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Virtual Workshop, June 2016
Cold Spring Harbor Laboratory’s DNA Learning Center (DNALC) invites you to apply to participate in a free 2-week online workshop for our NSF funded project, Infrastructure and Training to Bring Next-generation Sequence (NGS) Analysis Into Undergraduate Education. This s
will introduce the knowledge and tools needed to analyze an RNA-Seq experiment, and help participants develop teaching strategies and materials that use these experiments in the classroom. Applicants may either propose to obtain their own RNA-Seq data – which will be sequenced as part of the course – or propose to use existing datasets.
Who should apply?
We are recruiting faculty who will be committed to study differential gene expression and to use the knowledge and skills gained at the workshop to incorporate into undergraduate classroom-based or independent study projects during the 2016–17 school year. Forty-three faculty previously participated in our workshops and have developed RNA-Seq datasets, teaching materials, and assessment tools that will guide you as you develop lessons and activities.
When is the workshop? What is the time commitment? What is the format?
We are planning to hold the workshop either June 6–17 or June 13–24 (based on the consensus of accepted applicants). The estimated time commitment will not exceed 20 hours per week. This virtual workshop will consist of self-paced instruction based on expertly written tutorials, videos, and hands-on bioinformatics exercises for analyzing RNA-Seq data. In addition, there will be required attendance at live webinar sessions covering topics including implementation of RNA-Seq into classroom curricula, and participation in discussion forums where you will share your learning experience and interact with fellow workshop participants. Participants are required to have a computer, microphone/headset, and webcam.
What skills do I need and what will I learn?
This workshop is appropriate for faculty who have little or no experience with bioinformatics analysis of RNA-Seq data.Workshop participants will be guided through a bioinformatics workflow for analyzing data using the Green Line of DNA Subway and iPlant Collaborative Discovery Environment. Participants will also learn details of RNA-Seq experimental design and NGS technology, and how to teach modern genomics from expert educators. Following the workshop, participants will assist with classroom evaluation to gauge the impact of student participation, and are expected to help develop curriculum and website support materials that will be used for educational dissemination of the project.
What RNA-Seq dataset can I propose to analyze and use for teaching?
All applicants must propose to analyze and develop teaching materials for a specific RNA-Seq dataset. The options for a dataset are:
- Generate a new dataset as part of this workshop. We will fund and sequence a limited number of proposed projects. For applicants who would like to obtain new data, we currently support RNA-Seq experiments examining differential gene expression for eukaryotic organisms with fully sequenced and annotated genomes. Faculty are encouraged to submit project proposals that complement their ongoing research. Importantly, if you propose to obtain new data and your proposal is selected for sequencing, you must be able to submit high-quality RNA for sequencing by March 1, 2016 (no exceptions).
- Previously generated dataset developed by one of our past workshop participants. Applicants can choose to collaborate with and use data previously obtained by one of these past workshop participants: Drs. Ayme-Southgate, Brusslan, Enke, Makarevitch, Schwartz, Thurber, or Woody.
- Dataset independently obtained by applicant.
- Publicly available dataset from the Sequence Read Archive.
How do I apply?
Complete workshop applications require:
- Applicant Information Form (DOC) or (PDF), which includes a description of the courses and/or research contexts with which students will be involved
- Formatted RNA-Seq Project Proposal Guidelines
- Support letter from the Department head that demonstrates an institutional commitment to incorporate NGS analysis in appropriate courses during the 2016-17 academic year
Complete applications must be received by December 11, 2015. All proposals will be reviewed as received. Please feel free to share this notice with colleagues who may be interested in applying. If you have any questions, send an email to 
with “RNA-Seq Workshop 2016” as the subject.
