[Admin-all] [SWC] New workshop request: On behalf of the American Society for Microbiology, United States

amy-noreply at software-carpentry.org amy-noreply at software-carpentry.org
Fri Oct 28 10:19:02 CDT 2016

Submission date: Oct. 28, 2016, 10:19 a.m.
Workshop type: Software-Carpentry
Person: Jennifer Gardy <<a href="mailto:jennifer.gardy at bccdc.ca">jennifer.gardy at bccdc.ca</a>>
Affiliation: On behalf of the American Society for Microbiology
Location: New Orleans, LA
Country: United States
Alongside of a conference: Microbe 2017
Preferred date: Thursday, June 1
Workshop language: not specified
Approx. number of attendees: 20-40 (one room, two instructors)
Attendees' fields: Genetics, genomics, bioinformatics, Organismal biology (ecology, botany, zoology, microbiology), 
Attendees' academic level: Graduate, Post-doctorate, Faculty
Attendees' level of computing experience: Novice (uses a spreadsheet for data analysis rather than writing code)
Travel and accomodation costs covered by institution: yes
Administrative fee understanding: yes
Fee waiver requested: no
Travel reimbursement: Flat reimbursement fee of $1000 per instructor, instructors to arrange travel/accommodation if neede
Administrative fee payment option: Self-organized: no fee (please let us know if you wish to make a donation)
Comment: Hello!

I'm on the organizing committee for Microbe 2017, the American Society for Microbiology (ASM)'s big, annual conference. As the lone bioinformatician on the organizing committee, I've been fairly vocal in noting that we need a good "Beginning Bioinformatics" workshop as part of the conference. We often run workshops on using various bioinformatics platforms for data analysis, but these all presuppose a certain amount of command-line literacy that many of our attendees just don't have. This year I was finally successful in getting the committee to program a workshop we've tentatively titled "Beginning Bioinformatics: An Introduction to the Command Line", and I thought it would be ideal if we could engage Software Carpentry instructors - I really love the curriculum, the open-source aspect of the lessons, and the general ethos of the organization :)

We'd run this as a self-organized workshop (with a $500USD donation to Software Carpentry), as the ASM Meetings staff will be handling all the logistics of booking the room, contacting potential attendees, signing people up, etc... We just need instructors! 

I saw Hani Nakhoul and Tina O'Grady's names online - both are based in New Orleans, where Microbe 2017 will be held, and both work on computational genomics of viruses, so they'll be Microbe-type folks :) I think two instructors will be sufficient - I'm suspecting we'll have about 30-40 registrants, and if we end up getting more (we'll have an idea of numbers about two months before the workshop) we can add instructors as needed. 

The instructors will be treated as ASM workshop speakers - upon arriving at the meeting and picking up their instructor badge, they will receive a cheque for $1000. They are free to spend this as they like - if they are travelling, it is meant to cover airfare and accommodation, if they are local, they can use it for absolutely anything they like! If they wish to attend the full conference, they could use part of the money to cover their registration.

We are limited to the June 1 date - all ASM workshops will take place on that date - and it will be a half-day workshop - 3.5hrs in total (with as many breaks as desired in there). Lesson-wise, we'd want to cover all the material in The Unix Shell, then spend the rest of our time dabbling in a few other key areas attendees will find useful: basic regular expressions so people can do quick find and replace operations, introducing a few simple 'for h in *.foo; do something $h; done' examples to help them with basic automation; and then introducing how to install command-line software - a walkthrough of unpacking, running a make operation, etc...

I hope this will work out - I know there's a load of us amongst the Microbe organizing committee who could run something like this but we'd much rather support an awesome organization like Software Carpentry! :)

You can view the request here:

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