Merge pull request #4997 from dbrites/patch-4

Update 2024-06-10-mtb-ngs.html

_includes/tutorial_list.html

@@ -40,7 +40,7 @@
         <tr>
           {% assign hidetime = material.async | default: async%}
           {% if page.layout == 'event' and hidetimes != true %}
-          <td>{{material.time}}</td>
+          <td>{{material.time | markdownify }}</td>
           {% endif %}
 
           {% if material.layout == 'custom' %} <!-- e.g. for events -->

events/2024-06-10-mtb-ngs.html

@@ -86,39 +86,55 @@
     async: true
     tutorials:
     - type: custom
-      name: Icebreaker
+      name: "**Icebreaker**"
       description: |
-        Introduce yourself on Slack and tell us one fun fact about yourself.
+        **Introduce yourself on Slack and tell us one fun fact about yourself!**
+
         Post your answer to the [#event-mtb-ngs](https://gtnsmrgsbord.slack.com/archives/event-mtb-ngs)
+
         Please feel free to respond to each other here, this channel is for troubleshooting but also for getting to know each other! :)
 
 
     - type: custom
       name: "**Webinar**: Overview of NGS technologies & TB specific NGS solutions"
       description: |
-        This [webinar](https://www.youtube.com/watch?v=BcfBjCJRmUs) will introduce different sequencing technologies
-        and what applies best to what kind of problem.
+        Introduction to different sequencing technologiesand what applies best to what kind of problem.
+
+        [Watch webinar](https://www.youtube.com/watch?v=BcfBjCJRmUs) (1h)
 
         **Assessement***: Share your thoughts with us
         [here](https://docs.google.com/document/d/1Rd72luHh1Z33O-Le-FpEuPWi7X5yaBPTuVyB-oCSMQw/edit)
 
     - type: custom
       name: "**Webinar**: Implementation of NGS for TB- WHO documents and other considerations"
       description: |
-        [This webinar](https://youtu.be/eSWnPange8w) will summarize the recommendations and considerations
-        available from the WHO documents on the use of NGS for TB
+        Summary of the recommendations and considerations available from the WHO documents on the use of NGS for TB.
+
+        [Watch webinar](https://youtu.be/eSWnPange8w) (1h)
+
+        **Assessement***: Share your thoughts with us
+        [here] (https://docs.google.com/document/d/1M6lsXVHBipxJO84gRO0Lx-xGTrkDYOQmzaDuM19rAwY/edit#heading=h.bs9dcv9mioqd)
+
+    - type: custom
+      name: "**Webinar**: Updated WHO catalogue version 2"
+      description: |
+       Description of main changes introduced in the second version of the WHO catalogue on mutations associated with drug resistance released in November 2023.
+
+        [Watch webinar](https://www.youtube.com/watch?v=vxggV1wMLdk) (6 min)
 
     - type: custom
       name: "**Webinar**: WHO recommendations on targeted NGS (tNGS)"
       description: |
-        [This webinar](https://www.youtube.com/watch?v=UdolTwTnsz8) will summarize the recommendations from WHO on targeted sequencing.
+        Summary of the recommendations and considerations available from the WHO documents on the use of **targeted** NGS for TB
+
+        [Watch webinar](https://www.youtube.com/watch?v=UdolTwTnsz8) (15 min)
 
   - section:
     custom: true
     tutorials:
     - type: custom
       name: "**Meet the experts: Q&A session**"
-      time: "14:00-16:00 Central European Time"
+      time: "**14:00-16:00** Central European Time"
       description: |
         We would like to hear your opinion on the following questions
         and promote discussion in this Q&A session. Please let us know your thoughts on one or more of the following
@@ -131,11 +147,16 @@
         Also take the chance to ask us or write down in the shared notes other questions you might have.
 
         - Zoom: [link](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09)
-        - Shared Notes*: [link](https://docs.google.com/document/d/1VtGho4Zz0qFp5tzqD8rl7NU83xtYb4tCkLDitC3DrhQ/edit#heading=h.e69aqv1nq3gw)
+        - Shared Notes: [link](https://docs.google.com/document/d/1VtGho4Zz0qFp5tzqD8rl7NU83xtYb4tCkLDitC3DrhQ/edit#heading=h.e69aqv1nq3gw)
 
-        *Note*: The completion of the assessments is a requirement for the certificate of attendance.*
+        *The completion of the assessments is a requirement for the certificate of attendance.*
 
+  - section:
+    description: |
+        Optional webinars: These are produced outside this training by [tbnet](https://www.tbnet.eu/) and [Stop TB Partnership](https://www.stoptb.org/) and [FIND](https://www.finddx.org/), but might be of interest to you.
 
+        [Targeted next generation sequencing for the detection of drug resistant TB: intended use, challenges and research priorities](https://www.tbnet.eu/webinars)
+        [Implementing tNGS for detection of drug-resistant TB in high burden countries](https://www.stoptb.org/meetings-events/implementing-tngs-detection-of-drug-resistant-tb-high-burden-countries)
 
 
   - section: "Day 2: Mapping and variant calling"
@@ -163,7 +184,7 @@
       access to one, Galaxy is a very good alternative for data analysis.
 
     tutorials:
-      - name: Icebreaker
+      - name: "**Icebreaker**"
         type: custom
         description: |
            Come say Hi in Slack! Let us know you are joining today and are getting started!
@@ -200,7 +221,7 @@
 
       You are now ready for performing bioinformatic analysis in Galaxy. Before we start we would like you to watch a short video on how Illumina sequencing works. Following that video we have prepared a webinar on mapping and variant calling of Illumina applied to MTBC. After watching it you will be hopefully able to know; how a reference genome is chosen, why we typically ignore some regions of the MTBC genomes or what is the difference between a fixed and a variable SNP and why do we care about it (among other things).
     tutorials:
-      - name: Illumina sequencing
+      - name: "**Video:** Illumina sequencing"
         type: custom
         description: Please watch [this 5-minute video](https://youtu.be/fCd6B5HRaZ8) about the principles behind Illumina sequencing
       - name: "**Webinar**: Mapping and Variant calling"
@@ -220,11 +241,12 @@
     tutorials:
       - type: custom
         name: "**Meet the experts: Q&A session**"
-        time: "11:30-12:30 Central European Time"
+        time: "**11:30-12:30**  Central European Time"
         description: |
           Meet the experts! Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
 
   - section:
+    async: true
     tutorials:
       - name: tb-variant-analysis
         topic: variant-analysis
@@ -234,7 +256,7 @@
       - type: custom
         name: "**Meet the experts: Q&A session**"
         time: |
-          16:30-17:30
+          **16:30-17:30**
           Central European Time
         description: |
           Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
@@ -254,7 +276,7 @@
     async: true
     custom: true
     tutorials:
-      - name: Icebreaker
+      - name: "**Icebreaker**"
         type: custom
         description: |
            Come say Hi in Slack! Let us know you are joining today and are getting started!
@@ -288,15 +310,15 @@
 
           *The completion of the assessments is a requirement for the certificate of attendance.*
 
-      - name: "Webinar: Webinar: The concept of clustering"
+      - name: "**Webinar:** The concept of clustering"
         type: custom
         description: |
           Main aspects of clustering analysis to infer transmission in MTBC
 
           [Watch Webinar](https://youtu.be/l4cPUECJ7VU) (15 minutes)
 
 
-      - name: "**Webinar**: Webinar: Genetic distance thresholds"
+      - name: "**Webinar**: Genetic distance thresholds"
         type: custom
         description: |
           Clustering as an approximation to infer transmission
@@ -318,7 +340,7 @@
     tutorials:
       - type: custom
         name: "**Meet the experts: Q&A session**"
-        time: "11:30-12:30 Central European timeT"
+        time: "**11:30-12:30** Central European time"
         description: |
           Discussion with the experts! Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
 
@@ -352,7 +374,7 @@
     tutorials:
       - type: custom
         name: "**Meet the experts: Q&A session**"
-        time: "16:30-17:30 Central European Time"
+        time: "**16:30-17:30** Central European Time"
         description: |
           Discussion with the experts! Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
 
@@ -372,7 +394,7 @@
       MTBC sequence data and we’ll provide some examples of how these tools work and how to
       interpret the results.
     tutorials:
-      - name: Icebreaker
+      - name: "**Icebreaker**"
         type: custom
         description: |
            Come say Hi in Slack! Let us know you are joining today and are getting started!
@@ -393,7 +415,7 @@
 
           **Assessment**: Share your thoughts with us [here](https://docs.google.com/document/d/1QRnuHYXWGQnvf8fX5v6EIaynJh6AxkoOktS3VgL0Y8Q/edit)
 
-      - name: "Webinar: Introduction to the MTBseq pipeline"
+      - name: "**Webinar:** Introduction to the MTBseq pipeline"
         type: custom
         description: |
           Introduction to MTBseq pipeline, an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from whole genome sequence data of MTBC
@@ -405,7 +427,7 @@
     tutorials:
       - type: custom
         name: "**Meet the experts: Q&A session**"
-        time: "11:30-12:30 Central European Time"
+        time: "**11:30-12:30** Central European Time"
         description: |
           Discussion with the experts! Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
 
@@ -468,7 +490,7 @@
     tutorials:
       - type: custom
         name: "**Meet the experts: Q&A session**"
-        time: "16:30-17:30 Central European time"
+        time: "**16:30-17:30** Central European time"
         description: |
           Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
 
@@ -482,7 +504,7 @@
     tutorials:
       - type: custom
         name: "**Meet the experts:Q&A session**"
-        time: "10:00-12:30 Central European Time"
+        time: "**10:00-12:30** Central European Time"
         description: |
           Discussion with the experts! Join us on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09).
 
@@ -512,21 +534,18 @@
 
 ## Communication
 
-Chat on Slack channel [#event-mtb-ngs](https://gtnsmrgsbord.slack.com/?redir=%2Farchives%2FC01MNM98X9V%3Fname%3DC01MNM98X9V) (see "Setup" for instructions)
-Scheduled Questions & Answer sessions (Q&A) on [Zoom](https://swisstph.zoom.us/j/88614333103?pwd=OVVjeG04a2lVMXB0THUxMXoxNUNkdz09)
-
-The chat should be used to troubleshoot and to get to know each other.
-In the Q&A you can meet the intructors, discuss and ask questions. To know at what time each Q&A is taking place check the Program tab and be aware that all times are given the Central European Time-CET.
-If you are in Asia you can attend the Q&A sessions in the morning, if you are in America you can attend the sessions in the afternoon, no need to be there all the time.
+A Slack channel will allow participants to communicate in real-time via chat. The channel should be used to troubleshoot and to get to know each other.
+There will be scheduled zoom sessions (Q&A) every day where you can meet the experts, discuss and ask questions (check the program to know the time and be aware of the difference in time zone).
+If you are in Asia you can attend the zoom sessions in the morning, if you are in America you can attend the sessions in the afternoon, no need to be there all the time.
 
 ## Certificates
 
 Requirements for acquiring a certificate:
 - Being registered in the training
-- Join us on chat Slack #event-mtb-ngs! (see "Setup" for instructions)
-- Answer the assessments of days 1, 2 and 3
-- Fill the [Feedback Survey](https://forms.gle/6Xn8WudBvr3NMC3W7)
-- As you finish the **Galaxy** hands-on tutorials share your Galaxy history with us. See [how to do this here](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) and copy the url link in [this table](https://docs.google.com/document/d/1K2k_yzk14VIHjsedfHaUFJnLgq6JTweG2tqxmIKUM2M/edit?usp=sharing)
+- Join us on Slack! (see "Setup" for instructions)
+- Answer the assessments of days 1,2 and 3
+- Fill the [Feedback Survey](https://forms.gle/6Xn8WudBvr3NMC3W7	)
+- As you finish the hands-on tutorials share your Galaxy history with us. See [how to do this here](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) and copy the url link in [this table](https://docs.google.com/document/d/1K2k_yzk14VIHjsedfHaUFJnLgq6JTweG2tqxmIKUM2M/edit?usp=sharing)
 
 ## Start the Course