Technological advances produce data in greater quantity and complexity, generating demand for training in computer programming, data management, and data analysis. To overcome barriers to research progress and to take advantage of the novel methods of inquiry that new technologies present, biomedical researchers must engage in training that delivers both the conceptual knowledge and practical skills for managing and analyzing complex, large-scale data.
Researchers must obtain this training while also conducting research full-time, so the training must be of short duration, specific to their needs, and effective enough for them to apply it directly to their work. Absent relevant and directly applicable training, biomedical researchers are unable to surmount barriers to progress or benefit from the insights that new technologies promise.
Training in data science skills can unlock the potential of biomedical Big Data. To address the need for data science skills and knowledge at JAX, we offer a bioinformatics training program that equips researchers with critical data science skills.
For both efforts we rely on training methods employed by Software Carpentry and Data Carpentry, non-profit organizations with a shared mission to teach foundational coding and data science skills to researchers worldwide. The Carpentries, as they are called collectively, provide field-tested lesson material in introductory R, Python, the Unix shell, and data organization and management. These introductory topics prepare researchers to successfully approach more advanced topics including high performance computing, RNA sequence analysis, machine learning, image processing, and genetic mapping of Diversity Outbred mice.
The Carpentries instructor training provides background in research-based teaching principles and practice in applying these principles when teaching practical workshops. Live coding, in which the instructor writes code while learners code along, gives learners a guided opportunity to acquire a new skill. Frequent exercises alternate with sessions of live coding so that learners can practice newfound skills and instructors can gage whether or not a group has successfully grasped them. This kind of instruction is responsive to learners’ skill levels and their training needs, yet is rare in most research and higher education settings. The JAX bioinformatics training program grows effective instructors with training and practice in innovative teaching methods for applied skills workshops.
The bioinformatics training program grew from the teaching of two JAX staff located in the group. In 2015, Narayanan Raghupathy (now at Bristol Myers Squibb) and Susan McClatchy became certified Software Carpentry instructors and began teaching introductory R workshops with Dr. Churchill’s backing. The response from JAX researchers was overwhelming and JAX leadership took notice. The JAX officially launched in April 2016 with the goal of making JAX a data science powerhouse by building data science talent in-house and in the neighboring research community. We target predoctoral students and postdoctoral fellows primarily, though all are welcome to participate in training events.
The bioinformatics training program drives the growth of data science talent at JAX and changes the way researchers approach their work, making them more productive, efficient and able to interrogate their data from new perspectives. New means of inquiry can lead to breakthrough discoveries, placing JAX-educated scientists at the forefront of data science in biomedicine.