Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required.
The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover project setup, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.
Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.
Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.
Organizer: Adina Howe, Julian Trachsel, Heather Allen
Instructors: Adina Howe, Fan Yang
Assistants: Jin Choi, Julian Trachsel, Heather Allen
Who: The course is aimed at faculty, research staff, postdocs, graduate students, advanced undergraduates, and other researchers in any field. No prior computational experience is required.
Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (We will provide instructions on setting up the required software several days in advance, and the classroom will have computers with the software installed). There are no pre-requisites, and we will assume no prior knowledge about the tools. Participants are required to abide by Software Carpentry's Code of Conduct.
Data Carpentry is supported by the Gordon and Betty Moore Foundation and a partnership of several NSF-funded BIO Centers (NESCent, iPlant, iDigBio, BEACON and SESYNC) and Software Carpentry. The structure and objectives of the curriculum as well as the teaching style are informed by Software Carpentry. This workshop is sponsored by Iowa State University Microbiology Graduate Student Organization. We also thank for the Iowa State University College of Business for the colorful stickie notes!
Registration is through EventBrite, see below.
Updates will be posted to this website as they become available.
The etherpad for this workshop can be found HERE
All lessons and resources: https://datacarpentry.github.io/2015-08-24-ISU/lessons
|Monday||09:00 - 09:15||Introduction to Data Carpentry|
|Monday||09:15 - 09:30||Pre-class survey|
|9:30 - 10:00||Introduction on data ditiness|
|10:00 - 10:30||Introduction to cloud computing|
|10:30 - 11:00||Coffee break|
|11:00 - 11:30||Introducing Ecoli evolution experiment; Retreiving and examining SRA data and runtable|
|11:30 - 12:00||Unix file system|
|12:00 - 13:00||Lunch break|
|13:00 - 14:00||Seaching files; Know your data|
|14:00 - 14:30||Coffee break|
|14:30 - 15:00||Unix organization; Read QC|
|15:00 - 16:00||Shell automation; wrap-up|
|Tuesday||09:00 - 09:30||Before we start with R|
|09:30 - 10:00||Introduction to R|
|10:00 - 10:30||Coffee break|
|10:30 - 11:00||Starting with data|
|11:00 - 12:00||Data frames|
|12:00 - 13:00||Lunch Break|
|13:00 - 13:30||R automation|
|13:30 - 14:15||Data manipulation with dplyr|
|14:15 - 14:30||Coffee break|
|14:30 - 15:30||Data visualization|
|15:30 - 16:00||Review and wrap-up|
To participate in a Data Carpentry workshop, you will need working copies of the shell, R, RStudio, SQL and OpenRefine. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.
Please follow these Setup Instructions