Bioinformatics: Command Line/R Prerequisites Workshop
Dec. 16, 2019, 9 a.m. - Dec. 19, 2019, 4:30 p.m.
UC Davis Bioinformatics Core, firstname.lastname@example.org
UC Davis Student Community Center, Multipurpose room.
This workshop will cover the basic computational and statistical concepts needed before performing bioinformatics analysis.
- Access to a multi-core (24 cpu or greater), ‘high’ memory 64Gb or greater Linux server.
- Familiarity with the ’command line’ and constructing scripts/pipelines.
- Basic knowledge of how to install software
- Basic knowledge of R (or equivalent) and statistical programming
- Basic knowledge of Statistics and model building
The course will include experimental data organization, basic command line and high performance computing concepts, how to install software, use help, run applications, and the basics of building scripts and pipelines. Also covered will be basic R programming, working with data tables and generating figures, basic statistical concepts, and statistical model building. There are no prerequisites for this workshop other than an interest in bioinformatics! The workshop will be on the UC Davis campus, and will run from 9am to 4:30pm each day and include light breakfast, lunch, and snacks.
The registration fee for the entire workshop is $600 for UC and UC affiliates, $900 for other academic or non-profit participants and $1,200 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment. Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.
UNIX/COMMAND LINE CONCEPTS
- Introductory materials, Unix/bash command line basics.
- Environment variables, your bash profile
- Basic bash shell scripting.
- Introduction to cluster computing
- Basics of git
- Folder and experiment structure
- Installation and running of simple sequencing tools.
- Constructing and run a simple bioinformatics pipeline.
R/DATA PROGRAMMING CONCEPTS
- Introduction to the R programming language.
- R markdown and notebooks.
- Constructing metadata tables, data munging, excel to R
- Basics of the tidyverse, data frame manipulation (join/rename/pipes)
- Figures in R, ggplot2
- Statistical concepts and model building.
Who should attend? … Prior workshop participants have included faculty, post docs, grad students, staff, and industry researchers.
What are the prerequisites? … There are no prerequisites other than an enthusiasm for learning bioinformatics data analysis.
What do I need to bring? … You will need to bring your own laptop to use, which should have a recent version of R and R Studio, have a recent version of Java installed, and an application that will allow you to ssh into a server (e.g. Bash for windows, or terminal for Apple) as well as the ability to connect to the internet via wifi. Computational exercises will be performed on a remote server. We can help with setup early on in the workshop. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.
Can I bring my own data? … We will provide all experimental datasets for use during the workshop, as this helps to keep the workshop moving.
Where is the workshop? … It will be held on the UC Davis campus and will run from 9:30am to 4:30pm on the dates indicated.
How do I apply? … All registration is “first-come, first-served”. There is no application process. So, sign up as soon as possible to ensure your place in the workshop.
If you have any questions, please don’t hesitate to contact us at email@example.com