Difference between revisions of "20th Discussion-6 Feb 2018"
From BioWiki
Jump to navigationJump to search (Preparation for next discussion) |
|||
| Line 6: | Line 6: | ||
* Do you have any requirements to entry? | * Do you have any requirements to entry? | ||
* What are your favorite platforms for teaching or teaching tips? | * What are your favorite platforms for teaching or teaching tips? | ||
| + | |||
| + | How much training do you do? | ||
| + | * 2-3 full days modeled on software carpentry, done a few times, command line, RNA-seq | ||
| + | * Simon Andrews, Babraham Institute | ||
| + | ** huge amount of training, 50 courses a year, a day each | ||
| + | ** one of their core functions | ||
| + | ** internal / external / commercial venture | ||
| + | ** 5 regular teachers | ||
| + | * Matt Eldridge, Cambridge | ||
| + | ** Also a large amount of training | ||
| + | ** Part of a larger university program | ||
| + | ** demand is massive, long waiting list | ||
| + | ** perhaps have noticed routine analysis going down in volume | ||
| + | *** maybe that's fine, let routine stuff go and focus on harder analyses | ||
| + | * How much? free? | ||
| + | ** 50 pounds a day for postdocs, Phd students free | ||
| + | ** 178 pounds a day with a "day rate" | ||
| + | |||
| + | Curriculum? | ||
| + | * command line, common bioinfo tools | ||
| + | * RNA-seq / ChIP-seq / application specific | ||
| + | * someone suggested github / docker | ||
| + | * Simon said they do | ||
| + | ** statistics | ||
| + | ** core skills - unix, perl/python, R | ||
| + | ** RNA-seq / chIP-seq / methyl-seq | ||
| + | ** "creating figures" | ||
| + | ** gene set enrichment analysis | ||
| + | * Goblet was mentioned | ||
| + | ** but direct reuse is harder than it seems | ||
| + | * Environments are tricky | ||
| + | ** how do you ensure the same environment for everyone? | ||
| + | ** amazon - but then dependent on network | ||
| + | ** some people use docker - last part of course is getting things running on *your* laptop | ||
| + | ** Use a script to check that everything is installed and ready to go | ||
== Nanopore == | == Nanopore == | ||
Revision as of 09:26, 6 February 2018
Attendees
Training
- How much does your core do, and how do you schedule it?
- What do you teach?
- Do you have any requirements to entry?
- What are your favorite platforms for teaching or teaching tips?
How much training do you do?
- 2-3 full days modeled on software carpentry, done a few times, command line, RNA-seq
- Simon Andrews, Babraham Institute
- huge amount of training, 50 courses a year, a day each
- one of their core functions
- internal / external / commercial venture
- 5 regular teachers
- Matt Eldridge, Cambridge
- Also a large amount of training
- Part of a larger university program
- demand is massive, long waiting list
- perhaps have noticed routine analysis going down in volume
- maybe that's fine, let routine stuff go and focus on harder analyses
- How much? free?
- 50 pounds a day for postdocs, Phd students free
- 178 pounds a day with a "day rate"
Curriculum?
- command line, common bioinfo tools
- RNA-seq / ChIP-seq / application specific
- someone suggested github / docker
- Simon said they do
- statistics
- core skills - unix, perl/python, R
- RNA-seq / chIP-seq / methyl-seq
- "creating figures"
- gene set enrichment analysis
- Goblet was mentioned
- but direct reuse is harder than it seems
- Environments are tricky
- how do you ensure the same environment for everyone?
- amazon - but then dependent on network
- some people use docker - last part of course is getting things running on *your* laptop
- Use a script to check that everything is installed and ready to go
Nanopore
- How is your core supporting Nanopore sequencing?
- Which tools have you found useful thus far for analysis?
- Any particular quality control approaches you are using?
Other New Protocols or Approaches?
- Anything new happening at your institution that you would like to discuss?
