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Professional Development Opportunities this Summer

This summer we are offering two professional development workshops: GenomeSolver and Bioinformatics: Unlocking Life through Computation.  Both explore bioinformatics, microbial diversity and the implementation in the undergradauate or high school classrooms. 

The GenomeSolver workshop trains faculty on genome analysis. Workshop attendees will learn about general methodologies, standards, and processes used to annotate and analyze microbial genomes. The workshop contents will be available to aid the faculty in developing teaching modules. In addition, extensive documentation on methodologies and tools will be available via the online environment created for this project. On online web portal Genome Solver (www.genomesolver.org) will be a virtual space for development and sustaining of community. Genome Solver will assist faculty with technical issues and curricular design, as well as an online environment for the ongoing sharing of information including publication of student work. 

http://www.jcvi.org/cms/education/prodev/genome-solver-annotation-workshops

Bioinformatics: Unlocking Life through Computation is a new opportunity for high school teachers. Genomics and biotechnology are valuable tools in our quest to understand life and nature. However, introducing the science classroom to the computational and mathematical underpinnings of biology can be challenging. The goal of this workshop is to introduce a curriculum for mathematics and science education in the area of genomics (with a focus on the fascinating world of microbes). Educators will be introduced to the various analysis and computational challenges that arise in this discipline. Workflow examples illustrating comparative genomic analysis will be made available through the JCVI Metagenomics Report (METAREP) software infrastructure. The eventual aim is for the educational material to be integrated with local high school curricula requirements to expose students to both hypothesis-driven and discovery-based science.

 http://www.jcvi.org/cms/education/prodev/bioinformatics-unlocking-life-through-computation/

The 2014 Summer Internship Application is Open and Announcing the Genomics Scholar Program

The 2014 Summer Internship Application is now open.   Last summer, we hosted 49 interns from a pool of 424 applicants. They presented their research in the First Annual Summer Internship Poster Sessions held in San Diego and Rockville. The posters were judged by a team of volunteer JCVI scientists and the poster sessions were open to all employees, interns and their guests to share what great work they all participated in this summer.

 

 

2013 Intern Poster Session

2013 Intern Poster Session

We are also excited to announce the new Genomics Scholar Program beginning this summer and also accepting applications.  The Genomic Scholar Program (GSP) is a targeted research experience program to community college students in Rockville. Our program incorporates multiple avenues of support for students through the research experience with the Principal Investigators as mentors, and supplemental professional development provided by the JCVI.  Additionally, selected students will have the opportunity to participate in undergraduate research conferences.

The GSP is supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under award number R25DK098111.

Thule, Greenland – Day Three

Day three started with me missing breakfast. It seems that folks around here only eat breakfast between 5am and 8am. Today was a very rough day for sampling.  About an hour drive to the area near the site, about a three-mile hike to one spot another half-mile hike to another spot followed by the three and a half mile hike back to the truck. We sampled “rich” soil and “rich” soil from a lake. These two sites were sampled and categorized as “rich” due to the abundance of vegetation around and near the sites. The area surrounding Thule is very desolate so I can imagine the plants have a hard enough time growing.  It would be very interesting to see what microbes are present in these two sites to allow such vegetation to grow; even more interesting to see how water affects the microbial population. Samples were frozen once we got back to the on site lab. A small portion was saturated with AllProtect to ensure preservation of RNA for transcriptomics analysis.

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The day ended with a lecture from another NSF grant recipient to install a telescope on the Greenlandic ice cap. It was an interesting idea to coordinate radio imaging from other telescopes around the world to look at quantum singularities that were very far away. After speaking to some of the other scientists here I found out that our group, which includes myself and our collaborators Slava Epstein and Dawoon Jung, were the ONLY Microbiologists on the base. Everyone else was either a Geologist, Environmental Scientist, Astronomer, or Meteorologist. It was great to hear about everyone else’s projects.

Plant Bioinformatics Workshop

JCVI recently held its 3rd Annual Plant Bioinformatics Workshop from July 15-19th. During the week-long workshop, 20 scientists from the Plant Research community visited JCVI and learned many aspects of Bioinformatics from the members of Chris Town’s Plant Genome group. Attendees included undergraduate and graduate students, post-doctoral fellows, research scientists and faculty at various Universities throughout the United States as well as a biotech company. In addition to the on-site participants, we had 5 additional participants attend the workshop via WebEx. The virtual participants had the opportunity to sit in on the lectures and complete the hands on exercises by logging into an Amazon Cloud instance, which was set up specifically for this purpose. The topics covered during the workshop included UNIX tools for Bioinformatics, Genome Assembly, Structural and Functional Annotation, RNA-seq assembly and analysis and SNPs. In addition to JCVI’s instructors, we had additional sections covered by external instructors. Eric Lyons (University of Arizona and iPlant) presented on Comparative Genomics and the iPlant Infrastructure and Ann Loraine (UNC Charlotte) presented on Integrated Genome Browser. All sessions contained a hands-on component so the students would have the opportunity to use the tools that we discussed during the lecture portion.  Watch our website for future offerings!

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Building a Solid Foundation

The JCVI La Jolla construction site has been busy since earthwork began in 2011.  After grading the site to specified levels, a detailed excavation began to make room for the structural concrete footings, supporting slabs, and underground utilities.  With all of the holes in just the right place, crews began installing steel rebar to provide reinforcement for the large structural footings which will eventually carry the building’s weight.  Once the steel had been placed, it was inspected and filled with concrete.  The largest structural footing was so large that it took 45 concrete trucks to fill the hole!

Concrete wasn’t the only thing being placed under the building.  Of the many sustainable strategies included in the building’s design, two of these systems require large underground water tanks to operate.   The first is a rainwater harvesting system which will collect precipitation from the building roof and site.  Three tanks, totaling 90,000 gallons, collect the water so that it can be treated and then reused for toilets and irrigation.  This system will reduce the building’s potable water demand by 70% annually. Pictured here is a 5,000 gallon fiberglass tank being lowered into position.

5500 gallon rainwater storage tank is lowered into place

To become a net-zero building it is critical that electrical demands are minimized.  The new JCVI La Jolla building is being designed with an ultra-efficient mechanical system to help reduce the building’s energy profile.  At the core of this design are two 25,000 gallon thermal energy storage (TES) tanks.  These tanks will store both warm and cool water which will be used to either heat or cool the building depending on the building’s internal temperatures.  Using water to move heat in and out of the building uses 87% less energy than using air and allows the mechanical systems to operate at much higher energy efficiencies than standard building systems.

Single TES tank arrives by tractor trailer

Two 25,000 gallon TES tanks being installed

Most of the building structure is made with concrete and, after the underground work was complete, McCarthy wasted no time in constructing the vertical support walls.  The walls are architectural concrete because they are designed to complement the other materials such as wood that will make up the building’s exterior.  Using information from the concrete mock-ups (See Moving Dirt at JCVI La Jolla) the team selected a 30% fly-ash concrete mix.  Fly ash is a waste material from coal-fired power plants that lowers the amount of cement needed to make concrete, thus both lowers the energy and carbon dioxide emissions of manufacture and increases the overall volume of recycled content used in building.

Constructing architectural concrete is akin to making art.  Huge forms are built with meticulous detail using special materials, fastening methodologies, and custom routed grooves to create the desired finish.  Those forms are filled with steel rebar, filled with concrete at lightning speed, and then stripped (formwork is removed) at just the right time to produce the final product.  The work is even more challenging given the complex geometries of the building and the performance characteristics of using a 30% fly-ash concrete mix.

 

Erected concrete forms

As of September 2012, the team has almost completed the parking garage and podium deck upon which the building structure will sit. Concrete work will continue through the fall and is expected to complete in early 2013.

 

Mock-up of a single office window at the building’s exterior.

Water testing the window system

2012 JCVI Internship Program Is Now Accepting New Applications

Wow! Another year has gone by.  Its hard to think it is November – almost December with the warm weather we have been enjoying.  However it did not start that way.

Halloween Snow in Maryland!

The 2012 JCVI Internship Program is open to accept spring and summer applications. The application process includes the submission of a resume, essay and transcripts as one PDF file via our online application site. We no longer require letters of recommendation.

Information about the 2012 program can be found at http://www.jcvi.org/cms/education/internship-program/

For summer 2011, we received 544 applicants.  Of these applicants, 30 Interns were selected (10 in San Diego and 20 in Rockville):

  • 7 high school students
  • 9 undergraduate students
  • 13 graduate students
  • 1 secondary teacher

The intern projects ranged across the Institute:

  • A lethal set of virulence factors in uropathogenic E. coli ?
  • Expanding genome transplantation: Streptococcus thermophilus
  • Random Assembly for Use in Swapping as a Tool for Genome Minimization
  • Assembling terminators and promoters
  • Developing Galaxy Tools for the Ordination Analysis of Meta-genomic samples

Good luck to all the applicants this year!