-
Notifications
You must be signed in to change notification settings - Fork 13
/
Copy pathsessions.yaml
244 lines (216 loc) · 9.85 KB
/
sessions.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
# Sessions specifiy small modules of multiple videos on the same topic, often taught as a unit
# For example, a lecture video and a hands-on video of the same GTN tutorial
#
webinars:
title: "Webinar Series: Galaxy Resources For.."
description: In this webinar series, we cover resources for different types of Galaxy users and audiences.
videos:
- webinar/researchers
- webinar/educators
- webinar/tooldevs
- webinar/admins
tb-webinars:
title: "Webinar series: Concepts of drug-resistance prediction and mutation-based clustering"
videos:
- webinar/tb-drug-resistance
- webinar/tb-phylogenetic-mutations
- webinar/tb-clustering
- webinar/tb-genetic-distance
sequence-analysis/quality-control:
title: Quality Control
description: In this sesssion, we will walk you through the basics of quality checking your sequencing data. This session consists of a lecture followed by a hands-on tutorial.
videos:
- sequence-analysis/quality-control/slides
- sequence-analysis/quality-control/tutorial
sequence-analysis/mapping:
title: Mapping
description: In this sesssion, we will walk you through the basics of mapping your sequencing data to a reference genome. This session consists of a lecture followed by a hands-on tutorial.
videos:
- sequence-analysis/mapping/slides
- sequence-analysis/mapping/tutorial
assembly:
title: Genome Assembly
description: This session provides an introduction to Genome Assembly
videos:
- assembly/general-introduction/slides
- assembly/chloroplast-assembly/tutorial
variant-analysis/tb-variant-analysis:
title: Tuberculosis Variant Analysis
description: Variation in the genome of M. tuberculosis (Mtb) is associated with
changes in phenotype, for example drug resistance and virulence. It is also useful
for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a
sample can be used to build a phylogeny.
videos:
- variant-analysis/tb-variant-analysis/slides
- variant-analysis/tb-variant-analysis/tutorial
epigenetics/atac-seq:
title: "Epigenetics: ATAC-Seq"
description: |
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. This session will introduce ATAC-Seq and walk you through an analysis step by step.
videos:
- epigenetics/atac-seq/slides
- epigenetics/atac-seq/tutorial
single-cell/scrna-intro:
title: Introduction to Single-Cell RNA-seq Data Analysis
description: |
Single-cell RNA-seq analysis is a rapidly evolving field at the forefront
of transcriptomic research, used in high-throughput developmental studies
videos:
- single-cell/scrna-intro/slides
- single-cell/scrna-case_basic-pipeline/tutorial
transcriptomics/mirna-target-finder:
title: Whole transcriptome analysis of Arabidopsis thaliana
description: |
In plants, miRNAs can silence targets through RNA degradation as well as translational repression pathways, and unlike animals, a large proportion of miRNA and their targets have less than four mismatches. This feature has been exploited for developing miRNAs target prediction tools, providing an efficient approach to elucidate the miRNA-mediated regulatory networks, which can contribute to biotechnological solutions to improve crops productivity.
videos:
- transcriptomics/mirna-target-finder/slides
- transcriptomics/mirna-target-finder/tutorial
climate/fates:
title: Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
description: This session will provide a brief overview of FATES, and guide you through a Galaxy analysis step by step.
videos:
- climate/fates/slides
- climate/fates/tutorial
genome-annotation/annotation-with-prokka:
title: Genome Annotation with Prokka
description: This tutorial will introduce genome annotation process and give you hands-on experience with annotating a prokaryotic genome using Prokka.
videos:
- genome-annotation/annotation-with-prokka/slides
- genome-annotation/annotation-with-prokka/tutorial
genome-annotation/apollo:
title: Genome Annotation with Apollo
description: This session will introduce the Apollo genome annotation platform, and provide you hands-on experience with using Apollo in Galaxy.
videos:
- genome-annotation/apollo/slides
- genome-annotation/apollo/tutorial
genome-annotation/crispr-screen:
title: CRISPR Screen Analysis
description: This lecture will introduce the basic concepts involved in CRISPR screen analysis.
videos:
- genome-annotation/crispr-screen/slides
- genome-annotation/crispr-screen/tutorial
proteomics/encyclopedia:
title: EncyclopeDIA
description: |
Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the
reproducibility and throughput of proteomics studies. EncyclopeDIA is library search engine comprised of
several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries
or DIA-based chromatogram libraries.
videos:
- proteomics/encyclopedia/slides
- proteomics/encyclopedia/tutorial
proteomics/protegenomics:
title: ProteoGenomics
description: |
Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and
transcriptomics to aid in the discovery and identification of peptides
videos:
- proteomics/proteogenomics-dbcreation/tutorial
- proteomics/proteogenomics-dbsearch/tutorial
- proteomics/proteogenomics-novel-peptide-analysis/tutorial
microbiome/mothur-miseq-sop-short:
title: 16S taxonomic profiling
description: |
To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene
is often used. This allows us to identify the bacterial species present in our sample.
This lecture and practical session introduces you to 16S analysis in Galaxy using the
mothur tool suite.
videos:
- microbiome/introduction/slides
- microbiome/mothur-miseq-sop-short/tutorial
microbiome/nanopore:
title: Microbiome Analysis using Nanopore Sequencing
description: |
In this 3-part module, you will learn about Nanopore long-read sequencing for the
detection of antimicrobial resistance (AMR). There is a short video showing you the
wetlab steps involved in using the MinION sequencer. A talk about the clinical applications,
and finally a practical tutorial walking you through an AMR analysis in Galaxy.
videos:
- wetlab/miseq/demo
- microbiome/clinical-applications
- microbiome/plasmid-metagenomics-nanopore/tutorial
statistics/deeplearning:
title: Deep Learning Demystified
description: |
This 3-part session will introduce you to the world of deep learning and cover Feedforward
Neural Networks (FNN), Recurrent Neural Networks (FNN), and Convolutional Neural Networks
(CNN).
videos:
- statistics/FNN
- statistics/RNN
- statistics/CNN
galaxy-interface/ncbi-sarf:
title: SRA Aligned read format in Galaxy
description: This session will introduce the SRA Aligned Read format, and show you how to use this in Galaxy to analyze a SARS-CoV-2 dataset.
videos:
- galaxy-interface/ncbi-sarf/slides
- galaxy-interface/ncbi-sarf/tutorial
dev/architecture:
title: Galaxy Code Architecture Lecture Series
description: In this 9-part Lecture series, John Chilton will walk you through the Galaxy Code Architecture.
videos:
- dev/architecture/slides-ecosystem
- dev/architecture/slides-models-managers
- dev/architecture/slides-app-di
- dev/architecture/slides-project-management
- dev/architecture/slides-web-client
- dev/architecture/slides-pluggable-components
- dev/architecture/slides-principles
- dev/architecture/slides-web-requests
- dev/architecture/slides-files-directories
dev/debugging/tutorial:
title: Debugging Galaxy
description: This series of videos will guide (future) Galaxy contributors through the process of debugging Galaxy.
videos:
- dev/debugging/tutorial/intro
- dev/debugging/tutorial/unit-test-failure
- dev/debugging/tutorial/api-test-failure
- dev/debugging/tutorial/client-unit-test
- dev/debugging/tutorial/client-linter
- dev/debugging/tutorial/selenium
- dev/debugging/tutorial/runtime-error
- dev/debugging/tutorial/summary
galaxy/r:
title: Using R in Galaxy
description: Want a bit more control over your Analyses? You can run R in Rstudio directly within Galaxy
videos:
- data-science/rstudio-galaxy
- data-science/r-basics/tutorial
- data-science/r-advanced/tutorial
visualisation/circos:
title: Visualisation with Circos
description: |
Circos (Krzywinski et al. 2009) is a software package for visualizing data in a circular layout. This makes Circos ideal for exploring relationships between objects or positions. Circos plots have appeared in thousands of scientific publications. Although originally designed for visualizing genomic data, it can create figures from data in any field.
videos:
- visualisation/circos/slides
- visualisation/circos/tutorial
admin/ansible:
title: Ansible
description: Here you'll learn the basics of Ansible
videos:
- admin/ansible/slides
- admin/ansible/tutorial
admin/cvmfs:
title: CVMFS
description: Reference data management is easier than ever with CVMFS
videos:
- admin/cvmfs/slides
- admin/cvmfs/tutorial
admin/pulsar:
title: Pulsar
description: Remote compute made possible with Pulsar
videos:
- admin/pulsar/slides
- admin/pulsar/tutorial
admin/monitoring:
title: Monitoring
description: Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.
videos:
- admin/monitoring/slides
- admin/monitoring/tutorial
admin/tool-management:
title: Tool Management
description: Learn how to install and manage tools in Galaxy
videos:
- admin/tool-management/slides
- admin/tool-management/tutorial