Welcome to MiniBaz2020 (the COIVD19 version of Research Bazaar). This year we are running a selection of stand-alone workshops to pick and chose from. Sessions will be targeted towards a molecular biology/genetics background with one in the morning then one in the afternoon. You don’t need to sign up for everything, only those workshops that interest you.
These worshops are designed as tasters rather than being comprehensive on the given topics.
Sign up is at the bottom of the page link
Workshops are designed to be stand-alone but complementary, but some workshops do have expected prior knowledge.
| Duration | Monday | Tuesday | Wednesday | Thursday |
|---|---|---|---|---|
| 9:30 - 11:30 | Intro R | Genomic Data in R | Bash | Reproducible Report - Worked Example |
| 2:00 - 4:00 | HackMD / RMarkdown | Data Manipulation / Plotting in R | Regex | Snakemake |
The event will be in the Department of Biochemistry Ground Floor Seminar Room (room G13).
A laptop is required to participate for all workshops
Install instuctions for each of the workshop sessions are HERE
This session uses the Carpentries, Introduction to R lessons It is aimed at beginner users of R, who have little to no experience using R.
Expected prior knowledge: NONE
Required software: R and RStudio (refer to setup instructions)
By attending this workshop, learners should come away understanding:
link to more detailed setup instructions
End of workshop survey: https://tinyurl.com/minibaz2020-intro-r
Link to workshop material: https://github.com/mikblack/MiniBaz2020-HackMD
This workshop will introduce markdown which is a syntax for encoding formatting from which documents can be made in multiple output formats from a single source document.
HackMD is a realtime, multi-platform collaborative markdown knowledge base. You can write notes with other people on your desktop, tablet or even on the phone.
R Markdown is a tool for writing reproducible reports, document and presentations by combining markdown and R code.
Expected prior knowledge: Understanding of basic R syntax would be useful for the RMarkdown portion.
Required software: R and RStudio (refer to setup instructions)
End of workshop survey: https://tinyurl.com/minibaz2020-markdown
This workshop will introduce R can be used with genomic data, specifically how to manipulate genomic regions, and the use of genomic annotations from external sources.
Expected prior knowledge: basic R syntax (such as Intro to R)
Required software: R and RStudio (refer to setup instructions)
By attending this workshop, learners can expect to come away understanding:
Link to lesson underlying code
End of workshop survey: https://tinyurl.com/minibaz2020-genomic-r
This workshop introduces how to use R for manipulating datasets, and the beginning of plotting data. It is expected that attendees would have an understanding of basic R syntax (such as by attending the Intro to R workshop).
Expected prior knowledge: basic R syntax (such as Intro to R)
Required software: R and RStudio (refer to setup instructions)
By attending, learners can expect to understand:
ggplot2.Lessons can be found at
Link to manipulating data code
Link to the plotting code used
End of workshop survey: https://tinyurl.com/minibaz2020-data-r
This workshop aims to introduce the use of the Unix shell for the purposes of increasing reproducibility of tasks.
Expected prior knowledge: NONE
Required software: Unix shell (refer to setup instructions)
By attending this workshop, learners can expect to come away understanding
Lesson content: The Unix Shell
End of workshop survey: https://tinyurl.com/minibaz2020-bash
Practical Bash, using grep, sed and other tools to search and filter your data files on the command line
Expected prior knowledge: Intro to Bash or equivalent
Required software: Unix shell (refer to setup instructions)
By attending, learners can expect to understand:
grep and sedLesson materials: https://github.com/rikutakei/minibaz_regex
End of workshop survey: https://tinyurl.com/minibaz2020-regex
This workshop will use an example dataset to demonstrate best practices for project setup and creating a reproducible analysis document using RMarkdown.
This report will include examples of:
Expected prior knowledge: The Intro to R, HackMD/RMarkdown, and Data manipulation and plotting in R workshops, or equivalent experience.
Required software: R and RStudio (refer to setup instructions)
Data: Workshop Github which contains the workflow_data.zip file.
End of workshop survey: https://tinyurl.com/minibaz2020-workflow
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
This workshop is aimed at people who are already using tools such as the Unix shell and R as part of their workflows and will cover how to start creating a reproducible workflow of multiple steps using an example bioinformatics pipeline.
Expected prior knowledge: Understanding of Unix file system and running of commands.
Required software: Snakemake (refer to setup instructions)
End of workshop survey: https://tinyurl.com/minibaz2020-snakemake
Please select the workshops you would like to attend, numbers are limited to 25 for each session.
A laptop is required to participate in the workshops
If a particular workshop is full, please email carpentries@otago.ac.nz and we will see what we can do to accommodate you.
Register at Evenbrite HERE