A Data Carpentry Workshop
The Jackson Laboratory for Genomic Medicine
Apr 6-7, 2017
8:30am - 4:30pm
Instructors:
Sue McClatchy, Saira Kazmi, Shane Sanders, Sandeep Namburi, Pariksheet Nanda
Helpers:
Neil Kindlon, Ming Zhang, Aditya Kovuri, Max Harvey
Apr 6-7, 2017
8:30am - 4:30pm
Instructors: Sue McClatchy, Saira Kazmi, Shane Sanders, Sandeep Namburi, Pariksheet Nanda
Helpers: Neil Kindlon, Ming Zhang, Aditya Kovuri, Max Harvey
General Information
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.
We will cover Data organization in spreadsheets and OpenRefine, Introduction to Python, and Data analysis and visualization in Python. 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.
Who: The course is aimed at graduate students and other researchers.
Where: 10 Discovery Drive, Farmington, Connecticut. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.
Contact: Please mail susan.mcclatchy@jax.org for more information.
Preliminary Schedule
Surveys
Please be sure to complete these surveys before and after the workshop.
Day 1
| Morning | Data organization in spreadsheets and OpenRefine |
| Afternoon | Introduction to Python |
Day 2
| Morning | Data analysis and visualization in Python |
| Afternoon | Data analysis and visualization in Python (continued) |
Day 1
| 08:30 | Setup, introduction, and workshop overview |
| 09:00 | Data Organization in Spreadsheets |
| 10:30 | Coffee |
| 10:45 | Data Cleaning with OpenRefine |
| 12:00 | Lunch break |
| 13:00 | Short Introduction to Python |
| 13:30 | Starting with Data |
| 14:30 | Coffee |
| 14:45 | Indexing, Slicing and Subsetting DataFrames |
| 15:45 | Data Types and Formats |
| 16:15 | Wrap-up |
Day 2
| 08:30 | Merging Data |
| 10:30 | Coffee |
| 10:45 | Data Analysis Automation: Loops and Functions |
| 12:00 | Lunch break |
| 13:00 | Plotting with ggplot |
| 14:30 | Coffee |
| 14:45 | Putting It All Together |
| 15:30 | Accessing SQL using Python |
| 16:15 | Wrap-up |
Etherpad: http://pad.software-carpentry.org/2017-04-06-farmington.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Syllabus
Programming in Python
- Using libraries
- Working with arrays
- Reading and plotting data
- Creating and using functions
- Loops and conditionals
- Defensive programming
- Using Python from the command line
- Reference...
Setup
To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. 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 for spreadsheets and OpenRefine. For Python installation, please follow these installation instructions
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.