Data Carpentry Genomics Workshop Hackathon:
Curriculum & Assessment Development
Goal: Develop materials and assessment for a two day Data Carpentry workshop focusing on the skills needed to work with genomic data
Location: Cold Spring Harbor Laboratory, New York
Dates and times: March 23-25, 2015; 9 am - 5 pm each day
To apply: http://goo.gl/dqmkwI ; deadline January 30, 2015. Successful applicants will be notified by February 6th.
The challenge of analyzing and organizing genomic data is limiting research progress because many researchers have not had training in the data skills that will enable effective analysis. To address this, we are organizing a 3-day workshop aimed at developing a Data Carpentry genomics workshop curriculum, including corresponding assessment instruments, to teach the fundamental data analysis skills genomics researchers need to start working efficiently with their data, such as the command line, data organization, introductory scripting and the use of cloud or high performance computing resources. The event will be held March 23-25, in Cold Spring Harbor, NY, at the Cold Spring Harbor Lab (CSHL). We aim to assemble a diverse and interdisciplinary group of participants, and invite those interested to apply by Jan 30 at http://goo.gl/dqmkwI.
The availability of genome-scale sequencing data is rapidly increasing, generating enormous potential for biologists to use such data to address research questions. However, most researchers have not had the opportunity to learn fundamental data analysis skills that will help them manage, organize and analyze this data, in other words, the equivalent of good lab practices for data science. As a result, researchers spent weeks or months doing things that could be done in hours or days; do not know how trustworthy their results are; and are often unable to reproduce their own work, much less that of their colleagues.
Most researchers are keenly interested to address this issue and in improving the way they manage and analyze data. In a Bioinformatics Resource Australia EMBL 2013 Community Survey Report the most emphatic outcome was the overwhelming demand for training. More than 60% of researchers surveyed said that their greatest need was additional training, compared to only 5% who need access to additional compute power. However, training resources relevant to researchers looking to develop these skills are scarce, and training in data and computing skills is still largely absent in undergraduate and graduate programs for researchers in biology. Filling this gap is hampered by teaching materials typically being re-developed by instructors independently and with little or no coordination, community engagement, and collaborative refinement. Similarly it is challenging to develop and deploy the assessment needed to determine the effectiveness of these materials. Our goal is bring together people with interest and expertise in genomics, bioinformatics, instruction and assessment to develop high quality materials and formative assessment. The materials will be vetted by practiced instruction and can continue to be developed by the community and taught at workshops across universities and locations. The goal of the material is to teach researchers the fundamental data skills necessary for them to better utilize the research potential of genomics data. We do not plan to develop lessons on particular types of analysis, i.e. RNA-Seq, genome assembly, but to have the lessons in this workshop provide the fundamental skills that will enable researchers to use and connect the resources in analysis workflows.
We are organizing a 3-day workshop to develop a Data Carpentry workshop for skills, resources, and best practices for data science in genomics. The goal of the workshop is to identify and subsequently address the teaching needs and technological gaps that hinder data analysis in genomics. The material developed during this workshop will be openly licensed under CC-BY and be taught at two-day Data Carpentry Genomics workshops.
We aim to assemble a diverse and interdisciplinary group of scientists, educators, and developers, encompassing various levels of experience and a broad set of skills. This includes participants who are familiar with, or even involved with developing tools and technologies in bioinformatics, but also includes scientists and other people enthusiastic to learn more about data skills in genomics and who are interested in helping to shape the curriculum.
Applications are due January 30, 2015. Travel support is available, and the logistics for arranging travel and housing will be communicated to accepted applicants. Women and underrepresented minorities are especially encouraged to apply.
If you have any questions, feel free to contact anyone of the organizing committee.
Organizing committee