update for 2024

README.md

@@ -1 +1 @@
-# bioinformatics-spring-school-2023
+# bioinformatics-spring-school-2024

_config.yml

@@ -1,6 +1,6 @@
-title: Bioinformatics Spring School 2023
+title: Bioinformatics Spring School 2024
 email: [email protected]
-baseurl: "/2023/"
+baseurl: "/2024/"
 url: "https://otagobioinformaticsspringschool.github.io"
 theme: jekyll-theme-leap-day
 

_includes/curriculum.md

@@ -14,11 +14,9 @@
 - Draft assembly
 - Assembly QC
 
-#### Nanopore
+### RNA Seq
 
-- Base calling
-- Quality control
-- Variant calling
+### eDNA
 
 ### Computational Topics
 

_includes/schedule_day1.md

@@ -1,15 +1,13 @@
-### Monday 27th Nov
+### Monday 18th Nov
 
 | Time  |         What         |
 | ----- | :------------------: |
 | 09:30 |       Welcome        |
 | 10:00 | Introduction to NeSI |
 | 10:45 |        Break         |
-| 11:00 | Keynote: Phil Wilcox |
+| 11:00 |       Keynote:       |
 | 12:15 |        Lunch         |
 | 13:00 | Introduction to BASH |
 | 14:45 |        Break         |
 | 15:00 |      BASH cont.      |
 | 16:30 |      End of Day      |
-
-Evening: Penguins and sea lions outing for those who signed up

_includes/schedule_day2.md

@@ -1,10 +1,10 @@
-### Tuesday 28th Nov
+### Tuesday 19th Nov
 
 8am Breakfast (own cost) for those who signed up
 
 | Time  |           What            |
 | ----- | :-----------------------: |
-| 09:30 |   Speaker: Anna Gosling   |
+| 09:30 |         Speaker:          |
 | 10:00 |    DNA variant calling    |
 | 10:45 |           Break           |
 | 11:00 | DNA variant calling cont. |
@@ -13,5 +13,3 @@
 | 14:30 |           Break           |
 | 14:45 | DNA variant calling cont  |
 | 16:30 |        End of Day         |
-
-Evening: Penguins and sea lions outing for those who signed up

_includes/schedule_day3.md

@@ -1,13 +1,13 @@
-### Wednesday 29th Nov
+### Wednesday 20th Nov
 
-| Time  |              What               |
-| ----- | :-----------------------------: |
-| 9:30  |             Speaker             |
-| 10:30 | Introduction to Version Control |
-| 11:00 |              Break              |
-| 11:15 |      Version Control cont.      |
-| 12:15 |              Lunch              |
-| 13:00 |     Reproducible pipelines      |
-| 14:45 |              Break              |
-| 15:00 |  Reproducible pipelines cont.   |
-| 16:30 |           End of Day            |
+| Time  |    What    |
+| ----- | :--------: |
+| 9:30  |  Speaker   |
+| 10:30 |            |
+| 11:00 |   Break    |
+| 11:15 |            |
+| 12:15 |   Lunch    |
+| 13:00 |            |
+| 14:45 |   Break    |
+| 15:00 |            |
+| 16:30 | End of Day |

_includes/schedule_day4.md

@@ -1,15 +1,13 @@
-### Thursday 30th Nov
+### Thursday 21st Nov
 
-| Time  |      What       |
-| ----- | :-------------: |
-| 9:30  |     Speaker     |
-| 10:30 | Genome assembly |
-| 11:00 |      Break      |
-| 11:15 | Genome assembly |
-| 12:15 |      Lunch      |
-| 13:00 | Genome assembly |
-| 14:45 |      Break      |
-| 15:00 | Genome assembly |
-| 16:30 |   End of Day    |
-
-(Optional) Drinks/nibbles at own cost, 5pm Noisy Brewery - 7 Anzac Avenue, Central Dunedin, Dunedin.
+| Time  |    What    |
+| ----- | :--------: |
+| 9:30  |  Speaker   |
+| 10:30 |            |
+| 11:00 |   Break    |
+| 11:15 |            |
+| 12:15 |   Lunch    |
+| 13:00 |            |
+| 14:45 |   Break    |
+| 15:00 |            |
+| 16:30 | End of Day |

_includes/schedule_day5.md

@@ -1,16 +1,13 @@
-### Friday 1st Dec
+### Friday 22nd Nov
 
-| Time  |      What      |
-| ----- | ------------ |
-| 09:30 | Introduction to Nanopore Sequencing    |
-| 10:00 | Nanopore flowcell loading demo: Dr Augstine Chen  |
-| 10:15 | Basecalling with Dorado  |
-| **10:45** | **BREAK**      |
-| 11:00 | Basecalling continued |
-| 11:30 | QC with Nanoplot and FastQC |
-| **12:15** | **LUNCH**      |
-| 13:00 | Talk: Dr Michael Dunnet |
-| 13:30 | Alignment and Variant Calling |
-| **14:30** | **BREAK** |
-| 14:45 | Adaptive sampling |
-| **16:00** | **FINISH!**   |
+| Time  |    What    |
+| ----- | :--------: |
+| 9:30  |  Speaker   |
+| 10:30 |            |
+| 11:00 |   Break    |
+| 11:15 |            |
+| 12:15 |   Lunch    |
+| 13:00 |            |
+| 14:45 |   Break    |
+| 15:00 |            |
+| 16:30 | End of Day |

about.md

@@ -4,17 +4,17 @@ title: About
 permalink: /about/
 ---
 
-Bioinformatics Spring School 2023 is a week long training event for researchers, supported by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI).
+Bioinformatics Spring School 2024 is a week long training event for researchers, supported by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI).
 
 We will combine talks from researchers and hands on computational workshops (influenced by [The Carpentries](https://www.carpentries.org)), covering example workflows of DNA variant calling, Genome assembly, environmental DNA (eDNA), and Nanopore.
 
 This event is organised by:
 
 {% include organisers.md %}
 
-
 When and where?
-9:30 - 16:30, 27 November - 1 December 2023
+
+9:30 - 16:30, 18-22 November 2024
 University of Otago, Dunedin, New Zealand
 
 This is an in-person event.

index.md

@@ -1,10 +1,10 @@
 ---
-title: Bioinformatics Spring School 2023
+title: Bioinformatics Spring School 2024
 ---
 
 ## About
 
-Hosted at the University of Otago, the Bioinformatics Spring School 2023 is a week long training event for researchers, supported by [Genomics Aotearoa](https://www.genomics-aotearoa.org.nz) and the [New Zealand eScience Infrastructure (NeSI)](https://www.nesi.org.nz). This event is primarily targeted at researchers and students based in Aotearoa New Zealand. International applications will be considered but will need to be able to attend in-person.
+Hosted at the University of Otago, the Bioinformatics Spring School 2024 is a week long training event for researchers, supported by [Genomics Aotearoa](https://www.genomics-aotearoa.org.nz) and the [New Zealand eScience Infrastructure (NeSI)](https://www.nesi.org.nz). This event is primarily targeted at researchers and students based in Aotearoa New Zealand. International applications will be considered but will need to be able to attend in-person.
 
 We will combine talks from researchers and hands on computational workshops (influenced by [The Carpentries](https://www.carpentries.org)), covering example workflows using short and long read DNA sequencing technologies for variant calling and genome assembly.
 
@@ -16,18 +16,18 @@ Please email [[email protected]]([email protected]) for futher i
 
 ### When and where?
 
-- 9:30 - 16:30, 27 November - 1 December 2023
+- 9:30 - 16:30, 18-22 November 2024
 - University of Otago, Dunedin, New Zealand
 
 **This is an in-person event.**
 
-| Day       | Topic                         |
+<!-- | Day       | Topic                         |
 | --------- | ----------------------------- |
 | Monday    | Introduction NeSI / Bash      |
 | Tuesday   | Genomic variant calling       |
 | Wednesday | Workflows and Reproducibility |
 | Thursday  | Genome Assembly               |
-| Friday    | Nanopore                      |
+| Friday    | Nanopore                      | -->
 
 ### Cost?
 
@@ -39,24 +39,25 @@ This event is designed to give researchers (including students - 4th year and ab
 
 - DNA variant calling from next generation sequence data
 - Genome Assembly
-- Dealing with Nanopore data
+- RNAseq Analysis
+- eDNA Analysis
 
 along with computational topics such as:
 
 - Introduction to the Unix commandline (Bash)
-- Using version control (Git/Github)
-- Creating automated workflows
 - Introduction to working in a high performance computing environment (provided by NeSI)
 
 This week long event is designed to be an immersive experience so **we ask that you commit to the entire week.** We have chosen to interweave the computational topics throughout the week so that we can build on them throughout the entire week, so this ensures participants have the key knowledge at the right time.
 
 ### Expressions of Interest
 
-Expressions of interest applications are now open and will close midnight, Friday 29th September 2023.
+Expressions of interest Will open mid-August.
+
+<!-- Expressions of interest applications are now open and will close midnight, Friday 29th September 2024. -->
 
 <!-- **Please register your interest in attending by filling out [this form](https://docs.google.com/forms/d/e/1FAIpQLSd-k0o9J64C04fcc5Guui9KGoZ8zwuGpMlGR-q8fzJWqcfqSQ/viewform?usp=sf_link)** -->
 
-Applications closed midnight 29th September (NZ). Applicants will be notified of their outcome the week following the close of applications.
+Applications close midnight 27th September anywhere on earth. Applicants will be notified of their outcome the week following the close of applications.
 
 ---