Meeting Programmes

Meeting 54 — 24th July 2020

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Gillian Gibb & Julien Gaspar (Massey) --Kmers 101 and bird genome assembly
  • Tips, tricks, and new tools.

Meeting 53 — 26th June 2020

  • In person if we are at alert level 1. Otherwise video conference.
  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Monika Karmin (Massey) -- "Human paternal lineages of Island South East Asia, population history from Y chromosomal sequences."
  • Tips, tricks, and new tools.

Meeting 52 — 22nd May 2020

Meeting 51 — 24th April 2020

  • Moved to Video Conference rather than in person.
  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Emily Koot (PFR) -- "Genome-wide patterns of genetic differentiation and demographic history in mānuka (Leptospermum scoparium) grown on indigenous Māori land."
  • Tips, tricks, and new tools.

Cancelled — 27th March 2020

  • COVID-19 Level 4 Lockdown in place.

Meeting 50 — 28th February 2020

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • David Chagne (PFR) -- "Genome informed selection and gene editing in a Māori context" & "Sequence Database for Taonga Species"
  • Tips, tricks, and new tools.

Meeting 49 — 24th January 2020

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Matthieu Vignes & Patrick Biggs (Massey) -- "Teaching Statistical Genetics at Massey: what's the situation and how is the future like? More importantly, what is 'needed out there': statisticians aware of genetics concepts/issues and adequate techniques, computational biologists, what else?"
  • Tips, tricks, and new tools.

Meeting 48 — 22nd November 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Giulia Trauzzi (Vic) -- "Paua SNP development for monitoring recovery of paua populations affected by the Kaikoura earthquake "
  • Tips, tricks, and new tools.

Meeting 47 — 25th October 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Ange Hura and Malin Undin (Massey) -- "Whakapapa of Brown kiwi Part one, GBS data on the way, what do we do now?"
  • Tips, tricks, and new tools.

Meeting 46 — 27th September 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Patrick Biggs (Massey) -- Third in a series of discussions about creating an undergraduate bioinformatics curriculum.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.
  • Annual pot luck dinner -- Marking the start of year 5.

Meeting 45 — 23rd August 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Rob Elshire (TEG) -- Update on Cloud Computing Bioinformatics Project (Tool Repository Here)
    • Murray Cox & Patrick Biggs (Massey) -- Second in a series of discussions about creating an undergraduate bioinformatics curriculum.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 44 — 26th July 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Siouxsie Wiles (University of Auckland) -- Shedding light on antibiotic resistance and the evolution of superbugs - AKA help, we're drowning in data!
    • Murray Cox & Patrick Biggs (Massey) -- Second in a series of discussions about creating an undergraduate bioinformatics curriculum. Postponed until next month!
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 43 — 28th June 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Peter Lockhart (Massey) -- Investigating adaptive diversification in the NZ alpine buttercups
    • Murray Cox & Patrick Biggs (Massey) -- First in a series of discussions about creating an undergraduate bioinformatics curriculum.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 42 — 24th May 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Olivia Angelin-Bonnet (Massey) -- Simulating gene expression profiles with the R package sismonr (a package she wrote)
    • Interactive demonstration of sismonr. Everyone can try it:
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Special Workshop: Bioinformatics Cloud Computing Phase 1 — 18th April 2019

  1. Building blocks of cloud computing

    1. Hardware

      1. Number of processors
      2. Amount of RAM
      3. Amount / type of storage
      4. Network
    2. Software

      1. Operating system
      2. Software you need
    3. Data

      1. Storage
      2. Transfer
  2. Using the cloud

    1. SSH

      1. key pair
      2. logging in
    2.  Installing software
      1. apt
      2. compiling
    3. Getting some data
    4. Doing a basic analysis

Meeting 41 — 22nd March 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Mingshu Cao (AgR) -- Genotyping-by-Sequencing based Cytoplasmic Markers Underpin Population Structural Variation of Perennial Ryegrass (see also: https://github.com/AgResearch/cpmt )
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 40 — 22nd February 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Roger Moraga (TBB) -- PAG Conference Highlights
    • Rob Elshire (TEG) -- Introduction to Cloud Computing
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 39 — 25th January 2019

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Rose Collis (AgR) -- PhD research plan: Metagenomic analysis to identify antimicrobial resistance determinants in NZ dairy farm environments.
    • Roger Moraga (TBB) -- PAG Conference Highlights
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 38 — 23rd November 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Rob Elshire (TEG) -- GFANZ Cloud Computing Project
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 37 — 26th October 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Shanthi Parkar (PFR) -- Effect of curcumin on human gut microbiota.
    • Laura Payling (Riddet Institute) -- PhD Research Plan: How does fibre structure effect microbiota functionality
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 36 — 28th September 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • GFANZ & Travel Update (Rob)
  • Blast parameter issue discussion
  • Presenter
    • Richard Winkworth (Massey) -- DNA tests in a tea cup.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 35 — 24th August 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Our Third Anniversary!
  • Presenter
    • Richard Fong (Massey) -- The impact of genomics on clinical microbiology and public health practice
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 34 — 27th July 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenter
    • Gillian Gibb (Massey) -- Why fly when you can walk? Comparing genomes of flying and
      flightless birds
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 33 — 22nd June 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Shannon Ormond (Massey) -- Searching for human disease-causative genetic variants using whole exome sequencing
    • Roger Moraga (Tea Break Bioinformatics) -- What you can do with 1 lane of Illumina Sequencing.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 32 — 25th May 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Sean Bisset (Massey) -- Insights into an antimicrobial mode of action using transcriptomics.
    • David Winter (Massey) -- Marsden Grant Application Discussion
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 31 — 27th April 2018

Meeting 30 — 23rd March 2018

Meeting 29 — 23rd February 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Jibran Tahir (PFR) -- 3D genome assembly of Kiwifruit
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 28 — 26th January 2018

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Nicole Ferguson (CE REANNZ) -- REANNZ
    • Question for the group: (How?) Does the differential alignment of different sample files affect SNP calling. Compare TASSEL collapsing to unique reads before alignment with other methods.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 27 — 24th November 2017

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    •  Simon Zhang (Custom Science) -- DNA Sequencing Technologies
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 26 — 27th October 2017 

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    •  Full Group — MapNet Workshop Preparations
    • Technical Issues
    • Anything else
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 25 — 22nd September 2017

  •  Opening discussion and general catch up
  •  Welcome for new members
  •  Presenters
    •  GFANZ
      • GFANZ / GA Collaboration Discussion Report
      • GFANZ Constitutional Draft Objectives
    • Full Group — MapNet Workshop Preparations
      • Any changes / suggestions
      • Talk outlines / references needed?
  • Tips, tricks, and new tools.
  • Ideas about future meetings.
  • 2nd Birthday Potluck Dinner

 Meeting 24 — 25th August 2017 

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Full Group —  MapNet Workshop Preparations
      • Any changes / suggestions
      • Talk outlines / references needed?
      • Recording the work for future use.
    • Finlay Thompson (Dragonfly Data Science) — Discussion about reproducibility
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 23 — 29th July 2017

Meeting 22 — 23rd June 2017

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 21 — 19th May 2017

  • Opening discussion and general catch up
  • Welcome for new members
  • Presentation & Discussion
    • Bruno Lago (Catalyst IT) — Software testing and how you can ensure your code is producing the right results.
    • Everyone — What would a good workshop on 'How do we know that our software is doing what we expect it to do?' in the bioinformatics context (and  MapNet) look like?
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 20 — 28th April 2017

Meeting 19 — 24th March 2017

Meeting 18 — 24th February 2017

  • Opening discussion and general catch up
  • Welcome for new members
  • Data Science Workshop Announcement
  • Presenters
    • Rob Elshire TEG — Advanced Genomics Research Platform Update
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 17 — 27th January 2017

  • Opening discussion and general catch up
  • Welcome for new members
  • Moment for Lucy
  • Presenters
    • Helge Dzierzon PFR — NextFlow
    • Rob Elshire TEG — BBS @ PAG & AGP proposal overview
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 16 — 31st December 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters (everyone)
    • Drinks and nibbles.
    • Swimming
    • BBQ
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 15 — 25th November 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • David Winter Massey — Recent work
    • Helge Dzierzon PFR — NextFlow postponed.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 14 — 28th October 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Alison Stringer MFE — Open Data in NZ
    • Helge Dzierzon PFR — NextFlow postponed
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 13 — 23rd September 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
    • Matthieu Vignes Massey — Machine Learning
    • Tatiana Lomasko — Centre for Space Science and Technology
  • Tips, tricks, and new tools.
  • Ideas about future meetings.
  • Dish to pass in celebration of our first anniversary.

Meeting 12 — 26th August 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Reflections on the Open Source // Open Society Conference (Rob)
  • Presenters
    • Robyn Johnston TEG — laser microdissection derived RNA seq data to look at pattern formation in maize leaf development
    • Rob Elshire TEG — Kāki Genomics: approaches, code and outcomes.
  • Tips, tricks, and new tools.
  • Ideas about future meetings.

Meeting 11 — 29th July 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Pressing Events Discussion
    • AGR / NZGL GBS Service
    • GPSBE GBS Pipeline Code Release & Removal
    • Elshire offer of Open Source Assistance to GPSBE Programme
    • Implications of above for BBS collective
    • BBS Collective Next Steps
  • Presenters
  • Tips, tricks, and new tools.

Meeting 10 — 24th June 2016

  • Opening discussion and general catch up
  • Welcome for new members
  • Presenters
  • Tips, tricks, and new tools.

Meeting 9 — 27th May 2016

Meeting 8 — 29th April 2016

Meeting 7 — 18th March 2016

Meeting 6 — 19th February 2016

  • Opening discussion and general catch up
  • Roger Moraga (AGR) --
  • Patrick Bigs (Massey) — Cardashian Effect

Meeting 5 — 15th January 2016

Meeting 4 — 10th December 2015

Meeting 3 — 9th November 2015

  • Mauro GBS adapter set optimisation.
  • GitHub work.
    • Get started with editing files and pull requests.
    • Populate the appropriate sub projects with people, skills and interests

Meeting 2 — October 2015

  • Agenda lost in the mists of time.

Meeting 1 — September 2015

  • A preliminary get together to gauge interest and direction.

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