+
+ {{ topic.title }}
+ {{ topic.summary }}
+ {% if topic.requirements %}
+ Requirements
Before diving into this topic, we recommend you to have a look at:
- {% endif %}
-
-
- Material
-
-
-
- Lesson |
- Hands-on |
- Slides |
-
- {% if topic.type != "admin-dev" %}
- Input dataset |
- Galaxy tour |
- {% endif %}
-
-
- {% for material in topic.material %}
- {% if material.enable != "false" %}
-
- {{ material.title }} |
-
- {% if material.type == "introduction" %}
- |
-
- {% if material.slides == "yes" %}
- :mortar_board:
- {% endif %}
- |
- {% if topic.type != "admin-dev" %}
+ {% endif %}
+
+ Material
+
+
+ Lesson |
+ Hands-on |
+ Slides |
+
+ {% if topic.type != "admin-dev" %}
+ Input dataset |
+ Galaxy tour |
+ {% endif %}
+
+
+ {% for material in topic.material %}
+ {% if material.enable != "false" %}
+
+ {{ material.title }} |
+
+ {% if material.type == "introduction" %}
|
- |
- {% endif %}
-
- {% elsif material.type == "tutorial" %}
-
- {% if material.hands_on == "external" %}
- :link:
- {% elsif material.hands_on == "yes" %}
- :book:
- {% elsif material.hands_on == "github" %}
- :book:
- {% endif %}
- |
-
-
- {% if material.slides == "yes" %}
- :mortar_board:
+ |
+ {% if material.slides == "yes" %}
+
+ {% icon slides %}
+
+ {% endif %}
+ |
+ {% if topic.type != "admin-dev" %}
+ |
+ |
{% endif %}
-
-
- {% if topic.type != "admin-dev" %}
+ {% elsif material.type == "tutorial" %}
- {% if material.zenodo_link != "" %}
- :open_file_folder:
+ {% if material.hands_on == "external" %}
+
+ {% icon tutorial %}
+
+ {% elsif material.hands_on == "yes" %}
+
+ {% icon tutorial %}
+
+ {% elsif material.hands_on == "github" %}
+
+ {% icon tutorial %}
+
{% endif %}
|
- {% if material.galaxy_tour != "" %}
- :eyes:
+ {% if material.slides == "yes" %}
+
+ {% icon slides %}
+
{% endif %}
|
- {% endif %}
- {% endif %}
-
- {% endif %}
- {% endfor %}
-
- {% if topic.docker_image %}
-
- Galaxy instance
+ {% if topic.type != "admin-dev" %}
+
+ {% if material.zenodo_link != "" %}
+
+ {% icon zenodo_link %}
+
+ {% endif %}
+ |
+
+ {% if material.galaxy_tour != "" %}
+
+ {% icon interactive_tour %}
+
+ {% endif %}
+ |
+ {% endif %}
+ {% endif %}
+
+ {% endif %}
+ {% endfor %}
+
+ {% if topic.docker_image %}
+ Galaxy instance
For these tutorials, you can use the dedicated Docker image:
-
-
- docker run -d -p 8080:80 {{ topic.docker_image }}
-
-
+ docker run -d -p 8080:80 {{ topic.docker_image }}
It will launch a flavored Galaxy instance available on http://localhost:8080.
- {% endif %}
+ {% endif %}
- {% if topic.galaxy_instance %}
+ {% if topic.galaxy_instance %}
Galaxy instance
For these tutorials, use Galaxy instance at {{ topic.galaxy_instance }}.
- {% endif %}
+ {% endif %}
-
- Contributors
-
- This material is maintained by:
-
-
+ Contributors
+ This material is maintained by:
+
{% for maintainer in topic.maintainers %}
-
{% if maintainer.github_username != "" %}
@@ -133,41 +134,42 @@
Contributors
{% endif %}
{% endfor %}
-
-
- For any question related to this topic and the content, you can contact them.
-
- The following persons have contributed to this training material:
+
-
- {% for contributor in topic.contributors %}
- -
- {% if contributor.github_username != "" %}
- {{ contributor.name }}
- {% else %}
- {{ contributor.name }}
- {% endif %}
- {% if contributor.email != "" %}
- ({{ contributor.email }})
- {% endif %}
-
- {% endfor %}
-
+
+ For any question related to this topic and the content, you can contact them.
+
- {% if topic.references %}
-
- References
+ The following persons have contributed to this training material:
+
+ {% for contributor in topic.contributors %}
+ -
+ {% if contributor.github_username != "" %}
+ {{ contributor.name }}
+ {% else %}
+ {{ contributor.name }}
+ {% endif %}
+ {% if contributor.email != "" %}
+ ({{ contributor.email }})
+ {% endif %}
+
+ {% endfor %}
+
+ {% if topic.references %}
+ References
+
{% for reference in topic.references %}
-
- {{ reference.authors }}: {{ reference.title }}
-
- {% if reference.summary != "" %}
-
{{ reference.summary }}
- {% endif %}
-
+ -
+ {{ reference.authors }}: {{ reference.title }}
+ {% if reference.summary != "" %}
+
{{ reference.summary }}
+ {% endif %}
+
{% endfor %}
- {% endif %}
-
+
+ {% endif %}
+
+
-{% include main_footer.html %}
+{% include default-footer.html %}
diff --git a/templates/metadata.yaml b/templates/metadata.yaml
index 50d070a80c3e5c..3a24fcdf51fbc1 100644
--- a/templates/metadata.yaml
+++ b/templates/metadata.yaml
@@ -7,67 +7,6 @@ requirements:
title: "Galaxy introduction"
type: "internal"
link: "/Introduction/"
--
- title: "tutorial1"
- type: "tutorial"
- name: "tutorial1"
- zenodo_link: ""
- galaxy_tour: ""
- hands_on: "yes"
- slides: "no"
- questions:
- - ""
- - ""
- objectives:
- - ""
- - ""
- - ""
- time_estimation: "1d/3h/6h"
- key_points:
- - ""
- - ""
- - ""
- - "..."
- contributors:
- -
- name: "Contributor"
- github_username: "contributor"
- email: "contributor@galaxy.org"
- -
- name: "Contributor"
- github_username: "contributor"
- email: "contributor@galaxy.org"
--
- title: "tutorial2"
- type: "tutorial"
- name: "tutorial2"
- zenodo_link: ""
- galaxy_tour: ""
- hands_on: "yes"
- slides: "no"
- questions:
- - ""
- - ""
- objectives:
- - ""
- - ""
- - ""
- time_estimation: "1d/3h/6h"
- key_points:
- - ""
- - ""
- - ""
- - "..."
- contributors:
- -
- name: "Contributor"
- github_username: "contributor"
- email: "contributor@galaxy.org"
- -
- name: "Contributor"
- github_username: "contributor"
- email: "contributor@galaxy.org"
-
maintainers:
-
name: "Maintainer"
@@ -78,3 +17,12 @@ maintainers:
github_username: "maintainer"
email: "maintainer@galaxy.org"
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/admin/metadata.yaml b/topics/admin/metadata.yaml
index bf1890e8f111cf..d36bf7eab151c8 100644
--- a/topics/admin/metadata.yaml
+++ b/topics/admin/metadata.yaml
@@ -3,24 +3,12 @@ type: "admin-dev"
title: "Galaxy Server administration"
summary: "Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task"
docker_image: ""
+
material:
-
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Valentin Marcon"
- github_username: "ValentinMarcon"
- email: ""
-
title: "Move from dev instance to production instance"
type: "tutorial"
@@ -28,7 +16,6 @@ material:
zenodo_link: ""
galaxy_tour: ""
hands_on: "github"
- enable: false
slides: "no"
questions:
- ""
@@ -43,15 +30,6 @@ material:
- ""
- ""
- "..."
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Galaxy Database schema"
type: "tutorial"
@@ -72,23 +50,6 @@ material:
time_estimation: "2h"
key_points:
- "Be careful, when you interact with the Galaxy database. And make sure you always have a backup!"
- contributors:
- -
- name: "Hans-Rudolf Hotz"
- github_username: "hrhotz"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Docker and Galaxy"
type: "tutorial"
@@ -111,38 +72,12 @@ material:
- "Use Docker"
- "Integrate your tools into Galaxy"
- "Use Galaxy inside Docker to have a flavoured Galaxy instance"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Advanced customisation of a Galaxy instance"
type: "tutorial"
name: "advanced-galaxy-customisation"
slides: "yes"
- contributors:
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- -
- name: "Eric Rasche"
- github_username: "erasche"
- -
- name: "Martin Čech"
- github_username: "martenson"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+
maintainers:
-
@@ -153,13 +88,31 @@ maintainers:
name: "Martin Čech"
github_username: "martenson"
email: "marten@bx.psu.edu"
+
+contributors:
-
- name: "Bérénice Batut"
- github_username: "bebatut"
+ name: "Dave Clements"
+ github_username: ""
+ email: ""
+-
+ name: "Hans-Rudolf Hotz"
+ github_username: ""
+ email: ""
+-
+ name: "Olivier Inizan"
+ github_username: ""
email: ""
-
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
+ name: "Valentin Marcon"
+ github_username: ""
+ email: ""
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: ""
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
email: ""
references:
diff --git a/topics/admin/tutorials/advanced-galaxy-customisation/metadata.yaml b/topics/admin/tutorials/advanced-galaxy-customisation/metadata.yaml
new file mode 100644
index 00000000000000..26b5f3cb56b4bb
--- /dev/null
+++ b/topics/admin/tutorials/advanced-galaxy-customisation/metadata.yaml
@@ -0,0 +1,25 @@
+title: "Advanced customisation of a Galaxy instance"
+type: "tutorial"
+name: "advanced-galaxy-customisation"
+slides: "yes"
+maintainers:
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+-
+ name: "Eric Rasche"
+ github_username: "erasche"
+-
+ name: "Martin Čech"
+ github_username: "martenson"
+
+contributors:
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+-
+ name: "Eric Rasche"
+ github_username: "erasche"
+-
+ name: "Martin Čech"
+ github_username: "martenson"
diff --git a/topics/admin/tutorials/database-schema/metadata.yaml b/topics/admin/tutorials/database-schema/metadata.yaml
new file mode 100644
index 00000000000000..877cfea8b73b03
--- /dev/null
+++ b/topics/admin/tutorials/database-schema/metadata.yaml
@@ -0,0 +1,39 @@
+title: "Galaxy Database schema"
+type: "tutorial"
+name: "database-schema"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "github"
+slides: "no"
+questions:
+- ""
+- ""
+objectives:
+- ""
+- ""
+- ""
+time_estimation: "1d/3h/6h"
+key_points:
+- ""
+- ""
+- ""
+- "..."
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/admin/tutorials/dev-to-production/metadata.yaml b/topics/admin/tutorials/dev-to-production/metadata.yaml
new file mode 100644
index 00000000000000..8f6c52bf5c2ea3
--- /dev/null
+++ b/topics/admin/tutorials/dev-to-production/metadata.yaml
@@ -0,0 +1,39 @@
+title: "Move from dev instance to production instance"
+type: "tutorial"
+name: "dev-to-production"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "github"
+slides: "no"
+questions:
+- ""
+- ""
+objectives:
+- ""
+- ""
+- ""
+time_estimation: "1d/3h/6h"
+key_points:
+- ""
+- ""
+- ""
+- "..."
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/admin/tutorials/galaxy-docker/metadata.yaml b/topics/admin/tutorials/galaxy-docker/metadata.yaml
new file mode 100644
index 00000000000000..b8dd12e994d145
--- /dev/null
+++ b/topics/admin/tutorials/galaxy-docker/metadata.yaml
@@ -0,0 +1,40 @@
+title: "Docker and Galaxy"
+type: "tutorial"
+name: "galaxy-docker"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+- "Why Docker? What is it?"
+- "How to use Docker?"
+- "How to integrate Galaxy in Docker to facilitate its deployment?"
+objectives:
+- "Docker basics"
+- "Galaxy Docker image (usage)"
+- "Galaxy Docker (internals)"
+- "Galaxy flavours"
+time_estimation: "1d/3h/6h"
+key_points:
+- "Use Docker"
+- "Integrate your tools into Galaxy"
+- "Use Galaxy inside Docker to have a flavoured Galaxy instance"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/assembly/metadata.yaml b/topics/assembly/metadata.yaml
index 74394c331ce6ec..c4c91137331c11 100644
--- a/topics/assembly/metadata.yaml
+++ b/topics/assembly/metadata.yaml
@@ -1,4 +1,4 @@
-name: "assembly"
+name: "assembly"
type: "use"
title: "Assembly"
summary: "DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone."
@@ -20,11 +20,6 @@ material:
# title: "Introduction"
# type: "introduction"
# slides: "no"
-# contributors:
-# -
-# name: "Saskia Hiltemann"
-# github_username: "shiltemann"
-# email: ""
-
title: "Introduction to Genome Assembly"
@@ -44,19 +39,6 @@ material:
- "We assembled some Illumina fastq reads into contigs using a short read assembler called Velvet"
- "We showed what effect one of the key assembly parameters, the k-mer size, has on the assembly"
- "It looks as though there are some exploitable patterns in the metric data vs the k-mer size."
- contributors:
- -
- name: "Simon Gladman"
- github_username: "slugger70"
- email: "simon.gladman@unimelb.edu.au"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "De Bruijn Graph Assembly"
type: "tutorial"
@@ -78,33 +60,18 @@ material:
- "We learned about the strategies that assemblers use to make reference genomes"
- "We performed a number of assemblies with Velvet and SPAdes."
- "You should use SPAdes or another more modern assembler than Velvet for actual assemblies now."
- contributors:
- -
- name: "Simon Gladman"
- github_username: "slugger70"
- email: "simon.gladman@unimelb.edu.au"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
maintainers:
-
name: "Simon Gladman"
github_username: "slugger70"
email: "simon.gladman@unimelb.edu.au"
+
+contributors:
-
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
--
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
+ name: "Simon Gladman"
+ github_username: "slugger70"
+ email: "simon.gladman@unimelb.edu.au"
references:
-
diff --git a/topics/assembly/tutorials/debruijn-graph-assembly/metadata.yaml b/topics/assembly/tutorials/debruijn-graph-assembly/metadata.yaml
new file mode 100644
index 00000000000000..358f7516fc4c63
--- /dev/null
+++ b/topics/assembly/tutorials/debruijn-graph-assembly/metadata.yaml
@@ -0,0 +1,31 @@
+title: "De Bruijn Graph Assembly"
+type: "tutorial"
+name: "debruijn-graph-assembly"
+zenodo_link: "https://doi.org/10.5281/zenodo.582600"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "yes"
+questions:
+- "What are the factors that affect genome assembly?"
+- "How does Genome assembly work?"
+objectives:
+- "Perform an optimised Velvet assembly with theh Velvet Optimiser"
+- "Compare this assembly with those we did in the basic tutorial"
+- "Perform an assembly using the SPAdes assembler."
+time_estimation: "1d/3h/6h"
+key_points:
+- "We learned about how the choice of k-mer size will affect assembly outcomes"
+- "We learned about the strategies that assemblers use to make reference genomes"
+- "We performed a number of assemblies with Velvet and SPAdes."
+- "You should use SPAdes or another more modern assembler than Velvet for actual assemblies now."
+maintainers:
+-
+ name: "Simon Gladman"
+ github_username: "slugger70"
+ email: "simon.gladman@unimelb.edu.au"
+
+contributors:
+-
+ name: "Simon Gladman"
+ github_username: "slugger70"
+ email: "simon.gladman@unimelb.edu.au"
diff --git a/topics/assembly/tutorials/general-introduction/metadata.yaml b/topics/assembly/tutorials/general-introduction/metadata.yaml
new file mode 100644
index 00000000000000..f20f54b4dc2396
--- /dev/null
+++ b/topics/assembly/tutorials/general-introduction/metadata.yaml
@@ -0,0 +1,28 @@
+title: "Introduction to Genome Assembly"
+type: "tutorial"
+name: "general-introduction"
+zenodo_link: "https://doi.org/10.5281/zenodo.582600"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "How do we perform a very basic genome assembly from short read data?"
+objectives:
+- "assemble some paired end reads using Velvet"
+- "examine the output of the assembly."
+time_estimation: "30 minutes"
+key_points:
+- "We assembled some Illumina fastq reads into contigs using a short read assembler called Velvet"
+- "We showed what effect one of the key assembly parameters, the k-mer size, has on the assembly"
+- "It looks as though there are some exploitable patterns in the metric data vs the k-mer size."
+maintainers:
+-
+ name: "Simon Gladman"
+ github_username: "slugger70"
+ email: "simon.gladman@unimelb.edu.au"
+
+contributors:
+-
+ name: "Simon Gladman"
+ github_username: "slugger70"
+ email: "simon.gladman@unimelb.edu.au"
diff --git a/topics/chip-seq/metadata.yaml b/topics/chip-seq/metadata.yaml
index 46eee7c55f0297..50c210329a0a0a 100644
--- a/topics/chip-seq/metadata.yaml
+++ b/topics/chip-seq/metadata.yaml
@@ -1,4 +1,4 @@
-name: "chip-seq"
+name: "chip-seq"
type: "use"
title: "ChIP-Seq data analysis"
summary: "ChIP-sequencing is a method used to analyze protein interactions with DNA."
@@ -24,15 +24,6 @@ material:
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)"
type: "tutorial"
@@ -65,31 +56,6 @@ material:
- Sophisticated analysis of ChIP-seq data is possible using tools hosted by Galaxy
- Genomic dataset analyses require multiple methods of quality assessment to ensure that the data are appropriate for answering the biology question of interest.
- By using the sharable and transparent Galaxy platform, data analyses can easily be shared and reproduced
- contributors:
- -
- name: "Mallory Freeberg"
- github_username: "malloryfreeberg"
- email: ""
- -
- name: "Mo Heydarian"
- github_username: "MoHeydarian"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Vivek Bhardwaj"
- github_username: "vivekbhr"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email: ""
-
title: "ChIP-seq Galaxy Workshop"
type: "tutorial"
@@ -112,19 +78,6 @@ material:
- ""
- ""
- "..."
- contributors:
- -
- name: "Friederike Dündar"
- github_username: "friedue"
- email: ""
- -
- name: "Anika Exleben"
- github_username: "erxleben"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
maintainers:
-
@@ -135,22 +88,24 @@ maintainers:
name: "Mo Heydarian"
github_username: "MoHeydarian"
email: ""
+
+contributors:
-
- name: "Friederike Dündar"
- github_username: "friedue"
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
email: ""
-
- name: "Anika Exleben"
- github_username: "erxleben"
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
email: ""
-
- name: "Bérénice Batut"
- github_username: "bebatut"
+ name: "Friederike Dündar"
+ github_username: "friedue"
email: ""
-
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
references:
-
diff --git a/topics/chip-seq/tutorials/chip-seq/metadata.yaml b/topics/chip-seq/tutorials/chip-seq/metadata.yaml
new file mode 100644
index 00000000000000..94c2b283ee8c47
--- /dev/null
+++ b/topics/chip-seq/tutorials/chip-seq/metadata.yaml
@@ -0,0 +1,44 @@
+title: "ChIP-seq Galaxy Workshop"
+type: "tutorial"
+name: "chip-seq"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "github"
+slides: "no"
+
+questions:
+- ""
+- ""
+
+objectives:
+- ""
+- ""
+- ""
+
+time_estimation: ""
+
+key_points:
+- ""
+- ""
+- ""
+- "..."
+
+maintainers:
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: ""
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: ""
+
+contributors:
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: ""
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: ""
diff --git a/topics/chip-seq/tutorials/tal1-binding-site-identification/metadata.yaml b/topics/chip-seq/tutorials/tal1-binding-site-identification/metadata.yaml
new file mode 100644
index 00000000000000..a529a27db85c7e
--- /dev/null
+++ b/topics/chip-seq/tutorials/tal1-binding-site-identification/metadata.yaml
@@ -0,0 +1,56 @@
+title: "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)"
+type: "tutorial"
+name: "tal1-binding-site-identification"
+zenodo_link: "https://doi.org/10.5281/zenodo.197100"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+edam_ontology: "topic_3169"
+
+questions:
+- How is raw ChIP-seq data processed and analyzed?
+- What are the binding sites of Tal1?
+- Which genes are regulated by Tal1?
+
+objectives:
+- Inspect read quality with FastQC
+- Perform read trimming with Trimmomatic
+- Align trimmed reads with BWA
+- Assess quality and reproducibility of experiments
+- Identify Tal1 binding sites with MACS2
+- Determine unique/common Tal1 binding sites from G1E and Megakaryocytes
+- Identify unique/common Tal1 peaks occupying gene promoters
+- Visually inspect Tal1 peaks with Trackster
+
+requirements:
+-
+ title: "Trackster"
+ type: "external"
+ link: "https://wiki.galaxyproject.org/Learn/Visualization"
+
+time_estimation: "3h"
+
+key_points:
+- Sophisticated analysis of ChIP-seq data is possible using tools hosted by Galaxy
+- Genomic dataset analyses require multiple methods of quality assessment to ensure that the data are appropriate for answering the biology question of interest.
+- By using the sharable and transparent Galaxy platform, data analyses can easily be shared and reproduced
+
+maintainers:
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: ""
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: ""
+
+contributors:
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: ""
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: ""
diff --git a/topics/dev/metadata.yaml b/topics/dev/metadata.yaml
index 6c892f6a42149a..623efc32970464 100644
--- a/topics/dev/metadata.yaml
+++ b/topics/dev/metadata.yaml
@@ -3,29 +3,13 @@ type: "admin-dev"
title: "Development in Galaxy"
summary: "Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ..."
docker_image: ""
+
requirements:
material:
-
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Loraine Guéguen"
- github_username: "loraine-gueguen"
- email: ""
- -
- name: "Olivia Doppelt-Azeroual"
- github_username: "odoppelt"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Contributing with GitHub"
type: "tutorial"
@@ -36,24 +20,17 @@ material:
slides: "yes"
questions:
- ""
+ - ""
objectives:
- ""
+ - ""
+ - ""
time_estimation: "1d/3h/6h"
key_points:
- ""
- contributors:
- -
- name: "Cyril Monjeaud"
- github_username: "cmonjeau"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ - ""
+ - ""
+ - "..."
-
title: "Tool development and integration into Galaxy"
type: "tutorial"
@@ -81,35 +58,6 @@ material:
- "Use GitHub"
- "Use Travis"
- "No more excuse to develop crappy Galaxy tools"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Anthony Bretaudeau"
- github_username: "abretaud"
- email: ""
- -
- name: "John Chilton"
- github_username: "jmchilton"
- email: ""
- -
- name: "Nicola Soranzo"
- github_username: "nsoranzo"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Gildas Le Corguillé"
- github_username: "lecorguille"
- email: ""
-
title: "Tool Shed: sharing Galaxy tools"
type: "tutorial"
@@ -131,27 +79,6 @@ material:
key_points:
- "Use Planemo"
- "Contribute to the Main Tool Shed"
- contributors:
- -
- name: "Anthony Bretaudeau"
- github_username: "abretaud"
- email: ""
- -
- name: "Loraine Guéguen"
- github_username: "loraine-gueguen"
- email: ""
- -
- name: "Stéphanie Legras"
- github_username: "slegras"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "Galaxy Interactive Tours"
type: "tutorial"
@@ -172,19 +99,6 @@ material:
- "An Interactive Tour is easy to create: just a yaml file to fill"
- "Use the Developper Tools of find the JQuery Selector"
- "Help yourself by using the available web plugins and record an interactive tour"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Galaxy Interactive Environments"
type: "tutorial"
@@ -208,15 +122,6 @@ material:
key_points:
- "Interactive Environments offer access to third-party applications within Galaxy"
- "Interactive Environments run in a docker images for sandboxing and easy dependency management"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
-
title: "Visualizations: charts plugins"
type: "tutorial"
@@ -231,23 +136,6 @@ material:
key_points:
- "Charts is a pluggable extension system for JS-only visualisations"
- "With only 3 files we can integrate any JS-only visualizations into Galaxy"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Youri Hoogstrate"
- github_username: "yhoogstrate"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
-
title: "Galaxy Webhooks"
type: "tutorial"
@@ -268,27 +156,6 @@ material:
- "A Galaxy Webhook provides an easy way to customize the Galaxy UI with plugins"
- "Right now there are 4 entry points: tool, workflow, masthead, history-menu"
- "With a minimal amount of code you can extend Galaxy's user-interace."
- contributors:
- -
- name: "Clemens Blank"
- github_username: "blankclemens"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Martin Čech"
- github_username: "martenson"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
-
title: "Visualizations: generic plugins"
@@ -314,19 +181,6 @@ material:
- "Interactivity is what makes visualizations different from static tools"
- "Requires understanding of both the Galaxy ecosystem as well as HTML5/JS"
- "Performance is more important than for static Galaxy tools"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Youri Hoogstrate"
- github_username: "yhoogstrate"
- email: ""
-
title: "BioBlend module, a Python library to use Galaxy API"
type: "tutorial"
@@ -353,23 +207,6 @@ material:
- "Understand the job launching in Galaxy with BioBlend"
- "Understand the workflow launching in Galaxy with BioBlend"
- "Be able to adapt this knowledge to personal workflows"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
- -
- name: "Olivia Doppelt-Azeroual"
- github_username: "odoppelt"
- email: ""
- -
- name: "Fabien Mareuil"
- github_username: "fmareuil"
- email: ""
-
title: "Tool Dependencies and Conda"
type: "tutorial"
@@ -403,27 +240,6 @@ material:
- "Conda recipe skeletons, `conda build`, and with `planemo conda_install --conda_use_local` allow easy development of new Conda recipes at the same time as Galaxy tools that wrap them."
- "Bioconda is a Galaxy best practice Conda channel for recipe publication."
- "Bioconda has easy to follow contribution guidelines and is very welcoming to new contributors."
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Nicola Soranzo"
- github_username: "nsoranzo"
- email: ""
- -
- name: "John Chilton"
- github_username: "jmchilton"
- email: "jmchilton@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Hervé Ménager"
- github_username: "hmenager"
- email: ""
-
title: "Tool Dependencies and Containers"
type: "tutorial"
@@ -452,19 +268,6 @@ material:
- "You can explicitly define a container for your tool - but it is easier and more reproducible to let Galaxy find or build one using your tool's best practice requirements."
- "The Galaxy community will infrastructure to automatically build and/or publish containers for your tool as long as it defines best practice Conda dependencies."
- "Planemo makes it easy to test your tool inside of containers."
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "John Chilton"
- github_username: "jmchilton"
- email: "jmchilton@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
-
title: "Galaxy Code Architecture"
type: "tutorial"
@@ -481,25 +284,13 @@ material:
- "Understand the various top-level files and modules in Galaxy."
- "Understand how dependencies work in Galaxy's frontend and backend."
time_estimation: "2.5h"
- requirements:
+ requirements: []
key_points:
- "Galaxy runs out of the box and fetches all needed dependencies."
- "Running Galaxy in production requires work configuration."
- "The architecture is designed to be pluggable and extendable."
- "Learn more about different Galaxy aspects in our [development section](/topics/dev/)."
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "John Chilton"
- github_username: "jmchilton"
- email: "jmchilton@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
+
-
title: "Data source integration"
type: "tutorial"
@@ -530,13 +321,51 @@ maintainers:
name: "Bérénice Batut"
github_username: "bebatut"
email: ""
+
+contributors:
+-
+ name: "Anthony Bretaudeau"
+ github_username: "abretaud"
+ email: ""
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: ""
+-
+ name: "John Chilton"
+ github_username: "jmchilton"
+ email: "jmchilton@gmail.com"
+-
+ name: "Gildas Le Corguillé"
+ github_username: "lecorguille"
+ email: ""
+-
+ name: "Loraine Brillet-Guéguen"
+ github_username: "loraine-gueguen"
+ email: ""
+-
+ name: "Stéphanie Le Gras"
+ github_username: "slegras"
+ email: ""
-
name: "Saskia Hiltemann"
github_username: "shiltemann"
email: ""
-
- name: "Björn Grüning"
- github_username: "bgruening"
+ name: "Youri Hoogstrate"
+ github_username: "yhoogstrate"
+ email: ""
+-
+ name: "Olivia Doppelt-Azeroual"
+ github_username: "odoppelt"
+ email: ""
+-
+ name: "Fabien Mareuil"
+ github_username: "fmareuil"
+ email: ""
+-
+ name: "Nicola Soranzo"
+ github_username: "nsoranzo"
email: ""
-references:
+references:
diff --git a/topics/dev/tutorials/bioblend-api/metadata.yaml b/topics/dev/tutorials/bioblend-api/metadata.yaml
new file mode 100644
index 00000000000000..771d4b8d38aa66
--- /dev/null
+++ b/topics/dev/tutorials/bioblend-api/metadata.yaml
@@ -0,0 +1,44 @@
+title: "BioBlend module, a Python library to use Galaxy API"
+type: "tutorial"
+name: "bioblend-api"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "yes"
+questions:
+- "What is the use of BioBlend?"
+- "How to use Galaxy through command line?"
+objectives:
+- "Get familiar with BioBlend using IPython"
+- "Launch a Galaxy job / Visualize your actions with Galaxy"
+- "Launch a Galaxy workflow / Visualize your actions with Galaxy"
+requirements:
+-
+ title: "IPython"
+ type: "external"
+ link: "https://ipython.org"
+time_estimation: "2h"
+key_points:
+- "Play with IPython"
+- "Understand the job launching in Galaxy with BioBlend"
+- "Understand the workflow launching in Galaxy with BioBlend"
+- "Be able to adapt this knowledge to personal workflows"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/dev/tutorials/data-source-integration/metadata.yaml b/topics/dev/tutorials/data-source-integration/metadata.yaml
new file mode 100644
index 00000000000000..c81e4ff1f113d8
--- /dev/null
+++ b/topics/dev/tutorials/data-source-integration/metadata.yaml
@@ -0,0 +1,37 @@
+title: "Tutorial name"
+type: "tutorial"
+name: "tutorial1"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "First question addressed during the tutorial"
+- "Second question addressed during the tutorial"
+objectives:
+- "First learning objectives of the tutorial"
+- "Second learning objectives of the tutorial"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/dev/tutorials/github-contribution/metadata.yaml b/topics/dev/tutorials/github-contribution/metadata.yaml
new file mode 100644
index 00000000000000..b29721293762a4
--- /dev/null
+++ b/topics/dev/tutorials/github-contribution/metadata.yaml
@@ -0,0 +1,39 @@
+title: "Contributing with GitHub"
+type: "tutorial"
+name: "github-contribution"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+- ""
+- ""
+objectives:
+- ""
+- ""
+- ""
+time_estimation: "1d/3h/6h"
+key_points:
+- ""
+- ""
+- ""
+- "..."
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/dev/tutorials/interactive-environments/metadata.yaml b/topics/dev/tutorials/interactive-environments/metadata.yaml
new file mode 100644
index 00000000000000..11dda44423f207
--- /dev/null
+++ b/topics/dev/tutorials/interactive-environments/metadata.yaml
@@ -0,0 +1,41 @@
+title: "Galaxy Interactive Environments"
+type: "tutorial"
+name: "interactive-environments"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+- "What are Galaxy Interactive Environments (GIEs)?"
+- "How to enable GIEs in Galaxy?"
+- "How to develop your own GIE?"
+objectives:
+- "Implement a Hello-World Galaxy Interactive Environment"
+requirements:
+-
+ title: "Docker basics"
+ type: "external"
+ link: ""
+time_estimation: "1.5h"
+key_points:
+- "Interactive Environments offer acces to third-party applications within Galaxy"
+- "Interactive Environments run in a docker images for sandboxing and easy dependency management"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/dev/tutorials/interactive-tours/metadata.yaml b/topics/dev/tutorials/interactive-tours/metadata.yaml
new file mode 100644
index 00000000000000..8148b21e5ad935
--- /dev/null
+++ b/topics/dev/tutorials/interactive-tours/metadata.yaml
@@ -0,0 +1,38 @@
+title: "Galaxy Interactive Tours"
+type: "tutorial"
+name: "interactive-tours"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+- "What is a Galaxy Interactive Tour?"
+- "How to create a Galaxy Interactive Tour?"
+objectives:
+- "Discover what is a Galaxy Interactive Tour"
+- "Be able to create a Galaxy Interactive Tour"
+- "Be able to add a Galaxy Interactive Tour in a Galaxy instance"
+time_estimation: "3h"
+key_points:
+- "An Interactive Tour is easy to create: just a YAML file to fill"
+- "Use the Developer Tools to find the JQuery Selector"
+- "Help yourself by using the available web plugins and record an interactive tour"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/dev/tutorials/tool-integration/metadata.yaml b/topics/dev/tutorials/tool-integration/metadata.yaml
new file mode 100644
index 00000000000000..6a67fb4ed6c1da
--- /dev/null
+++ b/topics/dev/tutorials/tool-integration/metadata.yaml
@@ -0,0 +1,45 @@
+title: "Tool development and integration into Galaxy"
+type: "tutorial"
+name: "tool-integration"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "external"
+hands_on_url: "http://planemo.readthedocs.io/en/latest/writing_standalone.html"
+slides: "yes"
+questions:
+- "What is a tool for Galaxy?"
+- "How to build a tool/wrapper with the good practices?"
+- "How to deal with the tool environment?"
+objectives:
+- "Discover what is a wrapper and its structure"
+- "Use the Planemo utilities to develop a good wrapper"
+- "Deal with tool dependencies"
+- "Write functional tests"
+- "Make a tool ready for publishing on a ToolShed"
+time_estimation: "6h"
+key_points:
+- "Galaxy Tool Syntax"
+- "Use Planemo"
+- "Use Conda"
+- "Use GitHub"
+- "Use Travis"
+- "No more excuses to develop crappy Galaxy tools"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/dev/tutorials/toolshed/metadata.yaml b/topics/dev/tutorials/toolshed/metadata.yaml
new file mode 100644
index 00000000000000..64671e95d29115
--- /dev/null
+++ b/topics/dev/tutorials/toolshed/metadata.yaml
@@ -0,0 +1,39 @@
+title: "Tool Shed: sharing Galaxy tools"
+type: "tutorial"
+name: "toolshed"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "yes"
+questions:
+- "What is a Tool Shed?"
+- "How to install tools and workflows from a Tool Shed into a Galaxy instance?"
+- "What are the Tool Shed repository types?"
+- "How to publish with Planemo?"
+objectives:
+- "Discover what is a Tool Shed"
+- "Be able to install tools and workflows from a Tool Shed into a Galaxy instance"
+- "Be able to publish tools with Planemo"
+time_estimation: "3h"
+key_points:
+- "Use Planemo"
+- "Contribute to the Main Tool Shed"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/dev/tutorials/visualization-charts/metadata.yaml b/topics/dev/tutorials/visualization-charts/metadata.yaml
new file mode 100644
index 00000000000000..ee5911a95dab33
--- /dev/null
+++ b/topics/dev/tutorials/visualization-charts/metadata.yaml
@@ -0,0 +1,35 @@
+title: "Visualizations: charts plugins"
+type: "tutorial"
+name: "visualization-charts"
+hands_on: "yes"
+slides: "yes"
+
+questions:
+- "How can I make a custom plugin for Charts?"
+
+objectives:
+- "Learn how to add custom javascript plugins to the Galaxy Charts framework"
+
+time_estimation: "1h"
+
+key_points:
+- "Charts is a pluggable extension system for JS-only visualisations"
+- "With only 3 files we can integrate any JS-only visualizations into Galaxy"
+
+requirements:
+
+maintainers:
+-
+ name: "Aysam Guerler"
+ github_username: "guerler"
+ email: "aysam.guerler@gmail.com"
+
+contributors:
+-
+ name: "Aysam Guerler"
+ github_username: "guerler"
+ email: "aysam.guerler@gmail.com"
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
diff --git a/topics/dev/tutorials/visualization-generic/metadata.yaml b/topics/dev/tutorials/visualization-generic/metadata.yaml
new file mode 100644
index 00000000000000..73300a8dbb35a0
--- /dev/null
+++ b/topics/dev/tutorials/visualization-generic/metadata.yaml
@@ -0,0 +1,42 @@
+title: "Visualizations: generic plugins"
+type: "tutorial"
+name: "visualization-generic"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "yes"
+questions:
+- "How can visualization plugins benefit science?"
+objectives:
+- "Implement a first Galaxy visualization"
+- "Understand the client side vs. server side principle"
+requirements:
+-
+ title: "Javascript knowledge"
+ type: "external"
+ link: ""
+time_estimation: "1.5h"
+key_points:
+- "Visualizations require a different way of thinking: server and client side; downloading files rather than system level access"
+- "Interactivity is what makes visualizations different from static tools"
+- "Requires understanding of both the Galaxy ecosystem as well as HTML5/JS"
+- "Performance is more important than for static Galaxy tools"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/dev/tutorials/webhooks/metadata.yaml b/topics/dev/tutorials/webhooks/metadata.yaml
new file mode 100644
index 00000000000000..55582812f5234f
--- /dev/null
+++ b/topics/dev/tutorials/webhooks/metadata.yaml
@@ -0,0 +1,33 @@
+title: "Galaxy webhooks"
+type: "tutorial"
+name: "webhooks"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+- "What are Galaxy webhooks?"
+- "How to create them?"
+objectives:
+- "Understand basics of what Galaxy webhooks are"
+- "Be able to create a simple webhook"
+- "Be able to configure and activate webhooks in Galaxy"
+time_estimation: "1h"
+key_points:
+- "A Galaxy webhook provides a way to customize the Galaxy interface."
+- "Webhooks have to be attached to a pre-defined entry points."
+- "They are more simple to write than modifying Galaxy codebase."
+maintainers:
+-
+ name: "Martin Čech"
+ github_username: "martenson"
+ email: "marten@bx.psu.edu"
+
+contributors:
+-
+ name: "Clemens Blank"
+ github_username: "blankclemens"
+-
+ name: "Martin Čech"
+ github_username: "martenson"
+ email: "marten@bx.psu.edu"
diff --git a/topics/epigenetics/metadata.yaml b/topics/epigenetics/metadata.yaml
index a14e68b43f6db1..4eb93f67575dd2 100644
--- a/topics/epigenetics/metadata.yaml
+++ b/topics/epigenetics/metadata.yaml
@@ -1,4 +1,4 @@
-name: "epigenetics"
+name: "epigenetics"
type: "use"
title: "Epigenetics"
summary: "DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements."
@@ -24,23 +24,6 @@ material:
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email:
- -
- name: "Yvan Le Bras"
- github_username: "yvanlebras"
- email:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email:
-
title: "DNA Methylation data analysis"
type: "tutorial"
@@ -62,29 +45,14 @@ material:
- "The output of a methylation NGS is having a different distribution of the four bases. This is caused by the bisulfite treatment of the DNA."
- "If there is a different level of methylation in the loci of a gene this can be a hint that something is wrong."
- "To get useful results you need -- data, data and data!"
- contributors:
- -
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email:
- -
- name: "Devon Ryan"
- github_username: "dpryan79"
- email:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
maintainers:
-
name: "Bérénice Batut"
github_username: "bebatut"
email: "berenice.batut@gmail.com"
+
+contributors:
-
name: "Joachim Wolff"
github_username: "joachimwolff"
diff --git a/topics/epigenetics/tutorials/methylation-seq/metadata.yaml b/topics/epigenetics/tutorials/methylation-seq/metadata.yaml
new file mode 100644
index 00000000000000..ef7e38d500ffe4
--- /dev/null
+++ b/topics/epigenetics/tutorials/methylation-seq/metadata.yaml
@@ -0,0 +1,44 @@
+title: "DNA Methylation data analysis"
+type: "tutorial"
+name: "methylation-seq"
+zenodo_link: "https://zenodo.org/record/557099"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+edam_ontology: "topic_3173"
+
+questions:
+- "What is methylation and why it cannot be recognised by a normal NGS procedure?"
+- "Can a different methylation influence the expression of a gene? How?"
+- "Which tools you can use to analyse methylation data?"
+
+objectives:
+- "Learn how to analyse methylation data"
+- "Get a first intuition what are common pitfalls."
+
+time_estimation: "3h"
+
+key_points:
+- "The output of a methylation NGS is having a different distribution of the four bases. This is caused by the bisulfite treatment of the DNA."
+- "If there is a different level of methylation in the loci of a gene this can be a hint that something is wrong."
+- "To get useful results you need -- data, data and data!"
+
+maintainers:
+-
+ name: "Joachim Wolff"
+ github_username: "joachimwolff"
+ email:
+-
+ name: "Devon Ryan"
+ github_username: "dpryan79"
+ email:
+
+contributors:
+-
+ name: "Joachim Wolff"
+ github_username: "joachimwolff"
+ email:
+-
+ name: "Devon Ryan"
+ github_username: "dpryan79"
+ email:
diff --git a/topics/introduction/metadata.yaml b/topics/introduction/metadata.yaml
index 0acff34242388e..2747a9743cdb28 100644
--- a/topics/introduction/metadata.yaml
+++ b/topics/introduction/metadata.yaml
@@ -11,15 +11,6 @@ material:
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Galaxy 101"
type: "tutorial"
@@ -30,7 +21,7 @@ material:
slides: "no"
questions:
- "Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?"
-objectives:
+ objectives:
- "Familiarize yourself with the basics of Galaxy"
- "Learn how to obtain data from external sources"
- "Learn how to run tools"
@@ -44,35 +35,6 @@ objectives:
- "Workflows enable you to repeat your analysis on different data"
- "Galaxy can connect to external sources for data import and visualization purposes"
- "Galaxy provides ways to share your results and methods with others"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: "zazkia@gmail.com"
- -
- name: "Nicola Soranzo"
- github_username: "nsoranzo"
- email: ""
- -
- name: "Clemens Blank"
- github_username: "blankclemens"
- email: "blankclemens@gmail.com"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Anton Nekrutenko"
- github_username: "nekrut"
- email: "anton@nekrut.org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "From peaks to genes"
type: "tutorial"
@@ -98,15 +60,6 @@ objectives:
- "Workflows enable you to repeat your analysis on different data"
- "Galaxy can connect to external sources for data import and visualization purposes"
- "Galaxy provides ways to share your results and methods with others"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Multisample Analysis"
type: "tutorial"
@@ -126,19 +79,6 @@ objectives:
- "First take home message"
- "Second take home message"
- "Third take home message"
- contributors:
- -
- name: "Anton Nekrutenko"
- github_username: "nekrut"
- email: "anton@nekrut.org"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Options for using Galaxy"
type: "tutorial"
@@ -152,23 +92,6 @@ objectives:
objectives:
time_estimation:
key_points:
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Dave Clements"
- github_username: "tnabtaf"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Anthony Bretaudeau"
- github_username: "abretaud"
- email: ""
-
title: "IGV Introduction"
type: "tutorial"
@@ -188,23 +111,6 @@ objectives:
- "First take home message"
- "Second take home message"
- "Third take home message"
- contributors:
- -
- name: "Anton Nekrutenko"
- github_username: "nekrut"
- email: "anton@nekrut.org"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
-
title: "Visualization"
type: "tutorial"
@@ -218,23 +124,6 @@ objectives:
objectives:
time_estimation:
key_points:
- contributors:
- -
- name: "Nicola Soranzo"
- github_username: "nsoranzo"
- email: ""
- -
- name: "Clemens Blank"
- github_username: "blankclemens"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Getting data into Galaxy"
type: "tutorial"
@@ -247,11 +136,6 @@ objectives:
objectives:
time_estimation:
key_points:
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Collections"
type: "tutorial"
@@ -265,17 +149,22 @@ objectives:
objectives:
time_estimation:
key_points:
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
maintainers:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Clemens Blank"
+ github_username: "blankclemens"
+ email: "blankclemens@gmail.com"
+-
+ name: "Dave Clements"
+ github_username: "tnabtaf"
+ email: ""
+
+contributors:
-
name: "Bérénice Batut"
github_username: "bebatut"
@@ -289,8 +178,13 @@ maintainers:
github_username: "tnabtaf"
email: ""
-
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
+ name: "Nicola Soranzo"
+ github_username: "nsoranzo"
email: ""
-
+-
+ name: "Anne Pajon"
+ github_username: "pajanne"
+ email: ""
+
+
references:
diff --git a/topics/introduction/tutorials/galaxy-intro-101/metadata.yaml b/topics/introduction/tutorials/galaxy-intro-101/metadata.yaml
new file mode 100644
index 00000000000000..a3450aebb11b8f
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-101/metadata.yaml
@@ -0,0 +1,47 @@
+title: "Galaxy 101"
+type: "tutorial"
+name: "galaxy-intro-101"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?"
+objectives:
+- "Familiarize yourself with the basics of Galaxy"
+- "Learn how to obtain data from external sources"
+- "Learn how to run tools"
+- "Learn how histories work"
+- "Learn how to create a workflow"
+- "Learn how to share your work"
+time_estimation: "1-1.5h"
+key_points:
+- "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools"
+- "Galaxy keeps a full record of your analysis in a history"
+- "Workflows enable you to repeat your analysis on different data"
+- "Galaxy can connect to external sources for data import and visualization purposes"
+- "Galaxy provides ways to share your results and methods with others"
+requirements:
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
+-
+ name: "Nicola Soranzo"
+ github_username: "nsoranzo"
+ email: ""
+-
+ name: "Clemens Blank"
+ github_username: "blankclemens"
+ email: "blankclemens@gmail.com"
diff --git a/topics/introduction/tutorials/galaxy-intro-collections/metadata.yaml b/topics/introduction/tutorials/galaxy-intro-collections/metadata.yaml
new file mode 100644
index 00000000000000..abbc184eed24b4
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-collections/metadata.yaml
@@ -0,0 +1,31 @@
+title: "Collections"
+type: "tutorial"
+name: "galaxy-intro-collections"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+objectives:
+time_estimation:
+key_points:
+requirements:
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/introduction/tutorials/galaxy-intro-get-data/metadata.yaml b/topics/introduction/tutorials/galaxy-intro-get-data/metadata.yaml
new file mode 100644
index 00000000000000..e539f41923686e
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-get-data/metadata.yaml
@@ -0,0 +1,31 @@
+title: "Getting data into Galaxy"
+type: "tutorial"
+name: "galaxy-intro-get-data"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+objectives:
+time_estimation:
+key_points:
+requirements:
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/introduction/tutorials/galaxy-intro-peaks2genes/metadata.yaml b/topics/introduction/tutorials/galaxy-intro-peaks2genes/metadata.yaml
new file mode 100644
index 00000000000000..2d8822fd54d42e
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-peaks2genes/metadata.yaml
@@ -0,0 +1,44 @@
+title: "From peaks to genes"
+type: "tutorial"
+name: "galaxy-intro-peaks2genes"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "How to use Galaxy?"
+- "How to get from peak regions to a list of gene names?"
+objectives:
+- "Familiarize yourself with the basics of Galaxy"
+- "Learn how to obtain data from external sources"
+- "Learn how to run tools"
+- "Learn how histories work"
+- "Learn how to create a workflow"
+- "Learn how to share your work"
+time_estimation: "3h"
+key_points:
+- "Galaxy provides an easy-to-use graphical user interface for often complex commandline tools"
+- "Galaxy keeps a full record of your analysis in a history"
+- "Workflows enable you to repeat your analysis on different data"
+- "Galaxy can connect to external sources for data import and visualization purposes"
+- "Galaxy provides ways to share your results and methods with others"
+requirements:
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/introduction/tutorials/galaxy-intro-vis/metadata.yaml b/topics/introduction/tutorials/galaxy-intro-vis/metadata.yaml
new file mode 100644
index 00000000000000..ec86b972066942
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-vis/metadata.yaml
@@ -0,0 +1,31 @@
+title: "Visualization"
+type: "tutorial"
+name: "galaxy-intro-vis"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+objectives:
+time_estimation:
+key_points:
+requirements:
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/introduction/tutorials/igv-introduction/metadata.yaml b/topics/introduction/tutorials/igv-introduction/metadata.yaml
new file mode 100644
index 00000000000000..35a56507989041
--- /dev/null
+++ b/topics/introduction/tutorials/igv-introduction/metadata.yaml
@@ -0,0 +1,37 @@
+title: "IGV Introduction"
+type: "tutorial"
+name: "igv-introduction"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "First question addressed during the tutorial"
+- "Second question addressed during the tutorial"
+objectives:
+- "First learning objectives of the tutorial"
+- "Second learning objectives of the tutorial"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/introduction/tutorials/options-for-using-galaxy/metadata.yaml b/topics/introduction/tutorials/options-for-using-galaxy/metadata.yaml
new file mode 100644
index 00000000000000..1ce413996319be
--- /dev/null
+++ b/topics/introduction/tutorials/options-for-using-galaxy/metadata.yaml
@@ -0,0 +1,32 @@
+title: "Options for using Galaxy"
+type: "tutorial"
+name: "options-for-using-galaxy"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "no"
+slides: "yes"
+questions:
+- "Which Galaxy instance should I use?"
+objectives:
+time_estimation:
+key_points:
+requirements:
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
\ No newline at end of file
diff --git a/topics/introduction/tutorials/processing-many-samples-at-once/metadata.yaml b/topics/introduction/tutorials/processing-many-samples-at-once/metadata.yaml
new file mode 100644
index 00000000000000..8ac8f9c30b91db
--- /dev/null
+++ b/topics/introduction/tutorials/processing-many-samples-at-once/metadata.yaml
@@ -0,0 +1,37 @@
+title: "Multisample Analysis"
+type: "tutorial"
+name: "processing-many-samples-at-once"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "First question addressed during the tutorial"
+- "Second question addressed during the tutorial"
+objectives:
+- "First learning objectives of the tutorial"
+- "Second learning objectives of the tutorial"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/metagenomics/metadata.yaml b/topics/metagenomics/metadata.yaml
index e03bb68b48dd5e..55ac3507e6ed46 100644
--- a/topics/metagenomics/metadata.yaml
+++ b/topics/metagenomics/metadata.yaml
@@ -1,4 +1,4 @@
-name: "metagenomics"
+name: "metagenomics"
type: "use"
title: "Metagenomics"
summary: "Metagenomics is a discipline that enables the genomic study of uncultured microorganisms"
@@ -15,15 +15,6 @@ material:
-
title: "Introduction"
type: "introduction"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: "zazkia@gmail.com"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
-
title: "16S Microbial Analysis with Mothur"
type: "tutorial"
@@ -42,15 +33,6 @@ material:
- "Quality control and cleaning of your data is a crucial step in order to obtain optimal results"
- "Adding a mock community to serve as a control sample can help you asses the error rate of your experimental setup"
- "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: "zazkia@gmail.com"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
-
title: "Analyses of metagenomics data - The global picture"
type: "tutorial"
@@ -74,16 +56,7 @@ material:
- "With shotgun data, we can extract information about the studied community structure and also the functions realised by the community"
- "The tools used to analyze amplicon and shotgun data are different, except for the visualisation"
- "Metagenomics data analyses are complex and time-consuming"
- contributors:
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: "zazkia@gmail.com"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
-
+
maintainers:
-
name: "Bérénice Batut"
@@ -94,6 +67,16 @@ maintainers:
github_username: "shiltemann"
email: "zazkia@gmail.com"
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
+
references:
-
authors: "John C. Wooley, Adam Godzik, Iddo Friedberg"
diff --git a/topics/metagenomics/tutorials/general-tutorial/metadata.yaml b/topics/metagenomics/tutorials/general-tutorial/metadata.yaml
new file mode 100644
index 00000000000000..3a398e5e5e0b82
--- /dev/null
+++ b/topics/metagenomics/tutorials/general-tutorial/metadata.yaml
@@ -0,0 +1,41 @@
+title: "Analyses of metagenomic data - The global picture"
+type: "tutorial"
+name: "general-tutorial"
+zenodo_link: "https://doi.org/10.5281/zenodo.815875"
+galaxy_tour:
+hands_on: "yes"
+slides: "no"
+questions:
+- "How to analyze metagenomics data?"
+- "What information can be extracted of metagenomics data?"
+- "What is the difference between amplicon and shotgun data?"
+- "What are the difference in the analyses of amplicon and shotgun data?"
+objectives:
+- "Choosing the best approach to analyze metagenomics data"
+- "Selection of tools to analyze amplicon data or shotgun data"
+- "Visualisation of a community structure"
+time_estimation: "2h30"
+key_points:
+- "With amplicon data, we can extract information about the studied community structure"
+- "With shotgun data, we can extract information about the studied community structure and also the functions realised by the community"
+- "The tools used to analyze amplicon and shotgun data are different, except for the visualisation"
+- "Metagenomics data analyses are complex and time-consuming"
+maintainers:
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+
+contributors:
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
\ No newline at end of file
diff --git a/topics/metagenomics/tutorials/mothur-miseq-sop/metadata.yaml b/topics/metagenomics/tutorials/mothur-miseq-sop/metadata.yaml
new file mode 100644
index 00000000000000..e0e11a97cc5c03
--- /dev/null
+++ b/topics/metagenomics/tutorials/mothur-miseq-sop/metadata.yaml
@@ -0,0 +1,35 @@
+title: "16S Microbial Analysis with Mothur"
+type: "tutorial"
+name: "mothur-miseq-sop"
+zenodo_link: "https://doi.org/10.5281/zenodo.165147"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+
+questions:
+- "What is the effect of normal variation in the gut microbiome on host health?"
+
+objectives:
+- "Analyze of 16S rRNA sequencing data using the Mothur toolsuite in Galaxy"
+
+time_estimation: "3-4h"
+
+key_points:
+- "16S rRNA gene sequencing analysis results depend on the many algorithms used and their settings"
+- "Quality control and cleaning of your data is a crucial step in order to obtain optimal results"
+- "Adding a mock commutity to serve as a control sample can help you asses the error rate of your experimental setup"
+- "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations"
+
+requirements:
+
+maintainers:
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
+
+contributors:
+-
+ name: "Saskia Hiltemann"
+ github_username: "shiltemann"
+ email: "zazkia@gmail.com"
\ No newline at end of file
diff --git a/topics/proteomics/metadata.yaml b/topics/proteomics/metadata.yaml
index 35bbddd5683a47..3021b84128d826 100644
--- a/topics/proteomics/metadata.yaml
+++ b/topics/proteomics/metadata.yaml
@@ -1,4 +1,4 @@
-name: "proteomics"
+name: "proteomics"
type: "use"
title: "Proteomics"
summary: "Training material for proteomics workflows in Galaxy"
@@ -32,23 +32,6 @@ material:
- "You should always include a contaminant database."
- "It may be wise to include mycoplasma databases."
- "Depening on your search engine, you need to include a decoy database."
- contributors:
- -
- name: "Florian Christoph Sigloch"
- github_username: "Stortebecker"
- email: "sigloch [plus] github (at) mailbox {dot} org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "Metaproteomics tutorial"
type: "tutorial"
@@ -68,27 +51,6 @@ material:
- "Use dataset collections"
- "With SearchGUI and PeptideShaker you can gain access to multiple search engines"
- "Learning the basics of SQL queries can pay off"
- contributors:
- -
- name: "Timothy J. Griffin"
- github_username: ""
- email: "tgriffin@umn.edu"
- -
- name: "Pratik Jagtap"
- github_username: "PratikDJagtap"
- email: "pjagtap@umn.edu"
- -
- name: "James Johnson"
- github_username: "jj-umn"
- email: "jj@umn.edu"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Clemens Blank"
- github_username: "blankclemens"
- email: "blankclemens@gmail.com"
-
title: "Label-free versus Labelled - How to Choose Your Quantitation Method"
type: "tutorial"
@@ -105,23 +67,6 @@ material:
- "Label-free and labelled methods are not better or worse *per se*."
- "Different scientific question call for different quantitation methods."
- "Be wise in choosing the right method before starting your LC-MS/MS runs."
- contributors:
- -
- name: "Florian Christoph Sigloch"
- github_username: "Stortebecker"
- email: "sigloch [plus] github (at) mailbox {dot} org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "ntails"
type: "tutorial"
@@ -142,23 +87,6 @@ material:
- "First take home message"
- "Second take home message"
- "Third take home message"
- contributors:
- -
- name: "Florian Christoph Sigloch"
- github_username: "Stortebecker"
- email: "sigloch [plus] github (at) mailbox {dot} org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "Peptide and Protein ID"
type: "tutorial"
@@ -178,23 +106,6 @@ material:
- "LC-MS/MS raw files have to be converted before using GalaxyP on most GalaxyP servers."
- "SearchGUI can be used for running several peptide search engines at once."
- "PeptideShaker can be used to combine and evaluate the results, and to perform protein inference."
- contributors:
- -
- name: "Florian Christoph Sigloch"
- github_username: "Stortebecker"
- email: "sigloch [plus] github (at) mailbox {dot} org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "Secretome Prediction"
type: "tutorial"
@@ -214,23 +125,6 @@ material:
- "First take home message"
- "Second take home message"
- "Third take home message"
- contributors:
- -
- name: "Florian Christoph Sigloch"
- github_username: "Stortebecker"
- email: "sigloch [plus] github (at) mailbox {dot} org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
-
title: "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)"
type: "tutorial"
@@ -254,23 +148,6 @@ material:
- "Quantitations have to be mapped to PSMs."
- "PSM quantitations can be used to calculate protein quantitations."
- "Proper quantitation and mapping needs careful evaluation and optimization."
- contributors:
- -
- name: "Florian Christoph Sigloch"
- github_username: "Stortebecker"
- email: "sigloch [plus] github (at) mailbox {dot} org"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
maintainers:
-
@@ -285,14 +162,20 @@ maintainers:
name: "Clemens Blank"
github_username: "blankclemens"
email: "blankclemens@gmail.com"
+
+contributors:
-
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch+github@mailbox.org"
-
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: ""
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+-
+ name: "Clemens Blank"
+ github_username: "blankclemens"
+ email: "blankclemens@gmail.com"
references:
-
diff --git a/topics/proteomics/tutorials/database-handling/metadata.yaml b/topics/proteomics/tutorials/database-handling/metadata.yaml
new file mode 100644
index 00000000000000..a0dd2b6a1360f8
--- /dev/null
+++ b/topics/proteomics/tutorials/database-handling/metadata.yaml
@@ -0,0 +1,40 @@
+title: "Protein FASTA Database Handling"
+type: "tutorial"
+edam_ontology: "topic_0121"
+name: "database-handling"
+hands_on: "yes"
+slides: "no"
+questions:
+- "How to download protein FASTA databases of a certain organism?"
+- "How to download a contaminant database?"
+- "How to create a decoy database?"
+- "How to combine databases?"
+objectives:
+- "Creation of a protein FASTA database ready for use with database search algorithms."
+time_estimation: "30min"
+key_points:
+- "There are several types of Uniprot databases."
+- "You should always include a contaminant database."
+- "It may be wise to include mycoplasma databases."
+- "Depening on your search engine, you need to include a decoy database."
+requirements:
+-
+maintainers:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/proteomics/tutorials/labelfree-vs-labelled/metadata.yaml b/topics/proteomics/tutorials/labelfree-vs-labelled/metadata.yaml
new file mode 100644
index 00000000000000..e9e7978aa59073
--- /dev/null
+++ b/topics/proteomics/tutorials/labelfree-vs-labelled/metadata.yaml
@@ -0,0 +1,34 @@
+title: "Label-free versus Labelled - How to Choose Your Quantitation Method"
+type: "tutorial"
+name: "labelfree-vs-labelled"
+hands_on: "yes"
+slides: "no"
+questions:
+- "What are benefits and drawbacks of different quantitation methods?"
+- "How to choose which quantitation method bests suits my need?"
+objectives:
+- "Choose your quantitation method."
+time_estimation: "15min"
+key_points:
+- "Label-free and labelled methods are not better or worse *per se*."
+- "Different scientific question call for different quantitation methods."
+- "Be wise in chosing the right method before starting your LC-MS/MS runs."
+maintainers:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/proteomics/tutorials/metaproteomics/metadata.yaml b/topics/proteomics/tutorials/metaproteomics/metadata.yaml
new file mode 100644
index 00000000000000..77069bf1acc3be
--- /dev/null
+++ b/topics/proteomics/tutorials/metaproteomics/metadata.yaml
@@ -0,0 +1,49 @@
+title: "Metaproteomics"
+type: "tutorial"
+enable: "true"
+name: "metaproteomics"
+zenodo_link: "https://doi.org/10.5281/zenodo.839701"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?"
+- "How can I perform taxonomy analysis and visualize metaproteomics data?"
+- "How can I perform functional analysis on this metaproteomics data?"
+objectives:
+- "A taxonomy and functional analysis of metaproteomic mass spectrometry data."
+time_estimation: "2h"
+key_points:
+- "Use dataset collections"
+- "With SearchGUI and PeptideShaker you can gain access to multiple search engines"
+- "Learning the basics of SQL queries can pay off"
+
+requirements:
+-
+ title: "Galaxy introduction"
+ type: "internal"
+ link: "/introduction/"
+
+maintainers:
+-
+ name: "Clemens Blank"
+ github_username: "blankclemens"
+ email: "blankclemens@gmail.com"
+
+contributors:
+-
+ name: "Clemens Blank"
+ github_username: "blankclemens"
+ email: "blankclemens@gmail.com"
+-
+ name: "Timothy J. Griffin"
+ github_username: ""
+ email: "tgriffin@umn.edu"
+-
+ name: "Pratik Jagtap"
+ github_username: "PratikDJagtap"
+ email: "pjagtap@umn.edu"
+-
+ name: "James Johnson"
+ github_username: "jj-umn"
+ email: "jj@umn.edu"
\ No newline at end of file
diff --git a/topics/proteomics/tutorials/ntails/metadata.yaml b/topics/proteomics/tutorials/ntails/metadata.yaml
new file mode 100644
index 00000000000000..61d260574e1ea8
--- /dev/null
+++ b/topics/proteomics/tutorials/ntails/metadata.yaml
@@ -0,0 +1,38 @@
+title: "ntails"
+type: "tutorial"
+edam_ontology: "topic_0121"
+name: "ntails"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "First question addressed during the tutorial"
+- "Second question addressed during the tutorial"
+objectives:
+- "First learning objectives of the tutorial"
+- "Second learning objectives of the tutorial"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/proteomics/tutorials/protein-id-sg-ps/metadata.yaml b/topics/proteomics/tutorials/protein-id-sg-ps/metadata.yaml
new file mode 100644
index 00000000000000..39dfc68049a1a3
--- /dev/null
+++ b/topics/proteomics/tutorials/protein-id-sg-ps/metadata.yaml
@@ -0,0 +1,42 @@
+title: "Peptide and Protein ID"
+type: "tutorial"
+name: "protein-id-sg-ps"
+zenodo_link: "https://zenodo.org/record/546301"
+hands_on: "yes"
+slides: "no"
+questions:
+- "How to convert LC-MS/MS raw files?"
+- "How to identify peptides?"
+- "How to identify proteins?"
+- "How to evaluate the results?"
+objectives:
+- "Protein identification from LC-MS/MS raw files."
+time_estimation: "45min"
+key_points:
+- "LC-MS/MS raw files have to be converted before using GalaxyP on most GalaxyP servers."
+- "SearchGUI can be used for running several peptide search engines at once."
+- "PeptideShaker can be used to combine and evaluate the results, and to perform protein inference."
+requirements:
+-
+ title: "Protein FASTA Database Handling"
+ type: "internal"
+ link: "/Proteomics/tutorials/database-handling.md"
+maintainers:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/proteomics/tutorials/protein-quant-sil/metadata.yaml b/topics/proteomics/tutorials/protein-quant-sil/metadata.yaml
new file mode 100644
index 00000000000000..8ad2ad87ea2bfd
--- /dev/null
+++ b/topics/proteomics/tutorials/protein-quant-sil/metadata.yaml
@@ -0,0 +1,49 @@
+title: "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)"
+type: "tutorial"
+name: "protein-quant-sil"
+zenodo_link:
+hands_on: "yes"
+slides: "no"
+questions:
+- "What are MS1 features?"
+- "How to quantify based on MS1 features?"
+- "How to import peptide and protein IDs?"
+- "How to match quantitations and IDs?"
+- "How to evaluate and optimize the results?"
+objectives:
+- "MS1 feature quantitation and mapping of quantitations to protein IDs."
+time estimation: "1h"
+key_points:
+- "Stable isotopes result in multiple parallel MS1 ion traces."
+- "MS1 ion traces can be used to relatively quantify proteins of different samples in a sing
+- "Quantitations have to be mapped to PSMs."
+- "PSM quantitations can be used to calculate protein quantitations."
+- "Proper quantitation and mapping needs careful evaluation and optimization."
+requirements:
+-
+ title: "Protein FASTA Database Handling"
+ type: "internal"
+ link: "/Proteomics/tutorials/"
+-
+ title: "Peptide and Protein ID"
+ type: "internal"
+ link: "/Proteomics/tutorials/"
+maintainers:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/proteomics/tutorials/secretome-prediction/metadata.yaml b/topics/proteomics/tutorials/secretome-prediction/metadata.yaml
new file mode 100644
index 00000000000000..09e9a40d6d9a67
--- /dev/null
+++ b/topics/proteomics/tutorials/secretome-prediction/metadata.yaml
@@ -0,0 +1,37 @@
+title: "Secretome Prediction"
+type: "tutorial"
+name: "secretome-predicion"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "First question addressed during the tutorial"
+- "Second question addressed during the tutorial"
+objectives:
+- "First learning objectives of the tutorial"
+- "Second learning objectives of the tutorial"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Florian Christoph Sigloch"
+ github_username: "Stortebecker"
+ email: "sigloch [plus] github (at) mailbox {dot} org"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/sequence-analysis/metadata.yaml b/topics/sequence-analysis/metadata.yaml
index e9b6c7578353c6..c7ee434ac218b0 100644
--- a/topics/sequence-analysis/metadata.yaml
+++ b/topics/sequence-analysis/metadata.yaml
@@ -2,12 +2,12 @@ name: "sequence-analysis"
type: "use"
title: "Analysis of sequences"
summary: "Analyses of sequences"
-docker_image: ""
requirements:
-
title: "Galaxy introduction"
type: "internal"
link: "/introduction/"
+
material:
-
title: "Quality Control"
@@ -33,15 +33,6 @@ material:
- Run quality control on every dataset before running any other bioinformatics analysis
- Take care of the parameters used to improve the sequence quality
- Re-run FastQC to check the impact of the quality control
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Mapping"
type: "tutorial"
@@ -61,19 +52,6 @@ material:
- Know your data!
- Mapping is not trivial
- There are many mapping algorithms, it depends on your data which one to choose
- contributors:
- -
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email: "wolffj@informatik.uni-freiburg.de"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Genome Annotation"
type: "tutorial"
@@ -90,28 +68,9 @@ material:
- "Second learning objectives of the tutorial"
time_estimation: "1h/1d"
key_points:
- - ""
- contributors:
- -
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email: "wolffj@informatik.uni-freiburg.de"
- -
- name: "Anika Exleben"
- github_username: "erxleben"
- email: ""
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ - "First take home message"
+ - "Second take home message"
+ - "Third take home message"
-
title: "RAD-Seq Reference-based data analysis"
type: "tutorial"
@@ -128,20 +87,10 @@ material:
- "Calculate population genomics statistics from RAD sequencing data"
time_estimation: "1/2d"
key_points:
- - ""
- contributors:
- -
- name: "Yvan Le Bras"
- github_username: "yvanlebras"
- email: "yvan.le-bras@mnhn.fr"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ - "Simple sentence to sum up the first key point of the tutorial (Take home message)"
+ - "Second key point"
+ - "Third key point"
+ - "..."
-
title: "RAD-Seq de-novo data analysis"
type: "tutorial"
@@ -158,20 +107,10 @@ material:
- "Calculate population genomics statistics from RAD sequencing data"
time_estimation: "1/2d"
key_points:
- - ""
- contributors:
- -
- name: "Yvan Le Bras"
- github_username: "yvanlebras"
- email: "yvan.le-bras@mnhn.fr"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ - "Simple sentence to sum up the first key point of the tutorial (Take home message)"
+ - "Second key point"
+ - "Third key point"
+ - "..."
-
title: "RAD-Seq to construct genetic maps"
type: "tutorial"
@@ -188,304 +127,26 @@ material:
- "Create input files for genetic map building software"
time_estimation: "1/2d"
key_points:
- - ""
- contributors:
- -
- name: "Yvan Le Bras"
- github_username: "yvanlebras"
- email: "yvan.le-bras@mnhn.fr"
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
+ - "Simple sentence to sum up the first key point of the tutorial (Take home message)"
+ - "Second key point"
+ - "Third key point"
+ - "..."
maintainers:
-
- name: "Yvan Le Bras"
- github_username: "yvanlebras"
- email: "yvan.le-bras@mnhn.fr"
--
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
-
- name: "Joachim Wolff"
- github_username: "joachimwolff"
- email: "wolffj@informatik.uni-freiburg.de"
--
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
-references:
--
- authors: "Marco-Antonio Mendoza-Parra et al"
- title: "A quality control system for profiles obtained by ChIP sequencing"
- link: "http://nar.oxfordjournals.org/content/41/21/e196.short"
- summary: "Presents an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS."
--
- authors: "Ana Conesa et al"
- title: "A survey of best practices for RNA-seq data analysis"
- link: "http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8"
- summary: "Highlights the challenges associated with each step of RNA-seq data analysis."
--
- authors: "Yuval Benjamini1 et al"
- title: "Summarizing and correcting the GC content bias in high-throughput sequencing"
- link: "http://nar.oxfordjournals.org/content/40/10/e72.long"
- summary: "Summarizes the many possible sourced of GC bias for deeply sequenced samples."
--
- authors: "David Sims et al"
- title: "Sequencing depth and coverage: key considerations in genomic analyses"
- link: "http://www.nature.com/nrg/journal/v15/n2/abs/nrg3642.html"
- summary: "Discuss the issue of sequencing depth in the design of next-generation sequencing experiments."
--
- authors: "Frontiers in Genetics"
- title: "Quality assessment and control of high-throughput sequencing data"
- link: "http://journal.frontiersin.org/researchtopic/1683/quality-assessment-and-control-of-high-throughput-sequencing-data"
- summary: "Collection of papers on quality controls for various NGS applications"
--
- authors: "Frazer Meacham et al"
- title: "Identification and correction of systematic error in high-throughput sequence data"
- link: "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-451"
- summary: "Reviews and proposes correction for systematic base pair errors in deep sequencing"
--
- authors: "Guillaume Devailly et al"
- title: "Heat seq: an interactive web tool for high-throughput sequencing experiment comparison with public data"
- link: "http://biorxiv.org/content/early/2016/04/18/049254.abstract"
- summary: "Presents a web-tool that allows genome scale comparison of high throughput experiments"
--
- authors: "Amores, A., et al. 2011"
- title: "Genome evolution and meiotic maps by massively parallel DNA sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21828280"
--
- authors: "Catchen, J. M. et al. 2011"
- title: "Stacks: building and genotyping loci de novo from short-read sequences"
- link: "http://www.g3journal.org/content/1/3/171.full"
--
- authors: "Davey, J. W., et al. 2011"
- title: "Genome-wide genetic marker discovery and genotyping using next-generation sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21681211"
--
- authors: "Etter, P. D., et al. 2011"
- title: "SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658458/"
--
- authors: "Ekblom, R., and J. Galindo. 2010"
- title: "Applications of next generation sequencing in molecular ecology of non-model organisms"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21139633"
--
- authors: "Hohenlohe, P. A. et al. 2010"
- title: "Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags"
- link: "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862"
--
- authors: "Gompert, Z., and C. A. Buerkle. 2011a"
- title: "A hierarchical Bayesian model for next-generation population genomics"
- link: "http://www.genetics.org/content/187/3/903"
--
- authors: "Gompert, Z., and C. A. Buerkle. 2011b"
- title: "Bayesian estimation of genomic clines"
- link: "http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05074.x/abstract"
--
- authors: "Lynch, M. 2009"
- title: "Estimation of allele frequencies from high-coverage genome-sequencing projects"
- link: "http://www.genetics.org/content/182/1/295"
--
- authors: "Nielsen, R., et al. 2005"
- title: "Genomic scans for selective sweeps using SNP data"
- link: "http://genome.cshlp.org/content/15/11/1566.abstract"
--
- authors: "Hohenlohe, P. A., et al. 2010"
- title: "Using population genomics to detect selection in natural populations: Key concepts and methodological considerations"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21218185"
--
- authors: "Stapley, J., et al. 2010"
- title: "Adaptation genomics: the next generation"
- link: "http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00216-8"
--
- authors: "Luikart, G.,et al. 2003"
- title: "The power and promise of population genomics: from genotyping to genome typing"
- link: "http://www.nature.com/nrg/journal/v4/n12/full/nrg1226.html"
--
- authors: "Nielsen, R., et al. 2011"
- title: "Genotype and SNP calling from next-generation sequencing data"
- link: "http://www.nature.com/nrg/journal/v12/n6/full/nrg2986.html"
--
- authors: "Altshuler, D., et al. 2000"
- title: "An SNP map of the human genome generated by reduced representation shotgun sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/11029002"
--
- authors: "Baxter, S. W., et al. 2011"
- title: "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019315"
--
- authors: "Chutimanitsakun, Y., et al. 2011"
- title: "Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley"
- link: "http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-4"
--
- authors: "Gore, M. A., et al. 2009"
- title: "A first-generation haplotype map of maize"
- link: "http://science.sciencemag.org/content/326/5956/1115"
--
- authors: "Baird, N. A., et al. 2008"
- title: "Rapid SNP discovery and genetic mapping using sequenced RAD markers"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376"
--
- authors: "Emerson, K. J., et al. 2010"
- title: "Resolving postglacial phylogeography using high-throughput sequencing"
- link: "http://www.pnas.org/content/107/37/16196"
--
- authors: "Etter, P. D., et al. 2011"
- title: "Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018561"
--
- authors: "Hohenlohe, P. A., et al. 2011"
- title: "Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21429168"
--
- authors: "Miller, M. R., et al. 2007"
- title: "Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/17189378"
--
- authors: "Willing, E. M., et al. 2011"
- title: "Paired-end RAD-seq for de novo assembly and marker design without available reference"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21712251"
--
- authors: "Andolfatto, P., et al. 2011"
- title: "Multiplexed shotgun genotyping for rapid and efficient genetic mapping"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21233398"
--
- authors: "Elshire, R. J., et al. 2011"
- title: "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379"
--
- authors: "Rigola, D., et al. 2009"
- title: "High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology"
- links: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004761"
--
- authors: "van Orsouw, N. J., et al. 2007"
- title: "Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001172"
--
- authors: "van Tassell, C. P., et al. 2008"
- title: "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/18297082"
--
- authors: "Amores, A., et al. 2011"
- title: "Genome evolution and meiotic maps by massively parallel DNA sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21828280"
--
- authors: "Catchen, J. M. et al. 2011"
- title: "Stacks: building and genotyping loci de novo from short-read sequences"
- link: "http://www.g3journal.org/content/1/3/171.full"
--
- authors: "Davey, J. W., et al. 2011"
- title: "Genome-wide genetic marker discovery and genotyping using next-generation sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21681211"
--
- authors: "Etter, P. D., et al. 2011"
- title: "SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658458/"
--
- authors: "Ekblom, R., and J. Galindo. 2010"
- title: "Applications of next generation sequencing in molecular ecology of non-model organisms"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21139633"
--
- authors: "Hohenlohe, P. A. et al. 2010"
- title: "Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags"
- link: "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862"
--
- authors: "Gompert, Z., and C. A. Buerkle. 2011a"
- title: "A hierarchical Bayesian model for next-generation population genomics"
- link: "http://www.genetics.org/content/187/3/903"
--
- authors: "Gompert, Z., and C. A. Buerkle. 2011b"
- title: "Bayesian estimation of genomic clines"
- link: "http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05074.x/abstract"
--
- authors: "Lynch, M. 2009"
- title: "Estimation of allele frequencies from high-coverage genome-sequencing projects"
- link: "http://www.genetics.org/content/182/1/295"
--
- authors: "Nielsen, R., et al. 2005"
- title: "Genomic scans for selective sweeps using SNP data"
- link: "http://genome.cshlp.org/content/15/11/1566.abstract"
--
- authors: "Hohenlohe, P. A., et al. 2010"
- title: "Using population genomics to detect selection in natural populations: Key concepts and methodological considerations"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21218185"
--
- authors: "Stapley, J., et al. 2010"
- title: "Adaptation genomics: the next generation"
- link: "http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00216-8"
--
- authors: "Luikart, G.,et al. 2003"
- title: "The power and promise of population genomics: from genotyping to genome typing"
- link: "http://www.nature.com/nrg/journal/v4/n12/full/nrg1226.html"
--
- authors: "Nielsen, R., et al. 2011"
- title: "Genotype and SNP calling from next-generation sequencing data"
- link: "http://www.nature.com/nrg/journal/v12/n6/full/nrg2986.html"
--
- authors: "Altshuler, D., et al. 2000"
- title: "An SNP map of the human genome generated by reduced representation shotgun sequencing"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/11029002"
--
- authors: "Baxter, S. W., et al. 2011"
- title: "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019315"
--
- authors: "Chutimanitsakun, Y., et al. 2011"
- title: "Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley"
- link: "http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-4"
--
- authors: "Gore, M. A., et al. 2009"
- title: "A first-generation haplotype map of maize"
- link: "http://science.sciencemag.org/content/326/5956/1115"
--
- authors: "Baird, N. A., et al. 2008"
- title: "Rapid SNP discovery and genetic mapping using sequenced RAD markers"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376"
--
- authors: "Emerson, K. J., et al. 2010"
- title: "Resolving postglacial phylogeography using high-throughput sequencing"
- link: "http://www.pnas.org/content/107/37/16196"
--
- authors: "Etter, P. D., et al. 2011"
- title: "Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018561"
--
- authors: "Hohenlohe, P. A., et al. 2011"
- title: "Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21429168"
--
- authors: "Miller, M. R., et al. 2007"
- title: "Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/17189378"
--
- authors: "Willing, E. M., et al. 2011"
- title: "Paired-end RAD-seq for de novo assembly and marker design without available reference"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21712251"
--
- authors: "Andolfatto, P., et al. 2011"
- title: "Multiplexed shotgun genotyping for rapid and efficient genetic mapping"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/21233398"
--
- authors: "Elshire, R. J., et al. 2011"
- title: "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379"
--
- authors: "Rigola, D., et al. 2009"
- title: "High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology"
- links: (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004761"
+contributors:
-
- authors: "van Orsouw, N. J., et al. 2007"
- title: "Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes"
- link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001172"
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
-
- authors: "van Tassell, C. P., et al. 2008"
- title: "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries"
- link: "https://www.ncbi.nlm.nih.gov/pubmed/18297082"
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/sequence-analysis/tutorials/de-novo-rad-seq/metadata.yaml b/topics/sequence-analysis/tutorials/de-novo-rad-seq/metadata.yaml
new file mode 100644
index 00000000000000..0542dbbcd695d7
--- /dev/null
+++ b/topics/sequence-analysis/tutorials/de-novo-rad-seq/metadata.yaml
@@ -0,0 +1,180 @@
+title: "RAD-Seq de-novo data analysis"
+type: "tutorial"
+name: "de-novo-rad-seq"
+zenodo_link: "https://zenodo.org/record/61771#.WA9TyJN96EI"
+galaxy_tour: "de-novo-rad-seq"
+hands_on: "yes"
+slides: "no"
+
+questions:
+- "How to analyze RAD sequencing data without a reference genome for a population genomics sutdy?"
+
+objectives:
+- "Analysis of RAD sequencing data without a reference genome"
+- "SNP calling from RAD sequencing data"
+- "Calculate population genomics statistics from RAD sequencing data"
+
+time_estimation: "1/2d"
+
+key_points:
+- "Simple sentence to sum up the first key point of the tutorial (Take home message)"
+- "Second key point"
+- "Third key point"
+- "..."
+
+maintainers:
+-
+ name: "Yvan Le Bras"
+ github_username: "yvanlebras"
+ email: "yvan.le-bras@mnhn.fr"
+
+contributors:
+-
+ name: "Yvan Le Bras"
+ github_username: "yvanlebras"
+ email: "yvan.le-bras@mnhn.fr"
+
+-
+ authors: "Amores, A., et al. 2011"
+ title: "Genome evolution and meiotic maps by massively parallel DNA sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21828280"
+
+-
+ authors: "Catchen, J. M. et al. 2011"
+ title: "Stacks: building and genotyping loci de novo from short-read sequences"
+ link: "http://www.g3journal.org/content/1/3/171.full"
+
+-
+ authors: "Davey, J. W., et al. 2011"
+ title: "Genome-wide genetic marker discovery and genotyping using next-generation sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21681211"
+
+-
+ authors: "Etter, P. D., et al. 2011"
+ title: "SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658458/"
+
+-
+ authors: "Ekblom, R., and J. Galindo. 2010"
+ title: "Applications of next generation sequencing in molecular ecology of non-model organisms"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21139633"
+
+-
+ authors: "Hohenlohe, P. A. et al. 2010"
+ title: "Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags"
+ link: "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862"
+
+-
+ authors: "Gompert, Z., and C. A. Buerkle. 2011a"
+ title: "A hierarchical Bayesian model for next-generation population genomics"
+ link: "http://www.genetics.org/content/187/3/903"
+
+-
+ authors: "Gompert, Z., and C. A. Buerkle. 2011b"
+ title: "Bayesian estimation of genomic clines"
+ link: "http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05074.x/abstract"
+
+-
+ authors: "Lynch, M. 2009"
+ title: "Estimation of allele frequencies from high-coverage genome-sequencing projects"
+ link: "http://www.genetics.org/content/182/1/295"
+
+-
+ authors: "Nielsen, R., et al. 2005"
+ title: "Genomic scans for selective sweeps using SNP data"
+ link: "http://genome.cshlp.org/content/15/11/1566.abstract"
+
+-
+ authors: "Hohenlohe, P. A., et al. 2010"
+ title: "Using population genomics to detect selection in natural populations: Key concepts and methodological considerations"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21218185"
+
+-
+ authors: "Stapley, J., et al. 2010"
+ title: "Adaptation genomics: the next generation"
+ link: "http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00216-8"
+
+-
+ authors: "Luikart, G.,et al. 2003"
+ title: "The power and promise of population genomics: from genotyping to genome typing"
+ link: "http://www.nature.com/nrg/journal/v4/n12/full/nrg1226.html"
+
+-
+ authors: "Nielsen, R., et al. 2011"
+ title: "Genotype and SNP calling from next-generation sequencing data"
+ link: "http://www.nature.com/nrg/journal/v12/n6/full/nrg2986.html"
+
+-
+ authors: "Altshuler, D., et al. 2000"
+ title: "An SNP map of the human genome generated by reduced representation shotgun sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/11029002"
+
+-
+ authors: "Baxter, S. W., et al. 2011"
+ title: "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019315"
+
+-
+ authors: "Chutimanitsakun, Y., et al. 2011"
+ title: "Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley"
+ link: "http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-4"
+
+-
+ authors: "Gore, M. A., et al. 2009"
+ title: "A first-generation haplotype map of maize"
+ link: "http://science.sciencemag.org/content/326/5956/1115"
+
+-
+ authors: "Baird, N. A., et al. 2008"
+ title: "Rapid SNP discovery and genetic mapping using sequenced RAD markers"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376"
+
+-
+ authors: "Emerson, K. J., et al. 2010"
+ title: "Resolving postglacial phylogeography using high-throughput sequencing"
+ link: "http://www.pnas.org/content/107/37/16196"
+
+-
+ authors: "Etter, P. D., et al. 2011"
+ title: "Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018561"
+
+-
+ authors: "Hohenlohe, P. A., et al. 2011"
+ title: "Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21429168"
+
+-
+ authors: "Miller, M. R., et al. 2007"
+ title: "Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/17189378"
+
+-
+ authors: "Willing, E. M., et al. 2011"
+ title: "Paired-end RAD-seq for de novo assembly and marker design without available reference"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21712251"
+
+-
+ authors: "Andolfatto, P., et al. 2011"
+ title: "Multiplexed shotgun genotyping for rapid and efficient genetic mapping"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21233398"
+
+-
+ authors: "Elshire, R. J., et al. 2011"
+ title: "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379"
+
+-
+ authors: "Rigola, D., et al. 2009"
+ title: "High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology"
+ links: (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004761"
+
+-
+ authors: "van Orsouw, N. J., et al. 2007"
+ title: "Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001172"
+
+-
+ authors: "van Tassell, C. P., et al. 2008"
+ title: "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/18297082"
diff --git a/topics/sequence-analysis/tutorials/genetic-map-rad-seq/metadata.yaml b/topics/sequence-analysis/tutorials/genetic-map-rad-seq/metadata.yaml
new file mode 100644
index 00000000000000..e9a7653dace9f1
--- /dev/null
+++ b/topics/sequence-analysis/tutorials/genetic-map-rad-seq/metadata.yaml
@@ -0,0 +1,181 @@
+title: "RAD-Seq to construct genetic maps"
+type: "tutorial"
+name: "genetic-map-rad-seq"
+zenodo_link: "https://zenodo.org/record/61771#.WA9TyJN96EI"
+galaxy_tour: "genetic-map-rad-seq"
+hands_on: "yes"
+slides: "no"
+
+questions:
+- "How to analyze RAD sequencing data for a genetic map study?"
+
+objectives:
+- "SNP calling from RAD sequencing data"
+- "Find and correct haplotypes"
+- "Create input files for genetic map building software"
+
+time_estimation: "1/2d"
+
+key_points:
+- "Simple sentence to sum up the first key point of the tutorial (Take home message)"
+- "Second key point"
+- "Third key point"
+- "..."
+
+maintainers:
+-
+ name: "Yvan Le Bras"
+ github_username: "yvanlebras"
+ email: "yvan.le-bras@mnhn.fr"
+
+contributors:
+-
+ name: "Yvan Le Bras"
+ github_username: "yvanlebras"
+ email: "yvan.le-bras@mnhn.fr"
+
+references:
+-
+ authors: "Amores, A., et al. 2011"
+ title: "Genome evolution and meiotic maps by massively parallel DNA sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21828280"
+
+-
+ authors: "Catchen, J. M. et al. 2011"
+ title: "Stacks: building and genotyping loci de novo from short-read sequences"
+ link: "http://www.g3journal.org/content/1/3/171.full"
+
+-
+ authors: "Davey, J. W., et al. 2011"
+ title: "Genome-wide genetic marker discovery and genotyping using next-generation sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21681211"
+
+-
+ authors: "Etter, P. D., et al. 2011"
+ title: "SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658458/"
+
+-
+ authors: "Ekblom, R., and J. Galindo. 2010"
+ title: "Applications of next generation sequencing in molecular ecology of non-model organisms"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21139633"
+
+-
+ authors: "Hohenlohe, P. A. et al. 2010"
+ title: "Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags"
+ link: "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862"
+
+-
+ authors: "Gompert, Z., and C. A. Buerkle. 2011a"
+ title: "A hierarchical Bayesian model for next-generation population genomics"
+ link: "http://www.genetics.org/content/187/3/903"
+
+-
+ authors: "Gompert, Z., and C. A. Buerkle. 2011b"
+ title: "Bayesian estimation of genomic clines"
+ link: "http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05074.x/abstract"
+
+-
+ authors: "Lynch, M. 2009"
+ title: "Estimation of allele frequencies from high-coverage genome-sequencing projects"
+ link: "http://www.genetics.org/content/182/1/295"
+
+-
+ authors: "Nielsen, R., et al. 2005"
+ title: "Genomic scans for selective sweeps using SNP data"
+ link: "http://genome.cshlp.org/content/15/11/1566.abstract"
+
+-
+ authors: "Hohenlohe, P. A., et al. 2010"
+ title: "Using population genomics to detect selection in natural populations: Key concepts and methodological considerations"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21218185"
+
+-
+ authors: "Stapley, J., et al. 2010"
+ title: "Adaptation genomics: the next generation"
+ link: "http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00216-8"
+
+-
+ authors: "Luikart, G.,et al. 2003"
+ title: "The power and promise of population genomics: from genotyping to genome typing"
+ link: "http://www.nature.com/nrg/journal/v4/n12/full/nrg1226.html"
+
+-
+ authors: "Nielsen, R., et al. 2011"
+ title: "Genotype and SNP calling from next-generation sequencing data"
+ link: "http://www.nature.com/nrg/journal/v12/n6/full/nrg2986.html"
+
+-
+ authors: "Altshuler, D., et al. 2000"
+ title: "An SNP map of the human genome generated by reduced representation shotgun sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/11029002"
+
+-
+ authors: "Baxter, S. W., et al. 2011"
+ title: "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019315"
+
+-
+ authors: "Chutimanitsakun, Y., et al. 2011"
+ title: "Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley"
+ link: "http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-4"
+
+-
+ authors: "Gore, M. A., et al. 2009"
+ title: "A first-generation haplotype map of maize"
+ link: "http://science.sciencemag.org/content/326/5956/1115"
+
+-
+ authors: "Baird, N. A., et al. 2008"
+ title: "Rapid SNP discovery and genetic mapping using sequenced RAD markers"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376"
+
+-
+ authors: "Emerson, K. J., et al. 2010"
+ title: "Resolving postglacial phylogeography using high-throughput sequencing"
+ link: "http://www.pnas.org/content/107/37/16196"
+
+-
+ authors: "Etter, P. D., et al. 2011"
+ title: "Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018561"
+
+-
+ authors: "Hohenlohe, P. A., et al. 2011"
+ title: "Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21429168"
+
+-
+ authors: "Miller, M. R., et al. 2007"
+ title: "Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/17189378"
+
+-
+ authors: "Willing, E. M., et al. 2011"
+ title: "Paired-end RAD-seq for de novo assembly and marker design without available reference"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21712251"
+
+-
+ authors: "Andolfatto, P., et al. 2011"
+ title: "Multiplexed shotgun genotyping for rapid and efficient genetic mapping"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21233398"
+
+-
+ authors: "Elshire, R. J., et al. 2011"
+ title: "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379"
+
+-
+ authors: "Rigola, D., et al. 2009"
+ title: "High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology"
+ links: (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004761"
+
+-
+ authors: "van Orsouw, N. J., et al. 2007"
+ title: "Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001172"
+
+-
+ authors: "van Tassell, C. P., et al. 2008"
+ title: "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/18297082"
diff --git a/topics/sequence-analysis/tutorials/genome-annotation/metadata.yaml b/topics/sequence-analysis/tutorials/genome-annotation/metadata.yaml
new file mode 100644
index 00000000000000..9be2bdbd97ac0d
--- /dev/null
+++ b/topics/sequence-analysis/tutorials/genome-annotation/metadata.yaml
@@ -0,0 +1,37 @@
+title: "Genome Annotation"
+type: "tutorial"
+name: "genome-annotation"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "First question addressed during the tutorial"
+- "Second question addressed during the tutorial"
+objectives:
+- "First learning objectives of the tutorial"
+- "Second learning objectives of the tutorial"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/sequence-analysis/tutorials/mapping/metadata.yaml b/topics/sequence-analysis/tutorials/mapping/metadata.yaml
new file mode 100644
index 00000000000000..1657e655ebd3bb
--- /dev/null
+++ b/topics/sequence-analysis/tutorials/mapping/metadata.yaml
@@ -0,0 +1,30 @@
+title: "Mapping"
+type: "tutorial"
+name: "mapping"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- What two things are crucial for a correct mapping?
+- What is BAM?
+objectives:
+- You will learn what mapping is
+- A genome browser is shown that helps you to understand your data
+time_estimation: "1h"
+key_points:
+- Know your data!
+- Mapping is not trivial
+- There are many mapping algorithms, it depends on your data which one to choose
+
+maintainers:
+-
+ name: "Joachim Wolff"
+ github_username: "joachimwolff"
+ email: "wolffj@informatik.uni-freiburg.de"
+
+contributors:
+-
+ name: "Joachim Wolff"
+ github_username: "joachimwolff"
+ email: "wolffj@informatik.uni-freiburg.de"
diff --git a/topics/sequence-analysis/tutorials/quality-control/metadata.yaml b/topics/sequence-analysis/tutorials/quality-control/metadata.yaml
new file mode 100644
index 00000000000000..5eed0f1dfe1662
--- /dev/null
+++ b/topics/sequence-analysis/tutorials/quality-control/metadata.yaml
@@ -0,0 +1,72 @@
+title: "Quality Control"
+type: "tutorial"
+name: "quality-control"
+zenodo_link: ""
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- How to control quality of NGS data?
+- What are the quality parameters to check for each dataset?
+- How to improve the quality of a sequence dataset?
+objectives:
+- Manipulate FastQ files
+- Control quality from a FastQ file
+- Use FastQC tool
+- Understand FastQC output
+- Use tools for quality correction
+requirements:
+time_estimation: "1d/3h/6h"
+key_points:
+- Run quality control on every dataset before running any other bioinformatics analysis
+- Take care of the parameters used to improve the sequence quality
+- Re-run FastQC to check the impact of the quality control
+
+maintainers:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+
+references:
+-
+ authors: "Marco-Antonio Mendoza-Parra et al"
+ title: "A quality control system for profiles obtained by ChIP sequencing"
+ link: "http://nar.oxfordjournals.org/content/41/21/e196.short"
+ summary: "Presents an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS."
+-
+ authors: "Ana Conesa et al"
+ title: "A survey of best practices for RNA-seq data analysis"
+ link: "http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8"
+ summary: "Highlights the challenges associated with each step of RNA-seq data analysis."
+-
+ authors: "Yuval Benjamini1 et al"
+ title: "Summarizing and correcting the GC content bias in high-throughput sequencing"
+ link: "http://nar.oxfordjournals.org/content/40/10/e72.long"
+ summary: "Summarizes the many possible sourced of GC bias for deeply sequenced samples."
+-
+ authors: "David Sims et al"
+ title: "Sequencing depth and coverage: key considerations in genomic analyses"
+ link: "http://www.nature.com/nrg/journal/v15/n2/abs/nrg3642.html"
+ summary: "Discuss the issue of sequencing depth in the design of next-generation sequencing experiments."
+-
+ authors: "Frontiers in Genetics"
+ title: "Quality assessment and control of high-throughput sequencing data"
+ link: "http://journal.frontiersin.org/researchtopic/1683/quality-assessment-and-control-of-high-throughput-sequencing-data"
+ summary: "Collection of papers on quality controls for various NGS applications"
+-
+ authors: "Frazer Meacham et al"
+ title: "Identification and correction of systematic error in high-throughput sequence data"
+ link: "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-451"
+ summary: "Reviews and proposes correction for systematic base pair errors in deep sequencing"
+-
+ authors: "Guillaume Devailly et al"
+ title: "Heat seq: an interactive web tool for high-throughput sequencing experiment comparison with public data"
+ link: "http://biorxiv.org/content/early/2016/04/18/049254.abstract"
+ summary: "Presents a web-tool that allows genome scale comparison of high throughput experiments"
diff --git a/topics/sequence-analysis/tutorials/ref-based-rad-seq/metadata.yaml b/topics/sequence-analysis/tutorials/ref-based-rad-seq/metadata.yaml
new file mode 100644
index 00000000000000..2dac768b2e23d9
--- /dev/null
+++ b/topics/sequence-analysis/tutorials/ref-based-rad-seq/metadata.yaml
@@ -0,0 +1,187 @@
+title: "RAD-Seq Reference-based data analysis"
+type: "tutorial"
+name: "ref-based-rad"
+zenodo_link: "http://doi.org/10.5281/zenodo.218574"
+galaxy_tour: "ref-based-rad"
+hands_on: "yes"
+slides: "no"
+questions:
+- "How to analyze RAD sequencing data using a reference genome for a population genomics sutdy?"
+objectives:
+- "Analysis of RAD sequencing data using a reference genome"
+- "SNP calling from RAD sequencing data"
+- "Calculate population genomics statistics from RAD sequencing data"
+time_estimation: "1/2d"
+key_points:
+- "Simple sentence to sum up the first key point of the tutorial (Take home message)"
+- "Second key point"
+- "Third key point"
+- "..."
+
+requirements:
+-
+ title: "Mapping"
+ type: "internal"
+ link: "/NGS-mapping"
+-
+ title: "Trackster"
+ type: "internal"
+ link: "/Introduction/Trackster"
+
+maintainers:
+-
+ name: "Yvan Le Bras"
+ github_username: "yvanlebras"
+ email: "yvan.le-bras@mnhn.fr"
+
+contributors:
+-
+ name: "Yvan Le Bras"
+ github_username: "yvanlebras"
+ email: "yvan.le-bras@mnhn.fr"
+
+references:
+-
+ authors: "Amores, A., et al. 2011"
+ title: "Genome evolution and meiotic maps by massively parallel DNA sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21828280"
+
+-
+ authors: "Catchen, J. M. et al. 2011"
+ title: "Stacks: building and genotyping loci de novo from short-read sequences"
+ link: "http://www.g3journal.org/content/1/3/171.full"
+
+-
+ authors: "Davey, J. W., et al. 2011"
+ title: "Genome-wide genetic marker discovery and genotyping using next-generation sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21681211"
+
+-
+ authors: "Etter, P. D., et al. 2011"
+ title: "SNP Discovery and Genotyping for Evolutionary Genetics using RAD sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658458/"
+
+-
+ authors: "Ekblom, R., and J. Galindo. 2010"
+ title: "Applications of next generation sequencing in molecular ecology of non-model organisms"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21139633"
+
+-
+ authors: "Hohenlohe, P. A. et al. 2010"
+ title: "Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags"
+ link: "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000862"
+
+-
+ authors: "Gompert, Z., and C. A. Buerkle. 2011a"
+ title: "A hierarchical Bayesian model for next-generation population genomics"
+ link: "http://www.genetics.org/content/187/3/903"
+
+-
+ authors: "Gompert, Z., and C. A. Buerkle. 2011b"
+ title: "Bayesian estimation of genomic clines"
+ link: "http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05074.x/abstract"
+
+-
+ authors: "Lynch, M. 2009"
+ title: "Estimation of allele frequencies from high-coverage genome-sequencing projects"
+ link: "http://www.genetics.org/content/182/1/295"
+
+-
+ authors: "Nielsen, R., et al. 2005"
+ title: "Genomic scans for selective sweeps using SNP data"
+ link: "http://genome.cshlp.org/content/15/11/1566.abstract"
+
+-
+ authors: "Hohenlohe, P. A., et al. 2010"
+ title: "Using population genomics to detect selection in natural populations: Key concepts and methodological considerations"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21218185"
+
+-
+ authors: "Stapley, J., et al. 2010"
+ title: "Adaptation genomics: the next generation"
+ link: "http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00216-8"
+
+-
+ authors: "Luikart, G.,et al. 2003"
+ title: "The power and promise of population genomics: from genotyping to genome typing"
+ link: "http://www.nature.com/nrg/journal/v4/n12/full/nrg1226.html"
+
+-
+ authors: "Nielsen, R., et al. 2011"
+ title: "Genotype and SNP calling from next-generation sequencing data"
+ link: "http://www.nature.com/nrg/journal/v12/n6/full/nrg2986.html"
+
+-
+ authors: "Altshuler, D., et al. 2000"
+ title: "An SNP map of the human genome generated by reduced representation shotgun sequencing"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/11029002"
+
+-
+ authors: "Baxter, S. W., et al. 2011"
+ title: "Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019315"
+
+-
+ authors: "Chutimanitsakun, Y., et al. 2011"
+ title: "Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley"
+ link: "http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-4"
+
+-
+ authors: "Gore, M. A., et al. 2009"
+ title: "A first-generation haplotype map of maize"
+ link: "http://science.sciencemag.org/content/326/5956/1115"
+
+-
+ authors: "Baird, N. A., et al. 2008"
+ title: "Rapid SNP discovery and genetic mapping using sequenced RAD markers"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376"
+
+-
+ authors: "Emerson, K. J., et al. 2010"
+ title: "Resolving postglacial phylogeography using high-throughput sequencing"
+ link: "http://www.pnas.org/content/107/37/16196"
+
+-
+ authors: "Etter, P. D., et al. 2011"
+ title: "Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018561"
+
+-
+ authors: "Hohenlohe, P. A., et al. 2011"
+ title: "Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21429168"
+
+-
+ authors: "Miller, M. R., et al. 2007"
+ title: "Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/17189378"
+
+-
+ authors: "Willing, E. M., et al. 2011"
+ title: "Paired-end RAD-seq for de novo assembly and marker design without available reference"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21712251"
+
+-
+ authors: "Andolfatto, P., et al. 2011"
+ title: "Multiplexed shotgun genotyping for rapid and efficient genetic mapping"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/21233398"
+
+-
+ authors: "Elshire, R. J., et al. 2011"
+ title: "A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379"
+
+-
+ authors: "Rigola, D., et al. 2009"
+ title: "High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology"
+ links: (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004761"
+
+-
+ authors: "van Orsouw, N. J., et al. 2007"
+ title: "Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes"
+ link: "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001172"
+
+-
+ authors: "van Tassell, C. P., et al. 2008"
+ title: "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries"
+ link: "https://www.ncbi.nlm.nih.gov/pubmed/18297082"
diff --git a/topics/training/metadata.yaml b/topics/training/metadata.yaml
index 45f92275c502b0..81813a13bd6b80 100644
--- a/topics/training/metadata.yaml
+++ b/topics/training/metadata.yaml
@@ -10,12 +10,7 @@ material:
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
--
+-
title: "Creating a new tutorial - Writing content in markdown"
type: "tutorial"
name: "create-new-tutorial-content"
@@ -34,20 +29,7 @@ material:
- "Finding good training datasets is hard!"
- "You can highlight questions, tools and hints with a special syntax"
- "Self-learning can be done by questions and hidden answers"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
--
+-
title: "Creating a new tutorial - Defining metadata"
type: "tutorial"
name: "create-new-tutorial-metadata"
@@ -67,20 +49,7 @@ material:
- "Metadata are useful to find the tutorial and generate the webpage"
- "Learning objectives, time estimation and other pedagogic metadata are helpful for the instructors"
- "Learning objectives and other pedagogic metadata should be filled before starting developing the tutorial to know where to go"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
--
+-
title: "Creating a new tutorial - Setting up the infrastructure"
type: "tutorial"
name: "create-new-tutorial-jekyll"
@@ -97,19 +66,6 @@ material:
time_estimation: "15min"
key_points:
- "Checking the generated website can be done locally"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Creating a new tutorial - Creating Interactive Galaxy Tours"
@@ -129,20 +85,7 @@ material:
key_points:
- "The Interactive Tours are a good training object for self-learning at its own speed"
- "It is now easy to create an Interactive Tour and test it"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
--
+-
title: "Creating a new tutorial - Building a Docker flavor for a tutorial"
type: "tutorial"
name: "create-new-tutorial-docker"
@@ -164,20 +107,7 @@ material:
- "Tools, data and workflows can be easily integrated in a Docker flavor to have a useful technical support for a tutorial"
- "A Galaxy Docker flavor is a great support for training"
- "A Galaxy Docker flavor can be deployed 'anywhere' and is scalable"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
--
+-
title: "Good practices to run a workshop"
type: "tutorial"
name: "good-practices"
@@ -194,19 +124,6 @@ material:
key_points:
- "Prepare your workshop"
- "Take care of your trainees"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: "bjoern.gruening@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
maintainers:
-
@@ -217,3 +134,13 @@ maintainers:
name: "Björn Grüning"
github_username: "bgruening"
email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
diff --git a/topics/training/tutorials/good-practices/metadata.yaml b/topics/training/tutorials/good-practices/metadata.yaml
new file mode 100644
index 00000000000000..205a320d31f840
--- /dev/null
+++ b/topics/training/tutorials/good-practices/metadata.yaml
@@ -0,0 +1,36 @@
+title: "Good practices to run a workshop"
+type: "tutorial"
+name: "good-practices"
+zenodo_link:
+galaxy_tour:
+hands_on: "no"
+slides: "yes"
+questions:
+- "What do we need to take care when running a workshop?"
+- "What are the good practices?"
+objectives:
+- "Reflect on the things to do before, during and after a workshop"
+time_estimation: "1h/1d"
+key_points:
+- "First take home message"
+- "Second take home message"
+- "Third take home message"
+maintainers:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
+
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Björn Grüning"
+ github_username: "bgruening"
+ email: "bjoern.gruening@gmail.com"
\ No newline at end of file
diff --git a/topics/transcriptomics/metadata.yaml b/topics/transcriptomics/metadata.yaml
index ccf0fee481cd15..4c0a3e675f0248 100644
--- a/topics/transcriptomics/metadata.yaml
+++ b/topics/transcriptomics/metadata.yaml
@@ -1,8 +1,10 @@
-name: "transcriptomics"
+name: "transcriptomics"
type: "use"
title: "Transcriptomics"
summary: "Training material for all kinds of transcriptomics analysis."
docker_image: ""
+status: ""
+
requirements:
-
title: "Galaxy introduction"
@@ -18,23 +20,6 @@ material:
title: "Introduction"
type: "introduction"
slides: "yes"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Anika Exleben"
- github_username: "erxleben"
- email: ""
- -
- name: "Markus Wolfien"
- github_username: "mwolfien"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "De novo transcriptome reconstruction with RNA-seq"
type: "tutorial"
@@ -55,23 +40,6 @@ material:
- "De novo transcriptome reconstruction is the ideal approach for identifying differentially expressed known and novel transcripts."
- "Differential gene expression testing is improved with the use of replicate experiments and deep sequence coverage."
- "Visualizing data on a genome browser is a great way to display interesting patterns of differential expression."
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Mallory Freeberg"
- github_username: "malloryfreeberg"
- email: "mallory.freeberg@gmail.com"
- -
- name: "Mo Heydarian"
- github_username: "MoHeydarian"
- email: "mheydarian@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Reference-based RNA-seq data analysis"
type: "tutorial"
@@ -92,35 +60,6 @@ material:
- "Using a spliced mapping tool for eukaryotic RNA seq data"
- "Running a differential gene expression with taking care of the factors to study"
- "Running a differential exon usage with taking care of the factors to study"
- contributors:
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Mallory Freeberg"
- github_username: "malloryfreeberg"
- email: "mallory.freeberg@gmail.com"
- -
- name: "Mo Heydarian"
- github_username: "MoHeydarian"
- email: "mheydarian@gmail.com"
- -
- name: "Anika Exleben"
- github_username: "erxleben"
- email: ""
- -
- name: "Pavankumar Videm"
- github_username: "pavanvidem"
- email: ""
- -
- name: "Clemens Blank"
- github_username: "blankclemens"
- email: ""
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
title: "Differential abundance testing of small RNAs"
type: "tutorial"
@@ -141,23 +80,6 @@ material:
key_points:
- "Analysis of small RNAs is complex due to the diversity of small RNA subclasses."
- "Both alignment to references and transcript quantification approaches are useful for small RNA-seq analyses."
- contributors:
- -
- name: "Mallory Freeberg"
- github_username: "malloryfreeberg"
- email: "mallory.freeberg@gmail.com"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
- -
- name: "Bérénice Batut"
- github_username: "bebatut"
- email: "berenice.batut@gmail.com"
- -
- name: "Björn Grüning"
- github_username: "bgruening"
- email: ""
maintainers:
-
@@ -169,6 +91,20 @@ maintainers:
github_username: "malloryfreeberg"
email: "mallory.freeberg@gmail.com"
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: "mallory.freeberg@gmail.com"
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: "mheydarian@gmail.com"
+
references:
-
authors: "Shirley Pepke et al"
diff --git a/topics/transcriptomics/tutorials/de-novo/metadata.yaml b/topics/transcriptomics/tutorials/de-novo/metadata.yaml
new file mode 100644
index 00000000000000..417cf3660d944c
--- /dev/null
+++ b/topics/transcriptomics/tutorials/de-novo/metadata.yaml
@@ -0,0 +1,51 @@
+title: "De novo transcriptome reconstruction with RNA-seq"
+type: "tutorial"
+name: "de-novo"
+zenodo_link: "https://zenodo.org/record/254485#.WKODmRIrKRu"
+galaxy_tour: "..."
+hands_on: "yes"
+slides: "no"
+questions:
+- "What genes are differentially expressed between G1E cells and megakaryocytes?"
+- "How can we generate a transcriptome de novo from RNA sequencing data?"
+objectives:
+- "Analysis of RNA sequencing data using a reference genome"
+- "Reconstruction of transcripts without reference transcriptome (de novo)"
+- "Analysis of differentially expressed genes"
+time_estimation: "6h"
+key_points:
+- "De novo transcriptome reconstruction is the ideal approach for identifing differentially expressed known and novel transcripts."
+- "Differential gene expression testing is improved with the use of replicate experiments and deep sequence coverage."
+- "Vizualizing data on a genome browser is a great way to display interesting patterns of differential expression."
+requirements:
+-
+ title: "Mapping"
+ type: "internal"
+ link: "/NGS-mapping"
+-
+ title: "Trackster"
+ type: "external"
+ link: "https://wiki.galaxyproject.org/Learn/Visualization"
+maintainers:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Maintainer 2"
+ github_username: "maintainer2"
+ email: "maintainer2@maintainer2.com"
+
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: "mallory.freeberg@gmail.com"
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: "mheydarian@gmail.com"
diff --git a/topics/transcriptomics/tutorials/ref-based/metadata.yaml b/topics/transcriptomics/tutorials/ref-based/metadata.yaml
new file mode 100644
index 00000000000000..ad8f6f7eab76b0
--- /dev/null
+++ b/topics/transcriptomics/tutorials/ref-based/metadata.yaml
@@ -0,0 +1,51 @@
+title: "Reference-based RNA-seq data analysis"
+type: "tutorial"
+name: "ref-based"
+zenodo_link: "https://zenodo.org/record/290221"
+galaxy_tour: "ref_based_rna_seq"
+hands_on: "yes"
+slides: "no"
+questions:
+- "What are the effects of Pasilla (PS) gene depletion on splicing events?"
+- "How to analyze RNA sequencing data using a reference genome?"
+objectives:
+- "Analysis of RNA sequencing data using a reference genome"
+- "Analysis of differentially expressed genes"
+- "Identification of functional enrichment among differentially expressed genes"
+time_estimation: "1d"
+key_points:
+- "Using a spliced mapping tool for eukaryotic RNA seq data"
+- "Running a differential gene expression with taking care of the factors to study"
+- "Running a differential exon usage with taking care of the factors to study"
+requirements:
+-
+ title: "Mapping"
+ type: "internal"
+ link: "/NGS-mapping"
+-
+ title: "IGV"
+ type: "internal"
+ link: "/Introduction/IGV"
+maintainers:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Maintainer 2"
+ github_username: "maintainer2"
+ email: "maintainer2@maintainer2.com"
+
+contributors:
+-
+ name: "Bérénice Batut"
+ github_username: "bebatut"
+ email: "berenice.batut@gmail.com"
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: "mallory.freeberg@gmail.com"
+-
+ name: "Mo Heydarian"
+ github_username: "MoHeydarian"
+ email: "mheydarian@gmail.com"
diff --git a/topics/transcriptomics/tutorials/srna/metadata.yaml b/topics/transcriptomics/tutorials/srna/metadata.yaml
new file mode 100644
index 00000000000000..c9afdeb60950a3
--- /dev/null
+++ b/topics/transcriptomics/tutorials/srna/metadata.yaml
@@ -0,0 +1,38 @@
+title: "Differential abundance testing of small RNAs"
+type: "tutorial"
+name: "srna"
+zenodo_link: "url to Zenodo with input data"
+galaxy_tour: ""
+hands_on: "yes"
+slides: "no"
+questions:
+- "What small RNAs are expressed?"
+- "What RNA features have significantly different numbers of small RNAs targeting them between two conditions?"
+objectives:
+- "Process small RNA-seq datasets to determine quality and reproducibility."
+- "Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets."
+- "Differentiate between subclasses of small RNAs based on their characteristics."
+- "Identify differently abundant small RNAs and their targets."
+time_estimation: "3h"
+key_points:
+- "Analysis of small RNAs is complex due to the diversity of small RNA subclasses."
+- "Both alignment to references and transcript quantification approaches are useful for small RNA-seq analyses."
+maintainers:
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: "mallory@galaxyproject.org"
+-
+ name: "Maintainer"
+ github_username: "maintainer"
+ email: "maintainer@galaxy.org"
+
+contributors:
+-
+ name: "Mallory Freeberg"
+ github_username: "malloryfreeberg"
+ email: "mallory@galaxyproject.org"
+-
+ name: "Contributor"
+ github_username: "contributor"
+ email: "contributor@galaxy.org"
diff --git a/topics/usegalaxy/metadata.yaml b/topics/usegalaxy/metadata.yaml
index 9f052f00387292..a182d08d70eb5a 100644
--- a/topics/usegalaxy/metadata.yaml
+++ b/topics/usegalaxy/metadata.yaml
@@ -27,16 +27,8 @@ material:
- "Gain understanding on navigating and manipulating histories"
time_estimation: "30 min"
key_points:
- contributors:
- -
- name: "Anton Nekrutenko"
- github_username: "nekrut"
- email: "anton@nekrut.org"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
-
+ requirements:
+ references: ""
-
title: "Using dataset collection"
type: "tutorial"
@@ -52,15 +44,8 @@ material:
- "Understand and master dataset collections"
time_estimation: "30 min"
key_points:
- contributors:
- -
- name: "Anton Nekrutenko"
- github_username: "nekrut"
- email: "anton@nekrut.org"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ requirements:
+ references: ""
-
title: "NGS data logistics"
type: "tutorial"
@@ -76,15 +61,8 @@ material:
- "Learn about Fastq, SAM, and BAM."
time_estimation: "30 min"
key_points:
- contributors:
- -
- name: "Anton Nekrutenko"
- github_username: "nekrut"
- email: "anton@nekrut.org"
- -
- name: "Saskia Hiltemann"
- github_username: "shiltemann"
- email: ""
+ requirements:
+ references: ""
-
title: "Calling variants in non-diploid systems"
type: "tutorial"
@@ -104,15 +82,8 @@ material:
- "Nucleotide variants in haploid systems may have any frequency between 0 and 1."
- "Distinguishing true variants from noise is not easy and requires accounting