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Weekly Meeting #1

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pbranson opened this issue Mar 5, 2019 · 70 comments
Open

Weekly Meeting #1

pbranson opened this issue Mar 5, 2019 · 70 comments

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@pbranson
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pbranson commented Mar 5, 2019

This issue is for discussion about planning our weekly meetings and themes.

The format of the meetings will likely evolve, however some structure will help keep the meetings on track and on schedule.

The only principle is that themes for subsequent weeks will be decided from the quorum at a meeting (i.e. you have to be at the meeting to have a say!)
@dirkslawinski
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March-12-2019
This week I (Dirk Slawinski) will cover the list of links we are gathering for the group and asking others to contribute.

I'll also demo some basic online map making using "Shiny" which I've set up for some projects.

We'll also start a discussion on map making in R that will set the stage for a more in depth discussion in the future.

  • Dirk

@HayleaMiller
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HayleaMiller commented Mar 11, 2019 via email •
edited by pbranson
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@dirkslawinski
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dirkslawinski commented Mar 11, 2019 via email •
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@A-K-Cresswell
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It would be good if in a meeting soon someone could go through some github basics as I am just learning how it works.

Cheers,
Anna

@HayleaMiller
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HayleaMiller commented Mar 11, 2019 via email •
edited by pbranson
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@HayleaMiller
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HayleaMiller commented Mar 11, 2019 via email •
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@dirkslawinski
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dirkslawinski commented Mar 11, 2019 via email •
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@beckyfisher
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beckyfisher commented Mar 11, 2019 via email •
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@pbranson
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Yep good idea - will see if I can pull together some resources.

At the moment we are primarily just using it for discussion/coordination of the meeting and capturing details on a platform that is accessible to everyone.

So I wouldn't worry too much about understanding how to use it initially, from a source code versioning / control perspective. The version control side can seem intimidating as there are a number of concepts that are typically pretty foreign to scientists who havent had software development experience!

Having said that, it can be a a useful tool - a topic for us to discuss tomorrow possibly for the next meeting!

@dirkslawinski
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dirkslawinski commented Mar 11, 2019 via email •
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@beckyfisher
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beckyfisher commented Mar 11, 2019 via email •
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@beckyfisher
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Apologies in advance group, I am very unwell this week and away next week.

@pbranson
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No worries Becky!

As discussed last week I will be giving an introduction to git usage for scientists.

@ghost
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ghost commented Mar 19, 2019 •
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Hi guys,

we are meeting in Room 4.02 today as there is a conflicting booking (with our booking time) for the Ocean Works space once a month. If we don't want to contend with this clash, we can change our meeting day (Mondays, Wednesday and Fridays morning or afternoons on any day are free booking wise) or we can stick with Tuesdays morning and meet somewhere else once a month.
So please let me know works for you!
Hope you're feeling better soon Becky.

@beckyfisher
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bummer! If it is relevant to the meeting discussion I would vote for Friday lunchtime... or if everyone still insists we avoid lunch, perhaps later in the afternoon.

@ghost
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ghost commented Mar 26, 2019

Hi all,

There is a meeting clash for CSIRO folks today as we have an all staff meeting at 11 and the Ocean works space is also booked from 10:30-11:30 so we could reschedule for this afternoon? or those who can make it at 10:30 will need to find another meeting space.

@dirkslawinski
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dirkslawinski commented Mar 26, 2019 via email

@pbranson
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Im not going to make it due to said all staff meeting too - let us know if a time change happens, otherwise have a good meeting!

@ghost
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ghost commented Mar 26, 2019

It sounds like we are postponing this weeks meeting so I look fwd to catching everyone next Tuesday.

@ghost
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ghost commented Apr 2, 2019

Hi guys, we are meeting downstairs on Floor 1 in the OceanWorks meeting room at 10:30 for those who can make it!

@pbranson
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pbranson commented Apr 2, 2019 via email

@A-K-Cresswell
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A-K-Cresswell commented Apr 2, 2019 via email

@joannastrzelecki
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joannastrzelecki commented Apr 2, 2019 via email

@beckyfisher
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beckyfisher commented Apr 2, 2019 via email

@ghost
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ghost commented Apr 2, 2019

It was a small but enthusiastic group this morning! Between us we identified 2 discussion topics for next week. Topic 1 is producing publication quality maps in R and/or Python (@dirkslawinski put up his hand to facilitate this one) and Topic 2 is machine learning which Ben Mayne has kindly agreed to facilitate, but given Ben isn't here next week, do you mind facilitating Topic 1 next week Dirk? And perhaps we recruit Ben for the following week? or we discuss this at next weeks meeting?
I'm all for inviting Non-IOMRC people to join us @A-K-Cresswell & @beckyfisher. I don't see why we shouldn't expand the invite, but happy to hear others thoughts on this??

@dirkslawinski
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dirkslawinski commented Apr 3, 2019 via email

@ghost
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ghost commented Apr 16, 2019

Hi all, FYI the Oceanworks space is booked from 10:30-11:30 for those who can make it today. Unfortunately I can't make it today (or for the next few weeks).

@HayleaMiller
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HayleaMiller commented Apr 16, 2019 via email

@HayleaMiller
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Is there a meeting today? Or are most people on leave.

@dirkslawinski
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a useful ggplot post on r-bloggers:

https://www.r-bloggers.com/a-detailed-guide-to-the-ggplot-scatter-plot-in-r/

  • Dirk

@ghost
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ghost commented May 6, 2019 via email

@ghost
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ghost commented May 13, 2019

Hey all, we are postponing Bens talk until next Tuesday as something has come up for him and a few people who are keen to see his talk are away. So for those who are around and would like to meet, see you in the Ocean works space at 12.

@ghost
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ghost commented May 21, 2019

Hey all, sorry for the slightly late notice, but Ben Mayne will be facilitating a session on machine learning methods in R today so see you down stairs at 12!

@beckyfisher
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Sorry guys, wont make it this week.

@joannastrzelecki
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joannastrzelecki commented May 28, 2019 via email

@pbranson
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pbranson commented May 28, 2019 via email

@ghost
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ghost commented May 28, 2019 via email

@A-K-Cresswell
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A-K-Cresswell commented May 28, 2019 via email

@mrayson
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mrayson commented May 28, 2019 via email

@HayleaMiller
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HayleaMiller commented May 28, 2019 via email

@A-K-Cresswell
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A-K-Cresswell commented May 28, 2019 via email

@A-K-Cresswell
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A-K-Cresswell commented May 28, 2019 via email

@A-K-Cresswell
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A-K-Cresswell commented May 28, 2019 via email

@dirkslawinski
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dirkslawinski commented May 28, 2019 via email

@ghost
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ghost commented Jun 4, 2019

Hi all, sorry I won't make it today. Hope to see you next week.

@joannastrzelecki
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joannastrzelecki commented Jun 4, 2019 via email

@dirkslawinski
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dirkslawinski commented Jun 4, 2019 via email

@HayleaMiller
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Hi everyone,

We weren't sure if there was an agenda for tomorrows peacefulR topic, but me and Nick were talking around the work I’ve been doing atm and thinks we should do a topic on that.
I’ve just received my sequencing data for my eCells, but I need to modify the FASTAQ files to merge the sequencing reads into a single larger fragment of DNA. We are pretty sure I need to code to do this (rather than using a program call geneious which I have been using to manipulate the data already).
Nick was thinking we could do a session where we try and solve the problem on the fly? I don’t know how to solve the answer yet. So I won’t be a lot of help… but I’ll try.
Ben has experience working with this type of data and will try and help out too!
Hope that's cool with everyone!

Cheers,
Haylea

@ghost
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ghost commented Jun 11, 2019

Hi guys,

Sounds like a fun meeting today. Sorry I'm home sick and can't make it. Just wanted to let you know that I was told a few weeks ago that our usual meeting time and spot (the Oceanworks space) was booked by another group today so can someone please check with the Oceanworks people if that is still the case? and/or arrange an alternative meeting venue if need be?

Cheers,
Lucy

@HayleaMiller
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Hey Everyone,
As you know Lucy is away today. Turns out the woodside oceanworks room is not available for us today. And all the large meeting rooms on the booking system - libcal are fully booked for most of today.
I can book a small meeting room which seats 6 people if its a small group today, or if someone else knows of a place we can meet that would be great.
Let me know if the small meeting room would be enough

Cheers,
Haylea

@HayleaMiller
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HayleaMiller commented Jun 11, 2019 via email

@beckyfisher
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beckyfisher commented Jun 11, 2019 via email

@ghost
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ghost commented Jun 18, 2019

Hi all,

sorry I'm still out of action so unfortunately I won't make it to our meeting today.
Fyi - our usual meeting spot is free - last week was the only exception I'm aware of.

Cheers,
Lucy

@beckyfisher
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Sorry guys, I've been really slack - it's hard to keep momentum when things are so buys.
Next weeks meeting overlaps with an AIMS seminar being linked from our Townsville site. As the seminar is by BEN BOLKER!!!! I thought maybe you just want to come to that? I've submitted a booking for the lvl 3 boardroom....

Details below:

Speaker: Dr Ben Bolker
Affiliation: McMaster University

Title: Ecological synthesis: a case study of West Nile Virus spread in Texas bird communities

Date: Tuesday, 25 June at 2.30pm (AEST)
Venue: Lecture Theatre

Abstract: West Nile Virus (WNV), a mosquito-borne virus of birds, emerged in North America in 1999; the invading strain was then displaced within a few years by a novel mutant. In order to understand this competitive displacement event, and to predict transmission of WNV in bird communities comprising hundreds of species, we collected data on bird and mosquito infections, bird community composition, and mosquito biting preferences from lab experiments, field observations, and citizen-science databases. We use a Bayesian framework, including a method for phylogenetic imputation applied to species with missing data, to synthesize information across the entire disease life cycle and throughout the community.

About the speaker: Ben Bolker is a quantitative ecologist with broad interests in the ecology and evolution of host-pathogen interactions, ecological and statistical modeling of population dynamics, and mixed models. After a PhD in the epidemic dynamics of measles (Cambridge University) and postdoctoral work on ecosystem carbon dynamics and spatial plant competition (Princeton University), he worked at the University of Florida and moved in 2010 to McMaster University (Hamilton, Ontario, Canada), where he is jointly appointed in the departments of Biology and Mathematics & Statistics.

@ghost
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ghost commented Jun 25, 2019

Thanks for the heads up on the seminar Becky, unfortunately I wont be able to make it at 2:30 today, but am keen to catch up with anyone at our regular time (i.e. 12) in the Ocean works space to chat about setting up Python environments. I'm starting to use python now so thought it might be useful to share some of my recent experiences and to have a chat about using anaconda and PyCharm to hear from other python users about various pitfalls and benefits of different IDEs. Happy to chat about other topics that people might be interested in too.

@ghost
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ghost commented Jul 2, 2019

Hi everyone, I'm sick again so sorry I won't make it today, but the Ocean works space is free for us to use if anyone is keen to meet.

@ghost
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ghost commented Aug 12, 2019

Hi all,

It's been too long since we got together so if people are free, Melvine has offered to talk to us about processing and analysing drone images of turtles in python and future work that could use machine learning methods. Nick has also offered to talk about his time efficient methods for producing gridded bathymetry data from large datasets.
Hope you can join us in the Ocean works space at 12 tomorrow!

@joannastrzelecki
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joannastrzelecki commented Aug 12, 2019 via email

@pbranson
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Hi Everyone,

As discussed last week - tomorrow I will give an overview of Holoviews and Geoviews (some Python graphics libraries) that I have been using to interactively analyse large datasets via the browser. I am doing this due to the data residing remotely on HPC/Cloud, but the tools have compelling applicability for general purpose use.

Holoviews is for general data visualisation, Geoviews takes that and applies it to data with a geographic representation (i.e maps).

Look forward to seeing you there

@NickMortimer
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Tuesday 10th September

I'm good to run a session on using Pandas to get stuff done. It will be a live coding exploration of getting some data sets merged using Pandas (https://pandas.pydata.org/)

Pandas is the work horse of many Matlab defectors, Pandas originally started by Wes McKinney (https://wesmckinney.com/ ) is now one of the go-to tool kits for data science

See you there.

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8 participants
@dirkslawinski @NickMortimer @mrayson @pbranson @beckyfisher @A-K-Cresswell @HayleaMiller @joannastrzelecki