This workshop, facilitated by Software Carpentry, aims to teach scientists and researchers at the graduate level and above in science, engineering, and medicine the basic computing concepts and skills that will let them get more done in less time, and with less effort. Our two-day curriculum shows participants how to automate repetitive tasks with the Unix shell, how to grow a program from a few lines to a few hundred using Python or R, how to track and share their work using Git, and how to manage data using SQL. Lessons alternate with hands-on practical sessions, and instructors, who are all working scientists, draw on their own experience to show how these ideas are useful in real-world situations.
Stony Brook University
Jon is a PhD candidate in Ecology and Evolution at Stony Brook University. He is fascinated by the structure, dynamics, and evolution of ecological networks and the power of network tools to address ecological questions. He was first introduced to R in a Biometry course and found programming to be an incredibly useful tool in his research. He uses R to analyze ecological network structure, run simulations, and for permutation testing. Throughout his graduate career he has developed a passion for programming, and enjoys spreading the knowledge that he has gained.
Laura Graham, PhD
Stony Brook University
Laura Graham is an ecology postdoc at Stony Brook University. She is a spatial/computational ecologist interested in what impacts environmental changes have on species' distributions and how we can use this information in landscape and conservation planning to reduce detrimental effects. Having previously been a mathematician and database developer, she applies skills learned there to ecological questions.
Jason Pell, PhD
Jason Pell received his PhD in Computer Science & Quantitative Biology at Michigan State University in 2013 with C. Titus Brown (now at UC Davis) as his advisor. His research focused on making DNA sequence assembly algorithms more memory efficient, especially for metagenomics applications. After graduate school, he took on a role as a software engineer at Amazon Web Services on the ElastiCache team for almost two years. In October 2014, he took a software engineering position at Google’s NYC office where he currently works on processing pipelines for display advertising data.
Jason Williams, PhD
Cold Spring Harbor Laboratories
Jason Williams is the iPlant’s Education, Outreach, and Training Lead – Based out of Cold Spring Harbor Laboratory, Cold Spring Harbor NY, he has a background in plant molecular biology. For iPlant, Jason organizes, manages, and instructs more than a dozen annual bioinformatics workshops, conferences, and other events. He has been instructional staff at Cold Spring Harbor Laboratory's DNA Learning Center for the past 5 years, and been research staff at Cold Spring Harbor Laboratory for 5 years prior to that. Jason is also faculty at Yeshiva University – running a science immersion course at Yeshiva University High School for Girls, and is also a member of the Scientific Training Advisory Board for the Genome Analysis Centre in Norwich, UK.
This boot camp is designed for graduate students, postdocs, and faculty in the biomedical sciences.
Participants must bring a laptop with a few specific software packages installed. Links to download the software will be sent before the boot camp.
Prior to the course, registrants will be given a survey to assess their computing skills. Participants will then be separated into either a novice or intermediate class.
For more information about Software Carpentry please visit http://software-carpentry.org/
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