Posts in category Education

2015 Advanced Genomics, Metagenomics, and Bioinformatics Workshop Wrap-up

I was lucky enough to help set up and plan a workshop covering genomics, metagenomics, proteomics and bioinformatics at the University of the West Indies campus in St. Augustine, Trinidad & Tobago on February 19th and 20th. The workshop was sponsored by the National Institute of Allergy and Infectious Diseases through the Genomic Center for Infectious Diseases cooperative agreement. UWI was a co-sponsor and a gracious host. Participants included 60 individuals from Trinidad, England, Guyana and Barbados. On-line participants were from all over the world including Gambia, Ethiopia, Kenya, India, USA, and the Caribbean.

The team of presenters from the JCVI included Karen Nelson, Bill Nierman, Andrey Tovchigrechko, Rembert Pieper, and Shibu Yooseph.  Presenters from UWI included Drs. Christine Carrington and Adesh Ramsubhag.

Karen opened the workshop with a welcome message and overview. She has been a driving force behind the growing relationship between UWI and JCVI. Bill delivered very interesting talks on the history of research on the human microbiome and currently emerging infectious diseases. Rembert handled a presentation and tutorial on proteomic analysis strategies, which was a big hit. If time was not a factor, the question and answer period could have lasted longer than his talk. Finally, Andrey and Shibu presented and gave lessons on statistics, UNIX, and bioinformatics analyses for genomics, metagenomics, and microbiome work.

Dr. Carrington’s presentation on infectious diseases in Trinidad focused on Dengue Fever and Chickungunya, and dovetailed quite nicely with Bill’s presentation on emerging infectious diseases.

Dr. Ramsubhag described the results of his work examining the bacterial diversity of the Nariva Swamp in Trinidad, which uncovered many unique bacterial strains. Perhaps the most important portion of his talk described how important this type of workshop/collaboration is for UWI. Lessons from subject matter experts are invaluable to the undergraduate, graduate and faculty members that attended the workshop as students. In addition, Dr. Ramsuhbag described how a relationship that started through a workshop has given UWI access to cutting edge technologies and data analysis strategies that would be otherwise unavailable without the collaboration with the JCVI.

The students that attended the workshop were all very enthusiastic and eager to learn. They seemingly hung on every word from the presenters, and paid very close attention during the presentations and hands on informatics sessions. A few attendees even asked us to make the lunch break shorter so that the workshop time could be lengthened…but we needed that time to break down the video equipment, haul it to another building and set it up for the afternoon classes. It was a pleasure to help make this learning experience possible for the workshop students!

The workshop was the second time that staff from the JCVI have presented at the St. Augustine Campus of UWI. Tim Stockwell held an 8 hour workshop focused on viruses in 2013.  We look forward to working together in the future.

Special thanks to Tim Stayeas for handling all of the technology associated with on-line broadcasts of the meeting.

Watch all four training sessions below:

Day 1, AM Session

Day 1, PM Session

Day 2, AM Session

Day 2, PM Session

International Bioinformatics Workshop

20th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology (VEME) on behalf of the International Centre for Genetic Engineering and Biotechnology

The International Bioinformatics Workshop on VEME workshop is recognized as one of the best virus bioinformatics courses in the world and has so far been organized in Belgium, Brazil, Finland, Greece, Portugal, the USA, South Africa, The Netherlands, Serbia and Italy. The 20th edition will be held 9 – 14 August 2015 at the University of the West Indies (UWI) in Trinidad and Tobago. The workshop is co-organized by the UWI, J. Craig Venter Institute (JCVI) and the University of Leuven.

The workshop will provide intensive training in the mathematical principles and computer applications used in the study virus evolution and for conducting detailed molecular epidemiological investigations. The workshop will include lectures and computer practical session where students will have the opportunity to analyze their own research data. Teachers will include 24 world-renowned researchers (including Richard Scheuermann, Tim Stockwell and Karen E. Nelson from JCVI).

Note: the application deadline has been extended to March 29, 2015.

Detailed information and online applications may be accessed at:

http://rega.kuleuven.be/cev/veme-workshop/2015

OR

http://www.icgeb.org/trinidad-and-tobago-veme-bioinformatics-2015.html

H3Africa Update

The National Institutes of Health (NIH) and the UK-based Wellcome Trust, in partnership with the African Society of Human Genetics, developed a program to foster genomic and epidemiological research in African scientific institutions. The laboratory and computational infrastructure available to most scientists on the African continent is currently insufficient to keep up with the rapid developments in DNA sequencing technologies and the need to use advanced computationally intensive methods to analyze this data.

Through the H3Africa Consortium, a partnership between NIH and Wellcome Trust, funding has become available to support knowledge development and implementation of genomics-centered research in several African academic institutions. The first scientific paper to come from this effort, Enabeling the Genomic Revolution in Africa, was published in the journal Science in June 2014.

H3Africa Efforts at J. Craig Venter Institute (JCVI)

One of the main initiatives of H3Africa is to foster scientific exchange between US-based partners and their African-based consortium members. JCVI is involved in a number of such partnerships through training and research collaborations.

Tuberculosis Research with Addis Ababa University

Addis Ababa University is the only Ethiopian institution to receive a primary award from NIH under H3Africa. It is based on a collaboration with JCVI. Professor Gobena Ameni of Addis Ababa University and Dr. Rembert Pieper of JCVI developed a proposal on Systems Biology for Molecular Analysis of Tuberculosis in Ethiopia which was initiated earlier this year. The research focuses on genomic variability in M. tuberculosis strains in Ethiopian pastoralist societies and also has an oral microbiome and proteomic biomarker discovery component.

Bioinformatics Training for African Scientists

As part of H3Africa, JCVI is leveraging its recent GCID award, where appropriate, for training of African Scientists. As part of this effort Dr. Andrey Tovchigrechko  taught microbiome analysis to graduate students in Ibadan, Nigeria. The workshop was organized by the local H3Africa Bioinformatics Network node. The workshop took place in July, 2014 and comprised of students from Nigeria and other West and Central African countries.

Symposium presenters.

Symposium presenters.

Workshop student participants.

Workshop participants.

The workshop was held at IITA.

The workshop was held at IITA.

During the three day workshop, Dr. Tovchigrechko taught the students launching and controlling computing instances on Amazon cloud, the basics of Python and R programming, MG-RAST Web interface, MG-RAST R package matR and JCVI-developed R code MGSAT. MG-RAST tutorials were provided by one of its developers Andreas Wilke (ANL).

Dr. Tovchigrechko also gave a talk, along with a dozen other speakers, at a one-day symposium at the University of Ibadan that preceded the workshop and included approximately 200 participants. Special thanks go to Nash Oyekanmi, the organizer and manager of the whole event, for his relentless efforts.

Collaborations with University of Cape Town

Also as part of the H3Africa Consortium, Dr. William Nierman from JCVI and Dr. Mark Nicol from the University of Cape Town, South Africa are in collaboration to study the nasopharyngeal microbiome and respiratory disease in African children. Dr. Nierman’s group has conducted a month long in house microbiome training workshop with students from Dr. Nicol’s group.

The focus of the training was to teach students JCVI’s complete microbiome pipeline (including sample preparation, sequencing generation, and final association analysis). The aim of the training collaboration is to ensure that this complete pipeline can be performed at the University of Cape Town, to help build independent and sustainable capacity in this field within South Africa.

 

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/

JCVI Hosts South African Scientists to Share Microbiome Research Techniques

Two scientists from the University of Cape Town, South Africa have joined Dr. Bill Nierman’s lab for the next month as part of NIH’s Human Heredity and Health in Africa (H3Africa) Initiative, a training program designed to build out technical biological skills in the African research community. This training relates specifically to developing techniques around the area of microbiome analysis, a relatively new field in the biological sciences.

Microbiome analysis for the collaborative study is looking at entire community of microorganisms in the respiratory tract of South African infants to better understand how the microbiome is associated with infant pneumonia and wheezing episodes. The expectation is that the organisms that reside in the infant respiratory tract will provide protection from or a predisposition to the pneumonia or wheezing episodes.

 

The Nierman Group

The Nierman group left to right Sarah Lucas, Bill Nierman, Shantelle Claassen, Mamadou Kaba and Stephanie Mounaud (unpictured Jyoti Shanker and Lilliana Losada) welcomes visiting scientists Ms. Classeen and Dr. Kaba from University of Cape Town for a month long training in microbiome sequencing and analysis.

Mamado Kaba, MD, PhD and colleague Shantelle Claassen from the University of Cape Town will be working closely under the guidance of JCVI’s Stephanie Mounaud who is functioning as the project manager and coordinating the laboratory components of a similar project at JCVI studying the microbiomes of inafnts in the Philippines and also in South Africa. These studies are sponsored by the Bill and Melinda Gates Foundation. The training will focus initially on preparing samples for DNA sequencing on a modern DNA sequencing platform, the Illumina MiSeq instrument. Once the sequence reads are off the sequencer, the instructional focus will shift to analysis of the reads by means of an informatics pipeline that develop phylogenies, or family trees, of the microbes that are obtained from the infant respiratory tract so that the abundance and relatedness of the microbes can be established. The bioinformatics training will be provided by Jyoti Shankar, the statistical analyst working on the Gates Foundation Project.

Mamadou Kaba is a Wellcome Trust Fellow working in the Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town. Mamadou’s research interests include the molecular epidemiology of infectious diseases and the study of human microbiome in healthy and disease conditions. He has contributed in establishing a new research group conducting studies on how the composition of the upper respiratory tract, gastrointestinal, and the house dust microbial communities influences the development of respiratory diseases.

Prior to joining the University of Cape Town, Mamadou worked as Research Associate at the Laboratory of Medical Microbiology, Timone University Hospital, Marseille, France, where he studied the epidemiological characteristics of infection with hepatitis E virus in South-eastern France.

Shantelle Claassen is pursuing a Masters degree in the Division of Medical Microbiology at the University of Cape Town. She has completed a BSc (Med) Honours degree in Infectious Diseases and Immunology at the University of Cape Town, during which she examined the relative efficacy of extracting bacterial genomic DNA from human faecal samples using five commercial DNA extraction kits. The DNA extraction kits were evaluated based on their ability to efficiently lyse bacterial cells, cause minimal DNA shearing, produce reproducible results and ensure broad-range representation of bacterial diversity.

Mamadou and Shantelle are currently involved in an additional prospective, longitudinal study of which the primary objective is to investigate the association between fecal bacterial communities and recurrent wheezing during the first two years of life.

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 One

Arrived at Thule, Greenland after a 5 hr flight from Copenhagen.  It was pretty interesting seeing a long line of people all getting on a flight that was headed to a part of the world that usually has less than 600 people there at any given time.  Arrival was pretty straightforward, no jetway, no customs, no LCD screens telling you where to pick up your bag.  Just a few military personnel checking your documents to ensure that you have the approval from the Danish government and USAF to be on base.  First impression getting off the plane…it’s cold.  Not as cold as I expected it to be but it was just 90 degrees F when I left home a few days ago.  Today’s high was 39 degrees F.  Standing in the sun it’s not so bad but when the wind starts blowing it turns into a recipe for chapped lips and windburn.  Oh and did I mention the massive mosquitos here?  Not much wildlife in this part of the world but the mosquitos outnumbers the vertebrates probably a million to one.  They are also VERY aggressive; they even swarmed the trucks while we were driving around the base.  We were shown our living quarters, which were very nice, kind of reminded me of living in the dorms during undergrad.  There are individual rooms and a shared bathroom on each floor.  We toured the various sites that our collaborator Slava Epstein already pointed out as good sampling sites that vary in vegetation and proximity to water.  The land here is quite desolate, not much green, mostly moss and small shrubs growing.  Traditional trees are nonexistent but “ground trees” are actually common.  They are trees that grow outward on the grass and not upward.  The rest resembles pictures taken by the mars rover.  As the day goes by I noticed the sun was circling and I came to the realization that the typical artic summer was happening right in front of me.  The sun literally circles and will not go down until around September.  It was quite odd, getting in bed at midnight and seeing the sun still in the sky.  Tomorrow will be more interesting since we will be going further away from base to sample additional areas. 

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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.

The Next Generation Science Standards are Ready for Review

The second draft is ready for public comment through January 29th. Please be sure to take some time to review.

http://www.nextgenscience.org/next-generation-science-standards

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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