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mode 100644 index 0000000000000000000000000000000000000000..8c4525bf2a575ae63caa556fa822b65443a3c3bf --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/index.md @@ -0,0 +1,20 @@ +# IT101 - Working with computers +<br>IT101 - Working with computers<br> +## June 09th, 2020 + +<div style="top: 6em; left: 0%; position: absolute;"> + <img src="theme/img/lcsb_bg.png"> +</div> + +<div style="top: 5em; left: 60%; position: absolute;"> + <img src="slides/img/r3-training-logo.png" height="200px"> + <br><br><br><br> + <h3></h3> + <br><br><br> + <h4> + Vilem Ded<br> + Data Steward<br> + vilem.ded@uni.lu<br> + <i>Luxembourg Centre for Systems Biomedicine</i> + </h4> +</div> diff --git a/2020/2020-06-09_IT101-DM/slides/ingestion.md b/2020/2020-06-09_IT101-DM/slides/ingestion.md new file mode 120000 index 0000000000000000000000000000000000000000..05eea4bb716157d10f0da6a03388def8ec26bbc0 --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/ingestion.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/ingestion.md \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/introduction.md b/2020/2020-06-09_IT101-DM/slides/introduction.md new file mode 120000 index 0000000000000000000000000000000000000000..4b28996cbc4a67efe217f4e8faf785179bb2c93a --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/introduction.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/introduction.md \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/list.json b/2020/2020-06-09_IT101-DM/slides/list.json new file mode 120000 index 0000000000000000000000000000000000000000..1302be9d4466a9f5a41e41f83ae03619362a702b --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/list.json @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/list.json \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/overview.md b/2020/2020-06-09_IT101-DM/slides/overview.md new file mode 120000 index 0000000000000000000000000000000000000000..db510e2e96f4ef9708e8b5f919169676dfd6e0cb --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/overview.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/overview.md \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/problem_solving.md b/2020/2020-06-09_IT101-DM/slides/problem_solving.md new file mode 100644 index 0000000000000000000000000000000000000000..1f723a740e6c5b6d916561294d086e6011d1be44 --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/problem_solving.md @@ -0,0 +1,12 @@ +# Problem solving +A guide for solving computing issues + +1. Express the problem + * Write down what you want to achieve +2. Search for help + * Read **FAQs**, **help pages** and the **official documentation** well before turning to Google + * Use stack exchange, forums and related resources carefully +3. Ask an expert + * You have to submit the problem in writing + * Make the question interesting + * If you supply a trivial problem, it will stop answering diff --git a/2020/2020-06-09_IT101-DM/slides/r3_group.md b/2020/2020-06-09_IT101-DM/slides/r3_group.md new file mode 100644 index 0000000000000000000000000000000000000000..75c4c4391a2322b9f2d40c7c5322562f3dbf3f86 --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/r3_group.md @@ -0,0 +1,133 @@ +# Responsible and Reproducible Research (R<sup>3</sup>) +## What is R<sup>3</sup>? + + +A multi-facetted change management +process built on 3 pillars: + +- R3 pathfinder + +- R3 school + +- R3 accelerator + +Common link module: R3 clinic + +<div style="top: -1em; left: 50%; position: absolute;"> + <img src="slides/img/3pillars-full.png"> +</div> + +<br> +<br> +<br> +<br> + +<aside class="notes"> +Pathfinder - policies, data management changes<br> +School - courses, howtos, trainnings<br> +Accelerator - advanced teams and their boost/support, CI/CD setup<br> +Clinic - hands-on, meetings in groups, code review + suggestions<br> +</aside> + +## R<sup>3</sup> Training + * LCSB's Monthly Data Management and Data Protection training + * ELIXIR Luxembourg's trainings <br> + https://elixir-luxembourg.org/training + * R<sup>3</sup> school Git basics - every 4 months + <aside class="notes"> + Direct newcommers to this monthly training + </aside> + + + +# Responsible and Reproducible Research (R<sup>3</sup>) +<center><img src="slides/img/r3-training-logo.png" height="200px"></center> + +Your R<sup>3</sup> contacts: +<div style="display:block;text-align:center;position:relative"> +<div class="profile-container"> + + * Christophe Trefois + * <img src="slides/img/R3_profile_pictures/christophe_trefois.png"> + * R<sup>3</sup> coordination + +</div> +<div class="profile-container"> + + * Venkata Satagopam + * <img src="slides/img/R3_profile_pictures/venkata_satagopam.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Reinhard Schneider + * <img src="slides/img/R3_profile_pictures/reinhard_schneider.png"> + * Head of Bioinformatics Core + +</div> +<div class="profile-container"> + + * Pinar Alper + * <img src="slides/img/R3_profile_pictures/pinar_alper.png"> + * Data steward + +</div> +<div class="profile-container"> + + * Yohan Yarosz</li> + * <img src="slides/img/R3_profile_pictures/yohan_yarosz.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Laurent Heirendt</li> + * <img src="slides/img/R3_profile_pictures/laurent_heirendt.png"> + * Git, CI + +</div> +<div class="profile-container"> + + * Wei Gu</li> + * <img src="slides/img/R3_profile_pictures/wei_gu.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Sarah Peter</li> + * <img src="slides/img/R3_profile_pictures/sarah_peter.png"> + * HPC + +</div> +<div class="profile-container"> + + * Vilem Ded</li> + * <img src="slides/img/R3_profile_pictures/vilem_ded.png"> + * Data steward + +</div> +<div class="profile-container"> + + * Noua Toukourou</li> + * <img src="slides/img/R3_profile_pictures/noua_toukourou.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Alexey Kolodkin</li> + * <img src="slides/img/R3_profile_pictures/alexey_kolodkin.png"> + * Data steward + +</div> +<div class="profile-container"> + + * Maharshi Vyas</li> + * <img src="slides/img/R3_profile_pictures/maharshi_vyas.png"> + * R<sup>3</sup> Core + +</div> + +</div> diff --git a/2020/2020-06-09_IT101-DM/slides/reproducibility.md b/2020/2020-06-09_IT101-DM/slides/reproducibility.md new file mode 120000 index 0000000000000000000000000000000000000000..3c2445cfaf26dcb66e8ee207dd6465699625e33e --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/reproducibility.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/reproducibility.md \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/rudi_balling.jpg b/2020/2020-06-09_IT101-DM/slides/rudi_balling.jpg new file mode 120000 index 0000000000000000000000000000000000000000..94f5ee71a64577ee592b5f9ea00ccd20a51ba60c --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/rudi_balling.jpg @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/rudi_balling.jpg \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/storage_setup.md b/2020/2020-06-09_IT101-DM/slides/storage_setup.md new file mode 100644 index 0000000000000000000000000000000000000000..66aba999f56b75d617fc3bee905595d6b95ac7a2 --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/storage_setup.md @@ -0,0 +1,51 @@ +# Storage set-up + +* Download Anti-virus software +* Regualarly update your SW/OS +* Encrypt movable media + +### Passwords + +* Strong passwords +* Password manager +* Safe password exchange channels +* Expiration time on password share + +### Backup + * take care of your own backups! + * don't work on your backup copy! + * minimum is <b>3-2-1 backup rule</b> + + +<div style="position:absolute;right:10%;top:10%"> +<img src="slides/img/undraw_secure_server_s9u8.png" height="750px"> +</div> + + + +# Storage set-up +## Backup - Central IT/LCSB +<div style="position:relative"> +<img src="slides/img/LCSB_storages_backed-up.png" height="750px"> +</div> +<div style="position:absolute;left:65%;top:60%"> + +Server administrators take care of: +* server backups +* LCSB OwnCloud backups +* group/application server backups (not always) + +</div> + + + +# Storage set-up +## Backup - personal research data +<div style="position:relative"> +<img src="slides/img/LCSB_storages_backup.png" height="750px"> +</div> +<div style="position:absolute;left:55%;top:70%"> + +<font color="red">One version should reside on Atlas!</font> + +</div> diff --git a/2020/2020-06-09_IT101-DM/slides/thanks.md b/2020/2020-06-09_IT101-DM/slides/thanks.md new file mode 120000 index 0000000000000000000000000000000000000000..c81123046f3344f76f0902b149a4d9d7c070c184 --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/thanks.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/thanks.md \ No newline at end of file diff --git a/2020/2020-06-09_IT101-DM/slides/visualization.md b/2020/2020-06-09_IT101-DM/slides/visualization.md new file mode 120000 index 0000000000000000000000000000000000000000..82924b907833767bbd9460a245902e36775084a6 --- /dev/null +++ b/2020/2020-06-09_IT101-DM/slides/visualization.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/visualization.md \ No newline at end of file diff --git a/contribute.sh b/contribute.sh index 236fdf1e9c2a6c1e4ccf79bf78fd96182734c573..718f98405e6954dd3a3dea81730a60ee4c072b51 100755 --- a/contribute.sh +++ b/contribute.sh @@ -32,4 +32,4 @@ fi # launch the docker file cmd="python contribute.py --date=\"$parameterDate\" --name=\"$parameterName\"" -docker run -p $dockerPort:$dockerPort -it -v $(pwd)/:/presentation $dockerImg /bin/bash -c "$cmd" +docker run -p $dockerPort:$dockerPort --user $(id -u):$(id -g) -it -v $(pwd)/:/presentation $dockerImg /bin/bash -c "$cmd"