Commit e9435d7e authored by Laurent Heirendt's avatar Laurent Heirendt
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Merge branch '2021-07-27_IT101-DM' into 'develop'

Adding 2021-07-27_IT101-DM slide

See merge request !106
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......@@ -73,6 +73,13 @@ From Jenny Bryan by CC-BY
* Separate files you are actively working from the old ones
* Orient newcomers to the group's conventions
<div style="position:absolute;left:43%;top:10%">
<img src="slides/img/folder_structure.png" height="700px">
</div>
<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
<a href="https://riojournal.com/article/56508/" style="color:grey; font-size:0.8em;">Foundational Practices of Research Data Management</a>
</div>
# Data housekeeping
......
......@@ -4,50 +4,34 @@
<img src="slides/img/LCSB_storages_full.png" height="750px">
</div>
<div class='fragment' style="position:absolute">
<div class='fragment' style="position:relative">
<img src="slides/img/LCSB_storages_personal-crossed.png" height="750px">
</div>
<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
</div>
# Data ingestion/transfer
## Receiving and sending data
<img height="400px" style="position:relative;left:10%" src="slides/img/banned_exchange_channels.png"><br>
<div style="position:absolute; left:10%;width:30%">
<div style="position:absolute;left:65%;top:60%">
## E-mail is not for data transfer
* Avoid transfer of any data by e-mail
* E-mail is a poor repository
* Data can be read on passage
* Unless consortium/project has formally agreed to use a secure commercial cloud
</div>
<div class="fragment" style="left:50%; width:30%; position:absolute">
## Exchanging data
* Share on Atlas server
* OwnCloud share (LCSB - BioCore)
* DropIt service (SIU)
* LFT (IBM Aspera) share for sensitive data
</div>
</div>
<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-05" style="color:grey; font-size:0.8em;">Research Human Data Sharing Policy</a>
<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
</div>
# Data ingestion/transfer
# Data ingestion: Transfer and Integrity
* When sending data: <font color="red">Do not use emails, use secure platforms (Cloud, Aspera, Atlas share...)!</font>
<div class="fragment">
Data can be corrupted:
* (non-)malicious modification
* faulty file transfer
* disk corruption
</div>
<div class="fragment">
......@@ -55,8 +39,8 @@ Data can be corrupted:
* disable write access to the source data
* generate checksums!
<div style="position:absolute;left:40%">
<div style="position:absolute;left:40%;top:30%">
<img src="slides/img/checksum.png" width="500px">
</div>
</div>
......@@ -77,3 +61,33 @@ Data can be corrupted:
<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
</div>
# Data ingestion/Integrity
## Encryption
<div class='fragment' style="position:relative;left:25%;top:60%">
<img align="middle" height="300px" src="slides/img/encryption.png">
</div>
<div class='fragment'>
* Sensitive data protected by encryption
</div>
<div class='fragment'>
* Guaranted confidentiality
</div>
<div class='fragment'>
* Encryption key which need to be kept safe
</div>
<div class='fragment'>
* <font color= red>Loosing your encryption key means loosing your data!</font>
</div>
<div class='fragment'>
* Make a off-site backup of your data
</div>
......@@ -24,3 +24,5 @@ Prof. Dr. Rudi Balling, director
* Technicians
* Administrators
</div>
[
{"filename": "index.md"},
{"filename": "introduction.md"},
{"filename": "data-introduction.md"},
{"filename": "data_flow.md"},
{"filename": "ingestion.md"},
{"filename": "storage_setup.md"},
{"filename": "data-housekeeping.md"},
{"filename": "howtos.md"},
{"filename": "reproducibility.md"},
{"filename": "code_versioning.md"},
{"filename": "visualization.md"},
{"filename": "problem_solving.md"},
{"filename": "fair-principles.md"},
{"filename": "r3_group.md"},
{"filename": "thanks.md"}
]
{ "filename": "index.md" },
{ "filename": "introduction.md" },
{ "filename": "access_management.md" },
{ "filename": "data-introduction.md" },
{ "filename": "data_flow.md" },
{ "filename": "ingestion.md" },
{ "filename": "storage_setup.md" },
{ "filename": "data-housekeeping.md" },
{ "filename": "howtos.md" },
{ "filename": "reproducibility.md" },
{ "filename": "code_versioning.md" },
{ "filename": "visualization.md" },
{ "filename": "data_life_cycle.md" },
{ "filename": "problem_solving.md" },
{ "filename": "fair-principles.md" },
{ "filename": "r3_group.md" },
{ "filename": "thanks.md" }
]
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......@@ -94,3 +94,4 @@
<img src="slides/img/red-cross.png" width="700px"><br>
</div>
</div>
......@@ -4,12 +4,8 @@
* Regularly update your SW/OS
* Encrypt movable media
### Passwords
* Strong passwords
* Password manager
* Safe password exchange channels
* Expiration time on password share
<div class="fragment" >
### Backup
* take care of your own backups!
......@@ -24,6 +20,35 @@
<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
</div>
</div>
<div class="fragment">
### Passwords
* Strong passwords
* Password manager
* Safe password exchange channels
* Expiration time on password share
</div>
# Storage set-up
## Password exchange channels
<div style="position:relative">
<img src="slides/img/privateBin.png" height="350px">
</div>
<div style="position:absolute;left:65%;top:85%">
* Free service provided by LSCB at <a href="https://privatebin.lcsb.uni.lu" style="color:blue; font-size:0.8em;">privatebin.lcsb.uni.lu</a>
* **LUMS** account is required
* Set expiry period
* Can expire upon first access
* Password only accessible by sender and recipient
</div>
# Storage set-up
......
# 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 activate 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://gitlab.lcsb.uni.lu" style="color:blue; font-size:0.8em;">gitlab.lcsb.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>
../../2021-04-20_IT101-DM/slides/code_versioning.md
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../../2021-04-20_IT101-DM/slides/data-housekeeping.md
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../../2021-04-20_IT101-DM/slides/data-introduction.md
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../../2021-04-20_IT101-DM/slides/data_flow.md
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# 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>
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../../2021-04-20_IT101-DM/slides/fair-principles.md
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../../2021-04-20_IT101-DM/slides/howtos.md
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../../2021-04-20_IT101-DM/slides/img
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# 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>
../../2021-04-20_IT101-DM/slides/ingestion.md
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../../2021-04-20_IT101-DM/slides/introduction.md
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../../2021-04-20_IT101-DM/slides/list.json
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../../2021-04-20_IT101-DM/slides/overview.md
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# 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
# 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">
* Valentin Grouès</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>
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../../2021-04-20_IT101-DM/slides/thanks.md
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../../2021-04-20_IT101-DM/slides/visualization.md
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