From 4df810ede8e4a9c763d9d82f4f50ca06818252a5 Mon Sep 17 00:00:00 2001 From: "nene.barry" <nene.barry@uni.lu> Date: Fri, 23 Jul 2021 16:47:09 +0200 Subject: [PATCH] 2021-07-27_IT101-DM --- .../slides/access_management.md | 36 +++++ .../slides/code_versioning.md | 1 + .../slides/data-housekeeping.md | 1 + .../slides/data-introduction.md | 1 + 2021/2021-07-27_IT101-DM/slides/data_flow.md | 1 + .../slides/data_life_cycle.md | 23 +++ .../slides/fair-principles.md | 1 + 2021/2021-07-27_IT101-DM/slides/howtos.md | 1 + 2021/2021-07-27_IT101-DM/slides/img | 1 + 2021/2021-07-27_IT101-DM/slides/index.md | 20 +++ 2021/2021-07-27_IT101-DM/slides/ingestion.md | 1 + .../slides/introduction.md | 1 + 2021/2021-07-27_IT101-DM/slides/list.json | 1 + 2021/2021-07-27_IT101-DM/slides/overview.md | 1 + .../slides/problem_solving.md | 11 ++ 2021/2021-07-27_IT101-DM/slides/r3_group.md | 140 ++++++++++++++++++ .../slides/reproducibility.md | 1 + .../slides/storage_setup.md | 1 + 2021/2021-07-27_IT101-DM/slides/thanks.md | 1 + .../slides/visualization.md | 1 + 20 files changed, 245 insertions(+) create mode 100644 2021/2021-07-27_IT101-DM/slides/access_management.md create mode 120000 2021/2021-07-27_IT101-DM/slides/code_versioning.md create mode 120000 2021/2021-07-27_IT101-DM/slides/data-housekeeping.md create mode 120000 2021/2021-07-27_IT101-DM/slides/data-introduction.md create mode 120000 2021/2021-07-27_IT101-DM/slides/data_flow.md create mode 100644 2021/2021-07-27_IT101-DM/slides/data_life_cycle.md create mode 120000 2021/2021-07-27_IT101-DM/slides/fair-principles.md create mode 120000 2021/2021-07-27_IT101-DM/slides/howtos.md create mode 120000 2021/2021-07-27_IT101-DM/slides/img create mode 100644 2021/2021-07-27_IT101-DM/slides/index.md create mode 120000 2021/2021-07-27_IT101-DM/slides/ingestion.md create mode 120000 2021/2021-07-27_IT101-DM/slides/introduction.md create mode 120000 2021/2021-07-27_IT101-DM/slides/list.json create mode 120000 2021/2021-07-27_IT101-DM/slides/overview.md create mode 100644 2021/2021-07-27_IT101-DM/slides/problem_solving.md create mode 100644 2021/2021-07-27_IT101-DM/slides/r3_group.md create mode 120000 2021/2021-07-27_IT101-DM/slides/reproducibility.md create mode 120000 2021/2021-07-27_IT101-DM/slides/storage_setup.md create mode 120000 2021/2021-07-27_IT101-DM/slides/thanks.md create mode 120000 2021/2021-07-27_IT101-DM/slides/visualization.md diff --git a/2021/2021-07-27_IT101-DM/slides/access_management.md b/2021/2021-07-27_IT101-DM/slides/access_management.md new file mode 100644 index 00000000..f4e62651 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/access_management.md @@ -0,0 +1,36 @@ +# Access Management +<div style="display:grid;grid-gap:100px;grid-template-columns: 40% 40%"> +<div > + +## UNI-LU Account + * Mails services including web mail: <a href="https://owa.uni.lu" style="color:blue; font-size:0.8em;">owa.uni.lu</a> + * Microsoft Office & Teams: <a href="https://service.uni.lu" style="color:blue; font-size:0.8em;">service.uni.lu</a> + * SAP services: <a href="https://fiori.uni.lu/fiori" style="color:blue; font-size:0.8em;">fiori.uni.lu/fiori</a> + * University's Intranet: <a href="https://intranet.uni.lux" style="color:blue; font-size:0.8em;">intranet.uni.lux</a> + * All remote work services : Webex, Slack... + + +</div> +<div> +<div class="fragment"> + +## LUMS Account + * go to <a href="https://service.uni.lu" style="color:blue; font-size:0.8em;">service.uni.lu</a>: make a request and go to <a href="https://lcsb-cdc-lums-02.uni.lu" style="color:blue; font-size:0.8em;">lums.uni.lu</a> to active your account upon receiving credentials + + <div style="position:absolute;left:20%;top:90%"> + <img src="slides/img/access.png" height="400px"> + </div> + + <div style="position:absolute;left:60%;top:90%"> + <img src="slides/img/lums.png" height="400px"> + </div> +<div class="fragment"> + + * Owncloud: <a href="http://owncloud.lcsb.uni.lu" style="color:blue; font-size:0.8em;">owncloud.lcsb.uni.lu</a> + * R3 Gitlab: <a href="https://git-r3lab.uni.lu" style="color:blue; font-size:0.8em;">git-r3lab.uni.lu</a> + * Private Bin: <a href="https://privatebin.lcsb.uni.lu" style="color:blue; font-size:0.8em;">privatebin.lcsb.uni.lu</a> + * LCSB Wiki page, Webdav, LCSB Analytics page + + +</div> +</div> diff --git a/2021/2021-07-27_IT101-DM/slides/code_versioning.md b/2021/2021-07-27_IT101-DM/slides/code_versioning.md new file mode 120000 index 00000000..b5c7e06f --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/code_versioning.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/code_versioning.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md new file mode 120000 index 00000000..6146c008 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/data-housekeeping.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/data-introduction.md b/2021/2021-07-27_IT101-DM/slides/data-introduction.md new file mode 120000 index 00000000..a38b5e87 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/data-introduction.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/data-introduction.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/data_flow.md b/2021/2021-07-27_IT101-DM/slides/data_flow.md new file mode 120000 index 00000000..b7a2b316 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/data_flow.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/data_flow.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md b/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md new file mode 100644 index 00000000..a1f1d84b --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md @@ -0,0 +1,23 @@ + +# Some practical recommandations + +* Plan your data walking along the data life cycle + +<div class='fragment' style="position:relative;left:25%;top:60%"> +<img align="middle" height="300px" src="slides/img/rdm-cycle.png"> +</div> +<div class="fragment"> + +* Use data management tools: + * DMPonline <a href="https://dmponline.elixir-luxembourg.org/" style="color:blue; font-size:0.8em;">https://dmponline.elixir-luxembourg.org/</a> + <img src="slides/img/dmponline_logo.png" height="50px"> + * DS Wizard <a href="https://learning.ds-wizard.org/" style="color:blue; font-size:0.8em;">https://learning.ds-wizard.org/</a> + <img src="slides/img/dsw_logo.png" height="100px"> + +<div> + +<div class="fragment"> + +* Annotate your data and code using Ontologies and standardised metadata + +</div> \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/fair-principles.md b/2021/2021-07-27_IT101-DM/slides/fair-principles.md new file mode 120000 index 00000000..cb5bc476 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/fair-principles.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/fair-principles.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/howtos.md b/2021/2021-07-27_IT101-DM/slides/howtos.md new file mode 120000 index 00000000..4ff818a5 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/howtos.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/howtos.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/img b/2021/2021-07-27_IT101-DM/slides/img new file mode 120000 index 00000000..ad68bb48 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/img @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/img \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/index.md b/2021/2021-07-27_IT101-DM/slides/index.md new file mode 100644 index 00000000..6ac2ae37 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/index.md @@ -0,0 +1,20 @@ +# IT101 - Working with computers +<br>IT101 - Working with computers<br> +## July 27th, 2021 + +<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> + Nene Barry<br> + Data Steward<br> + nene.barry@uni.lu<br> + <i>Luxembourg Centre for Systems Biomedicine</i> + </h4> +</div> diff --git a/2021/2021-07-27_IT101-DM/slides/ingestion.md b/2021/2021-07-27_IT101-DM/slides/ingestion.md new file mode 120000 index 00000000..57dfd695 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/ingestion.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/ingestion.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/introduction.md b/2021/2021-07-27_IT101-DM/slides/introduction.md new file mode 120000 index 00000000..f4837a3c --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/introduction.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/introduction.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/list.json b/2021/2021-07-27_IT101-DM/slides/list.json new file mode 120000 index 00000000..df07566d --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/list.json @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/list.json \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/overview.md b/2021/2021-07-27_IT101-DM/slides/overview.md new file mode 120000 index 00000000..50f8000f --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/overview.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/overview.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/problem_solving.md b/2021/2021-07-27_IT101-DM/slides/problem_solving.md new file mode 100644 index 00000000..f34e0a2b --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/problem_solving.md @@ -0,0 +1,11 @@ +# 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 + * Submit the problem in writing + * Make the question interesting diff --git a/2021/2021-07-27_IT101-DM/slides/r3_group.md b/2021/2021-07-27_IT101-DM/slides/r3_group.md new file mode 100644 index 00000000..f652c8c5 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/r3_group.md @@ -0,0 +1,140 @@ +# 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> + +<aside class="notes"> +Pathfinder - policies, finding optimal 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 + * First steps with R (2021-07-27) + * Statistical tests and statistical learning for omics data (2021-09-14) + * 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>) +<section data-transition="none" data-background-image="slides/img/r3-training-logo.png" data-background-size="1000px" data-background-opacity="0.1"> +</section> +<div style="display:block;text-align:center;position:relative;" > +<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"> + * Datasteward + +</div> +<div class="profile-container"> + + * Yohan Yarosz</li> + * <img src="slides/img/R3_profile_pictures/yohan_yarosz.png"> + * Development + +</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"> + + * Sarah Peter</li> + * <img src="slides/img/R3_profile_pictures/sarah_peter.png"> + * Infrastructure + +</div> +<div class="profile-container"> + + * Valentine Groues</li> + * <img src="slides/img/R3_profile_pictures/valentine_groues.png"> + * Development + +</div> +<div class="profile-container"> + + * Vilem Ded</li> + * <img src="slides/img/R3_profile_pictures/vilem_ded.png"> + * Datasteward + +</div> +<div class="profile-container"> + + * Noua Toukourou</li> + * <img src="slides/img/R3_profile_pictures/noua_toukourou.png"> + * Infrastructure + +</div> +<div class="profile-container"> + + * Alexey Kolodkin</li> + * <img src="slides/img/R3_profile_pictures/alexey_kolodkin.png"> + * Datasteward + +</div> +<div class="profile-container"> + + * Maharshi Vyas</li> + * <img src="slides/img/R3_profile_pictures/maharshi_vyas.png"> + * Infrastructure + +</div> + +<div class="profile-container"> + + * Nene Barry</li> + * <img src="slides/img/R3_profile_pictures/nene_barry.png"> + * Datasteward + +</div> + +<div class="profile-container"> + + * Karim Chaouch</li> + * <img src="slides/img/R3_profile_pictures/karim_chaouch.png"> + * Development + +</div> +<div class="profile-container"> + + * Christophe Trefois + * <img src="slides/img/R3_profile_pictures/christophe_trefois.png"> + * R<sup>3</sup> team lead + +</div> +</div> diff --git a/2021/2021-07-27_IT101-DM/slides/reproducibility.md b/2021/2021-07-27_IT101-DM/slides/reproducibility.md new file mode 120000 index 00000000..8f6e4d1f --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/reproducibility.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/reproducibility.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/storage_setup.md b/2021/2021-07-27_IT101-DM/slides/storage_setup.md new file mode 120000 index 00000000..9fe2d27f --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/storage_setup.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/storage_setup.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/thanks.md b/2021/2021-07-27_IT101-DM/slides/thanks.md new file mode 120000 index 00000000..85dc36b8 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/thanks.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/thanks.md \ No newline at end of file diff --git a/2021/2021-07-27_IT101-DM/slides/visualization.md b/2021/2021-07-27_IT101-DM/slides/visualization.md new file mode 120000 index 00000000..d946af68 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/visualization.md @@ -0,0 +1 @@ +../../2021-04-20_IT101-DM/slides/visualization.md \ No newline at end of file -- GitLab