Next Generation Sequencing: Opportunities and Resources

As part of the iConnect team, I had the good fortune to go to several workshops during the conference Plant Biology 2014 organized by the American Society of Plant Biologists.


ASPB offers a diverse set of venues to acquire new skills and improve our careers by encouraging networking and initiation of collaborations. This year, for the Next Generation Sequencing workshop, ASPB organizers invited seven (the magic number?) experts with different levels of experience on bioinformatics. The event was sponsored by the ASPB Membership Committee and the speakers were Jason Williams and Christos Noutsos  from Cold Spring Harbor Laboratory, Nicole Hopkins from University of Arizona who is also working on iPlant Collaborative initiative (, Todd Mockler from Donald Danforth Plant Science Center, Kranthi Mandadi from Texas A&M University, Pankaj Jaiswal from Oregon State University and David Horvath from ARS-USDA. I have included a picture of them. They all are very photogenic!

Next Generation Sequencing Workshop Speakers
Next Generation Sequencing Workshop Speakers. (from left) Kranthi Mandadi, Pankaj Jaiswal, Christos Noutsos, Nicole Hopkins, Jason Williams, Todd Mockler, and David Horvath.

David Horvath, the workshop organizer, welcomed us, introduced all the speakers, mentioned each one’s expertise, and talked about iPlant Collaborative initiative, a National Science Foundation supported project aiming to provide “a place at the cyberspace where the power of high performance computing and data resources are available for life scientists”, therefore deep analysis of large sets of bioinformatics data is now possible in one place that is constantly curated and improved.


The common feeling among my colleagues and I was that due to the increasing availability of platforms, software and tools for bioinformatics analysis, it can be very confusing and challenging if you do not have a place where to start and have advice. iPlant Collaborative initiative offers several means of support to the very beginner and the more advanced user. It contains contact information of experts and places to put your questions and obtain answers from a community willing to help. Also, it contains confidentiality and security settings and links to other databases as GenBank and European Nucleotide Archive, in addition to the most trusted tools and software that are currently validated for use and publication.


The objective of the workshop was basically to know where the resources were and how to start and continue learning. We were around 50 people attending the workshop, with broad interests and projects but with the common goal to apply bioinformatics to the analysis of our data. We sat in groups of around six people, to allow a very dynamic round table discussion driven by one of the speakers, who changed table every 15 minutes. Each one of the speakers provided a unique perspective about the use of different tools and their own experiences. At the end, we concluded that we should not be overwhelmed for the large set of data to analyze, because there are places where to look and ask for help. iPlant Collaborative initiative is a very good place to go as it contains a complete set of settings to help us.


At the end I would like to thank the organizers and the speakers for a very helpful workshop. I hope to see you again in the near future.

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