as software designers, but also to improve their communication and management skills by bringing together students from a variety of backgrounds including Biology, Mathematics, Computer Science, and Chemistry.

MiBioSoft competes annually in the software track of the iGEM competition, where research teams from around the world present their results over the course of a three-day conference. During the first two years at the competition, the team was awarded bronze medals. In 2016, MiBioSoft received Best Software Project award as well as a gold medal for their protocol catalog, ProtoCat, in a competition that featured over 300 teams from more than 40 countries, with more than 5,000 participants in total.

About Protocat

Protocat is protocol catalog software developed by MiBioSoft students to address the issue of reproducibility in synthetic biology. Like many innovative ideas, it began because of a problem. Studies have estimated that only 10-25% of published scientific results are reproducible. A 2014 survey conducted by the Michigan Software team confirmed that the repeatability problem exists in synthetic biology, with every scientist surveyed reporting prior struggles with replicating protocols.

ProtoCat 3.0 is a free database of crowd-sourced protocols designed to make existing protocols more repeatable and enable more accurate computational models of biological systems. MiBioSoft believes this can most efficiently be accomplished with a commitment to open source protocols and a broader more active community of digital troubleshooters. ProtoCat 3.0 works to establish such a community by giving anyone with an internet connection or smartphone access to a repository of synthetic biology protocols collected from all over the world. Additionally, ProtoCat 3.0 encourages the development of higher quality, more repeatable protocols by allowing users to document, rate, review, and edit existing methods.

[SC2] HPC resources available to U-M students

By | Educational, Flux, SC2 | No Comments

Brock Palen, Associate Director of Advanced Research Computing-Technology Services, joined the SC2 to talk about all the high performance computing (HPC) resources available to U-M graduate and undergraduate students. A summary of his presentation is here.

Resources:

Available at/through Michigan

  1. Flux for Undergraduates: Undergraduates can use the local flux computing cluster FOR FREE! Please visit the page for more information
    • ARC-Connect: use for Jupyter notebooks and VNC (remote desktop) access of flux resources, useful for remote visualization of big data or just getting a feel for working on linux and flux.
  2. Amazon Web Services: Michigan students get $100/year in amazon web services. While not as cost-effective for some things, very good resource to be aware of.
  3. Hadoop: Michigan’s Hadoop cluster is available for free (I believe you have to apply/demonstrate a need, but you don’t have to pay if it’s accepted). This upcoming workshop will go over the basics, read more if you are interested.

Available via Grant

Brock has an up-to-date webpage linking to and detailing various resources you can apply for.

Highlights:
  1. XSEDE:
    • Startup and teaching allocations are available continuously
    • Research allocations accepts 4x/year
  2. Great Lakes Consortium:
    • Alternate way to get some time on Blue Waters
  3. Amazon/Microsoft/Google:

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