diff --git a/lectures/containers/containers.Rmd b/lectures/containers/containers.Rmd
deleted file mode 100644
index 574f19f0..00000000
--- a/lectures/containers/containers.Rmd
+++ /dev/null
@@ -1,286 +0,0 @@
----
-title: "Containerization with Docker and Singularity"
-subtitle: "Tools for Reproducible Research NBIS course"
-output:
- xaringan::moon_reader:
- self-contained: true
- seal: false
- css: ["default", "../template.css"]
- nature:
- slideNumberFormat: ""
----
-
-layout: true
-
-
-
----
-
-class: center, middle
-
-*Making self-contained, distributable projects with*
-
-.pull-left[
-
-
-
-]
-
-.pull-right[
-
-
-Singularity
-]
-
----
-# What is Docker?
-
-* Standardized packaging for software and dependencies
-* Docker lets you create and run applications securely isolated in a **container**, packaged with all its dependencies and libraries.
-
----
-
-# Docker in lifescience
-
-Docker containers can be used to allow others to reproduce a complete analysis:
-
-> To further support reproducibility, we bundled all tools and dependencies into one Docker container available on DockerHub [19]. *docker run* executes the aforementioned Makefile inside the container.
-
-.small[(click [here](https://github.com/metagenomics/2015-biogas-cebitec/blob/master/Dockerfile) to see the Dockerfile)]
-
-```bash
-docker run metagenomics/2015-biogas-cebitec
-```
-
-.small[Bremges *et al* GigaScience (2015) 4:33, [doi:10.1186/s13742-015-0073-6](https://doi.org/10.1186/s13742-015-0073-6)]
-
----
-
-# Docker in lifescience
-
-Docker can also be used to define software environments and settings for benchmarking studies
-
-[CAMI Challenge](https://data.cami-challenge.org/): an independent evaluation of several tools in the field of metagenomics
-
->... we defined standards for submitting the software itself, along with parameter settings and required databases and implemented them in Docker container templates...
-
-.small[
-Sczyrba *et al* Nature Methods (2017) 14:1063–1071, [doi.org/10.1038/nmeth.4458](https://doi.org/10.1038/nmeth.4458)
-]
-
----
-
-# Docker in lifescience
-
-Docker can also be used to define software environments and settings for benchmarking studies
-
-[2nd CAMI Challenge](https://www.microbiome-cosi.org/cami/cami/cami2)
-
-> For reproducibility, participants could submit a Docker container containing the complete workflow, a bioconda script or a software repository with detailed installation instructions...
-
-.small[
-Meyer *et al* Nature Methods (2022) 19:429-440,
-[https://doi.org/10.1038/s41592-022-01431-4](https://doi.org/10.1038/s41592-022-01431-4)
-]
-
----
-
-# Docker nomenclature
-
---
-
-* A Docker .green[file] is a recipe used to build a Docker .green[image]
-
---
-
-* A Docker .green[image] is a standalone executable package of software
-
---
-
-* A Docker .green[container] is a standard unit of software run on the Docker Engine.
-
---
-
-* .green[Docker Hub] is an online service for sharing docker images
-
----
-
-# Images and containers
-
-Example: Use a different OS
-
-.pull-right[]
-
---
-
-.pull-left[
-
-.small[Check OS on local machine]
-
-```bash
-$ uname -a
-Darwin johnsmbp.local 19.6.0 \
-Darwin Kernel Version 19.6.0: \
-Tue Jan 12 22:13:05 PST 2021; \
-root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64
-```
-
-.small[Pull Ubuntu (Linux) image]
-
-```bash
-$ docker pull ubuntu:16.04
-16.04: Pulling from library/ubuntu
-22dc81ace0ea: Pull complete
-...
-Digest: sha256:e348fbbea0e0a0e73ab0370de151e7800684445c509d46195aef73e090a49bd6
-Status: Downloaded newer image for ubuntu:16.04
-```
-
-.small[Run a container and check OS version]
-
-```bash
-$ docker run -it ubuntu:16.04
-root@407b0fd13fe5:/# uname -a
-Linux 407b0fd13fe5 4.9.60-linuxkit-aufs #1 SMP Mon Nov 6 16:00:12 UTC
-2017 x86_64 x86_64 x86_64 GNU/Linux
-```
-]
-
----
-
-# Mounting volumes
-
-
-`$ docker run -it -v $PWD/data:/home/data ubuntu:16.04`
-
-.pull-left[
-
-.tiny[Local project directory:]
-
-```
-$ ls project/
-
-|- doc/
-|
-|- data/
-| |- raw_external/
-| |- raw_internal/
-| |- meta/
-|
-|- code/
-|- notebooks/
-|
-|- intermediate/
-|- scratch/
-|- logs/
-|
-|- results/
-| |- figures/
-| |- tables/
-| |- reports/
-|
-|- Snakefile
-|- config.yml
-|- environment.yml
-|- Dockerfile
-```
-]
-.pull-right[
-.tiny[Docker image file system]
-```
-$ ls /
-
-|- bin/
-|- boot/
-|- dev/
-|- etc/
-|- home/
-| |- data/ # data folder mounted under home/
-| |- raw_external/
-| |- raw_internal/
-| |- meta/
-|- lib/
-|- lib64/
-|- media/
-|- opt/
-|- proc/
-|- root/
-|- run/
-|- sys/
-|- tmp/
-|- usr/
-|- var/
-```
-]
-
----
-
-# What can I use Docker for?
-
---
-
-* As an advanced .green[environment] manager
-
-```bash
-docker run -it -v $PWD:/home my_image /bin/bash
-```
-
---
-
-* To package your .green[code] with the .green[environment] it needs
-
-```bash
-docker run \
--v $PWD/data:/home/data \
--v $PWD/results:/home/results \
-my_image snakemake report.pdf
-```
-
---
-
-* To package a whole workflow with .green[environment], .green[code] and .green[data] (*e.g.* to accompany a manuscript).
-
-```bash
-docker run \
--v $PWD/results:/home/results \
-my_image snakemake report.pdf
-```
-
-* and much more...
-
----
-# What is Singularity?
-
-
-
-an open source container platform suitable for HPC clusters
-
-[https://sylabs.io/guides/latest/user-guide/](https://sylabs.io/guides/latest/user-guide/)
-
->Singularity was created to run complex applications on HPC clusters in a simple, portable, and reproducible way.
-
----
-# What is Apptainer?
-
-
-
-In 2021 Singularity joined the Linux Foundation and became Apptainer.
-
-The company Sylabs still maintains **Singularity**
-
----
-
-# Docker vs. Singularity
-
-| | |
-| ------ | ----------- |
-| runs as a daemon process with superuser privileges | runs as regular user |
-| images stored centrally | image files that you can move around. No layers! |
-| isolates the host and container file system by default | containers have access to host file system |
-| well supported on Mac/Linux/Windows | limited support on Mac/Windows |
-
----
-
-class: center, middle
-
-# Questions?
diff --git a/lectures/containers/containers.html b/lectures/containers/containers.html
new file mode 100644
index 00000000..ff9d1f7e
--- /dev/null
+++ b/lectures/containers/containers.html
@@ -0,0 +1,2623 @@
+
+
+
+
+
+
+
+
+
+
+
+
+ Working with containers
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Working with containers
+
+
+
+
+
+
+
What is Docker?
+
+
+
Standardized packaging for software, dependencies as well as the operating system
+
Docker lets you create and run applications securely isolated in containers
+
+
+
+
+
Docker in life science
+
Docker containers can be used to allow others to reproduce a complete analysis:
+
+
To further support reproducibility, we bundled all tools and dependencies into one Docker container available on DockerHub. docker run executes the aforementioned Makefile inside the container. 1
+
+
+
+
Reproducing the paper can now be done with one command:
+
docker run metagenomics/2015-biogas-cebitec
+
+
+
+
Docker in life science
+
Docker can also be used to define software environments and settings for benchmarking studies:
+
+
CAMI Challenge: an independent evaluation of several tools in the field of metagenomics.
+
+
[…] We defined standards for submitting the software itself, along with parameter settings and required databases and implemented them in Docker container templates … 1
+
+
+
+
Docker in life science
+
Docker can also be used to define software environments and settings for benchmarking studies:
For reproducibility, participants could submit a Docker container containing the complete workflow, a Bioconda script or a software repository with detailed installation instructions […] 1
+
+
+
+
Docker nomenclature
+
+
+
A Docker image is a stand-alone executable package of software
+
A Docker container is an instance of a Docker image
+
A Dockerfile is a recipe used to build a Docker image
+
Docker Hub is an online service for hosting Docker images
+
+
+
+
+
+
+
+
+
+
+
+
An example: using a different OS
+
+
Check OS on local machine
+
$ uname -a
+Darwin johnsmbp.local 19.6.0 Darwin Kernel Version 19.6.0: [...] x86_64
+
+
+
Pull Ubuntu (Linux) image
+
$ docker pull ubuntu:16.04
+16.04: Pulling from library/ubuntu
+22dc81ace0ea: Pull complete
+...
+Digest: sha256:e348fbbea0e0a0e73ab0370de151e7800684445c509d46195aef73e090a49bd6
+Status: Downloaded image for ubuntu:16.04
+
+
+
Run the container interactively and check OS version
+
$ docker run -it ubuntu:16.04
+root@407b0fd13fe5:/## uname -a
+Linux 407b0fd13fe5 4.9.60-linuxkit-aufs [...] x86_64 GNU/Linux
To package a whole project with environment, code and data (e.g. to accompany a manuscript).
+
+
docker run \
+-v$PWD/results:/home/results \
+ my_image snakemake report.pdf
+
+
+
+
What is Singularity?
+
+
+
+
+
+
+
+
Another software for working with containers, similar to Docker
+
A Singularity image is contained in a single file, facilitating portability
+
Does not require root access, making it suitable for work at HPCs
+
+
+
+
+
What is Apptainer?
+
+
+
+
In 2021 Singularity joined the Linux Foundation and became Apptainer.
+
The company Sylabs still maintains Singularity as a commercial piece of software.
+
SingularityCE is an Open Source project supported by Sylabs.
+
The three versions are similar today, but will diverge with time.
+
Apptainer is the most commonly adopted version of the scientific community.
+
+
+
+
+
Docker vs. Apptainer
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Runs as a daemon process with superuser privileges
+
Runs as a regular user
+
+
+
Images stored centrally
+
Image files that you can move around.
+
+
+
Isolates the host and container file system by default
+
Containers have access to host file system
+
+
+
Well-supported on Mac, Linux and Windows
+
Limited support on Mac and Windows
+
+
+
+
+
+
Questions?
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/lectures/containers/containers.pdf b/lectures/containers/containers.pdf
deleted file mode 100644
index 8a10bdc1..00000000
Binary files a/lectures/containers/containers.pdf and /dev/null differ
diff --git a/lectures/containers/containers.qmd b/lectures/containers/containers.qmd
new file mode 100644
index 00000000..db819bfd
--- /dev/null
+++ b/lectures/containers/containers.qmd
@@ -0,0 +1,238 @@
+---
+title: 'Working with containers
+
+
+ '
+format: nbis-revealjs
+---
+
+## What is [Docker]{.green}?
+
+::: {.incremental}
+- Standardized packaging for software, dependencies as well as the operating
+ system
+- Docker lets you create and run applications securely isolated in
+ [containers]{.green}
+:::
+
+## Docker in life science
+
+Docker containers can be used to allow others to reproduce a complete analysis:
+
+> To further support reproducibility, we bundled all tools and dependencies into
+> one Docker container available on DockerHub. `docker run` executes the
+> aforementioned Makefile inside the container. ^[_Bremges et al GigaScience
+> (2015) 4:33, [doi:10.1186/s13742-015-0073-6](https://doi.org/10.1186/s13742-015-0073-6)_]
+
+
+
+::: {.fragment}
+Reproducing the paper can now be done with one command:
+```bash
+docker run metagenomics/2015-biogas-cebitec
+```
+:::
+
+## Docker in life science
+
+Docker can also be used to define software environments and settings for
+benchmarking studies:
+
+
+
+[CAMI Challenge](https://data.cami-challenge.org/): an independent evaluation of
+several tools in the field of metagenomics.
+
+> [...] We defined standards for submitting the software itself, along with
+> parameter settings and required databases and implemented them in Docker
+> container templates ... ^[_Sczyrba et al Nature Methods (2017) 14:1063–1071,
+> [doi.org/10.1038/nmeth.4458](https://doi.org/10.1038/nmeth.4458)_]
+
+## Docker in life science
+
+Docker can also be used to define software environments and settings for
+benchmarking studies:
+
+
+
+[2nd CAMI Challenge](https://www.microbiome-cosi.org/cami/cami/cami2)
+
+> For reproducibility, participants could submit a Docker container containing
+> the complete workflow, a Bioconda script or a software repository with
+> detailed installation instructions [...] ^[_Meyer et al Nature Methods (2022)
+> 19:429-440, [https://doi.org/10.1038/s41592-022-01431-4](https://doi.org/10.1038/s41592-022-01431-4)_]
+
+## Docker nomenclature
+
+::: {.incremental}
+- A Docker [image]{.green} is a stand-alone executable package of software
+- A Docker [container]{.green} is an instance of a Docker image
+- A [Dockerfile]{.green} is a recipe used to build a Docker image
+- [Docker Hub]{.green} is an online service for hosting Docker images
+:::
+
+::: {.fragment}
+{height=350 fig-align="center"}
+:::
+
+## An example: using a different OS
+
+::: {.fragment}
+Check OS on local machine
+```{.bash code-line-numbers="|1|2"}
+$ uname -a
+Darwin johnsmbp.local 19.6.0 Darwin Kernel Version 19.6.0: [...] x86_64
+```
+:::
+
+::: {.fragment}
+Pull Ubuntu (Linux) image
+```{.bash code-line-numbers="|1|2-6"}
+$ docker pull ubuntu:16.04
+16.04: Pulling from library/ubuntu
+22dc81ace0ea: Pull complete
+...
+Digest: sha256:e348fbbea0e0a0e73ab0370de151e7800684445c509d46195aef73e090a49bd6
+Status: Downloaded image for ubuntu:16.04
+```
+:::
+
+::: {.fragment}
+Run the container interactively and check OS version
+```{.bash code-line-numbers="|1|2|3"}
+$ docker run -it ubuntu:16.04
+root@407b0fd13fe5:/## uname -a
+Linux 407b0fd13fe5 4.9.60-linuxkit-aufs [...] x86_64 GNU/Linux
+```
+:::
+
+## Mounting volumes
+
+:::: {.columns height=90%}
+
+::: {.column}
+::: {.fragment}
+Local `project/` directory:
+```{.bash code-line-numbers="1|2-16|3-6"}
+$ ls
+|- doc/
+|- data/
+| |- raw_external/
+| |- raw_internal/
+| |- meta/
+|- code/
+|- notebooks/
+|- intermediate/
+|- scratch/
+|- logs/
+|- results/
+|- Snakefile
+|- config.yml
+|- environment.yml
+|- Dockerfile
+```
+:::
+:::
+
+::: {.column}
+::: {.fragment}
+Docker container file system:
+```{.bash code-line-numbers="1-3|4-16|7-11"}
+$ docker run \
+ -v $PWD/data:/home/data \
+ ubuntu:16.04 ls
+|- bin/
+|- dev/
+|- etc/
+|- home/
+| |- data/
+| |- raw_external/
+| |- raw_internal/
+| |- meta/
+|- lib/
+|- opt/
+|- run/
+|- sys/
+|- usr/
+```
+:::
+:::
+
+::::
+
+## What can I use Docker for?
+
+::: {.fragment}
+- As an advanced [environment]{.green} manager
+
+```bash
+docker run -it -v $PWD:/home my_image /bin/bash
+```
+:::
+
+::: {.fragment}
+- To package your [code]{.green} with the environment it needs
+
+```bash
+docker run \
+ -v $PWD/data:/home/data \
+ -v $PWD/results:/home/results \
+ my_image snakemake report.pdf
+```
+:::
+
+::: {.fragment}
+- To package a [whole project]{.green} with environment, code and data (_e.g._
+ to accompany a manuscript).
+
+```bash
+docker run \
+ -v $PWD/results:/home/results \
+ my_image snakemake report.pdf
+```
+:::
+
+## What is Singularity?
+
+{height=250 fig-align=center}
+
+::: {.incremental}
+- Another software for working with containers, similar to Docker
+- A Singularity image is contained in a single file, facilitating portability
+- Does not require `root` access, making it suitable for work at HPCs
+:::
+
+## What is Apptainer?
+
+{fig-align=center}
+
+::: {.incremental}
+- In 2021 Singularity joined the Linux Foundation and became
+ [Apptainer]{.green}.
+- The company [Sylabs]{.green} still maintains Singularity as a commercial
+piece of software.
+- [SingularityCE]{.green} is an Open Source project supported by Sylabs.
+- The three versions are similar today, but will diverge with time.
+- [Apptainer]{.green} is the most commonly adopted version of the scientific
+ community.
+:::
+
+## Docker vs. Apptainer
+
+:::: {.columns}
+::: {.column}
+{height=150 fig-align=center}
+:::
+::: {.column}
+{height=150 fig-align=center}
+:::
+::::
+
+| | |
+| ------------------------------------------------------- | -------------------------------------------------------- |
+| Runs as a daemon process with superuser privileges | Runs as a regular user |
+| Images stored centrally | Image files that you can move around. |
+| Isolates the host and container file system by default | Containers have access to host file system |
+| Well-supported on Mac, Linux and Windows | Limited support on Mac and Windows |
+
+# Questions?
diff --git a/lectures/containers/images/docker-logo.webp b/lectures/containers/images/docker-logo.webp
new file mode 100644
index 00000000..88bd2d7d
Binary files /dev/null and b/lectures/containers/images/docker-logo.webp differ
diff --git a/lectures/containers/template.css b/lectures/containers/template.css
deleted file mode 100644
index 47a1ac43..00000000
--- a/lectures/containers/template.css
+++ /dev/null
@@ -1,124 +0,0 @@
-/* CSS style general NBIS presentations using Xaringen and RMarkdown */
-
-/* Import Google font */
-@import url('https://fonts.googleapis.com/css?family=Open+Sans&display=swap');
-
-/* Fonts */
-body,p,h1,h2,h3,h4,h5,h6 {
- font-family: 'Open Sans', sans-serif;
- font-weight: 400;
- font-size: 20px;
- color: #333333;
-}
-
-/* Header 1 font size */
-h1 {
- font-size: 1.7em !important;
-}
-
-/* Header 2 font size */
-h2 {
- font-size: 1.2em !important;
-}
-
-/* Header 3 font size */
-h3 {
- font-size: 0.9em !important;
-}
-
-/* Custom font sizes */
-.micro { font-size: 25% }
-.tiny { font-size: 50% }
-.small { font-size: 75% }
-.large { font-size: 125% }
-.huge { font-size: 150% }
-.Huge { font-size: 200% }
-.HUGE { font-size: 250% }
-
-.remark-code { font-size: 66% }
-
-/* Custom colours */
-.green { color: #85be42; font-weight: bold }
-.dark-green { color: #487a2d; font-weight: bold }
-.blue { color: #0099c2; font-weight: bold }
-.dark-blue { color: #015491; font-weight: bold }
-.light-grey { color: #999999 }
-.grey { color: #666666 }
-.dark-grey { color: #333333 }
-
-/* Set the maximum figure size to 100% of the slide */
-img, video, iframe {
- max-width: 100%;
- max-height: 100%;
-}
-
-table_rot {
- color: black;
- text-transform: uppercase;
- @include transform(rotate(270deg))
- @include transform-origin(0 0);
-}
-
-/* SciLifeLab logo in bottom left corner */
-div.scilife-logo {
- content: "";
- background-image: url("https://www.scilifelab.se/wp-content/uploads/2020/09/SciLifeLab_Logotype_Green_POS_large-copy-1536x334.png");
- background-repeat: no-repeat;
- background-size: contain;
- position: absolute;
- bottom: 10px;
- left: 15px;
- height: 50px;
- width: 200px;
-}
-
-/* NBIS logo in bottom right corner */
-div.nbis-logo {
- content: "";
- background-image: url("https://nbis.se/assets/img/logos/nbislogo-green.svg");
- background-repeat: no-repeat;
- background-size: contain;
- position: absolute;
- bottom: 23px;
- right: 27px;
- height: 35px;
- width: 100px;
-}
-
-/* Blockquotes */
-blockquote {
- border-left: 5px solid #85be42;
- background: #f9f9f9;
- font-style: italic;
- padding: 0.01em;
- padding-left: 12px;
- padding-right: 12px;
- margin-left: 12px;
- margin-right: 12px;
- border-radius: 0 5px 5px 0;
-}
-
-/* Link colour */
-a {
- color: #85be42;
- text-decoration: none;
-}
-
-/* Underline links when hovering */
-a:hover {
- text-decoration: underline;
-}
-
-/* Inline code color and border */
-.remark-inline-code {
- background: #f2f2f2;
- border-radius: 3px;
- margin-right: 2px;
- padding: 2px 3px 1px;
- font-size: 80% !important;
-}
-
-.image-with-text {
- display: inline-block;
- vertical-align: middle;
-}
-
-
]
-
---
-
-.pull-left[
-
-.small[Check OS on local machine]
-
-```bash
-$ uname -a
-Darwin johnsmbp.local 19.6.0 \
-Darwin Kernel Version 19.6.0: \
-Tue Jan 12 22:13:05 PST 2021; \
-root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64
-```
-
-.small[Pull Ubuntu (Linux) image]
-
-```bash
-$ docker pull ubuntu:16.04
-16.04: Pulling from library/ubuntu
-22dc81ace0ea: Pull complete
-...
-Digest: sha256:e348fbbea0e0a0e73ab0370de151e7800684445c509d46195aef73e090a49bd6
-Status: Downloaded newer image for ubuntu:16.04
-```
-
-.small[Run a container and check OS version]
-
-```bash
-$ docker run -it ubuntu:16.04
-root@407b0fd13fe5:/# uname -a
-Linux 407b0fd13fe5 4.9.60-linuxkit-aufs #1 SMP Mon Nov 6 16:00:12 UTC
-2017 x86_64 x86_64 x86_64 GNU/Linux
-```
-]
-
----
-
-# Mounting volumes
-
-
-`$ docker run -it -v $PWD/data:/home/data ubuntu:16.04`
-
-.pull-left[
-
-.tiny[Local project directory:]
-
-```
-$ ls project/
-
-|- doc/
-|
-|- data/
-| |- raw_external/
-| |- raw_internal/
-| |- meta/
-|
-|- code/
-|- notebooks/
-|
-|- intermediate/
-|- scratch/
-|- logs/
-|
-|- results/
-| |- figures/
-| |- tables/
-| |- reports/
-|
-|- Snakefile
-|- config.yml
-|- environment.yml
-|- Dockerfile
-```
-]
-.pull-right[
-.tiny[Docker image file system]
-```
-$ ls /
-
-|- bin/
-|- boot/
-|- dev/
-|- etc/
-|- home/
-| |- data/ # data folder mounted under home/
-| |- raw_external/
-| |- raw_internal/
-| |- meta/
-|- lib/
-|- lib64/
-|- media/
-|- opt/
-|- proc/
-|- root/
-|- run/
-|- sys/
-|- tmp/
-|- usr/
-|- var/
-```
-]
-
----
-
-# What can I use Docker for?
-
---
-
-* As an advanced .green[environment] manager
-
-```bash
-docker run -it -v $PWD:/home my_image /bin/bash
-```
-
---
-
-* To package your .green[code] with the .green[environment] it needs
-
-```bash
-docker run \
--v $PWD/data:/home/data \
--v $PWD/results:/home/results \
-my_image snakemake report.pdf
-```
-
---
-
-* To package a whole workflow with .green[environment], .green[code] and .green[data] (*e.g.* to accompany a manuscript).
-
-```bash
-docker run \
--v $PWD/results:/home/results \
-my_image snakemake report.pdf
-```
-
-* and much more...
-
----
-# What is Singularity?
-
-
-
-an open source container platform suitable for HPC clusters
-
-[https://sylabs.io/guides/latest/user-guide/](https://sylabs.io/guides/latest/user-guide/)
-
->Singularity was created to run complex applications on HPC clusters in a simple, portable, and reproducible way.
-
----
-# What is Apptainer?
-
-
-
-In 2021 Singularity joined the Linux Foundation and became Apptainer.
-
-The company Sylabs still maintains **Singularity**
-
----
-
-# Docker vs. Singularity
-
-| 
+
+ 
'
+format: nbis-revealjs
+---
+
+## What is [Docker]{.green}?
+
+::: {.incremental}
+- Standardized packaging for software, dependencies as well as the operating
+ system
+- Docker lets you create and run applications securely isolated in
+ [containers]{.green}
+:::
+
+## Docker in life science
+
+Docker containers can be used to allow others to reproduce a complete analysis:
+
+> To further support reproducibility, we bundled all tools and dependencies into
+> one Docker container available on DockerHub. `docker run` executes the
+> aforementioned Makefile inside the container. ^[_Bremges et al GigaScience
+> (2015) 4:33, [doi:10.1186/s13742-015-0073-6](https://doi.org/10.1186/s13742-015-0073-6)_]
+
+