diff --git a/2021/2021-04-20_IT101-DM/slides/data-housekeeping.md b/2021/2021-04-20_IT101-DM/slides/data-housekeeping.md
index ab2cca61ce38875fd70e9cd34ee325d0c4160b7a..8cb4d014ea2b7732e1aa2b6913379a74021cf527 100644
--- a/2021/2021-04-20_IT101-DM/slides/data-housekeeping.md
+++ b/2021/2021-04-20_IT101-DM/slides/data-housekeeping.md
@@ -73,13 +73,6 @@ 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
diff --git a/2021/2021-04-20_IT101-DM/slides/ingestion.md b/2021/2021-04-20_IT101-DM/slides/ingestion.md
index 8e377655a556d2575809edaa63de35fe63d948ee..7d168db8c9e03e261196b436ccae1b460f49fc4e 100644
--- a/2021/2021-04-20_IT101-DM/slides/ingestion.md
+++ b/2021/2021-04-20_IT101-DM/slides/ingestion.md
@@ -4,34 +4,50 @@
<img src="slides/img/LCSB_storages_full.png" height="750px">
</div>
-<div class='fragment' style="position:relative">
+<div class='fragment' style="position:absolute">
<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
-<div style="position:absolute;left:65%;top:60%">
+<img height="400px" style="position:relative;left:10%" src="slides/img/banned_exchange_channels.png"><br>
+<div style="position:absolute; left:10%;width:30%">
-* Unless consortium/project has formally agreed to use a secure commercial cloud
+## 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
</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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+<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>
</div>
-
-# 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 ingestion/transfer
Data can be corrupted:
-
* (non-)malicious modification
* faulty file transfer
* disk corruption
-</div>
<div class="fragment">
@@ -39,8 +55,8 @@ Data can be corrupted:
* disable write access to the source data
* generate checksums!
-
-<div style="position:absolute;left:40%;top:30%">
+
+<div style="position:absolute;left:40%">
<img src="slides/img/checksum.png" width="500px">
</div>
</div>
@@ -61,33 +77,3 @@ 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>
-
-
diff --git a/2021/2021-04-20_IT101-DM/slides/introduction.md b/2021/2021-04-20_IT101-DM/slides/introduction.md
index fed0b0971b7d1f868f2fd8213461c724834da16a..95e30815a03c5be0f1dd409701ec0edc15d2aa73 100644
--- a/2021/2021-04-20_IT101-DM/slides/introduction.md
+++ b/2021/2021-04-20_IT101-DM/slides/introduction.md
@@ -24,5 +24,3 @@ Prof. Dr. Rudi Balling, director
* Technicians
* Administrators
</div>
-
-
diff --git a/2021/2021-04-20_IT101-DM/slides/list.json b/2021/2021-04-20_IT101-DM/slides/list.json
index 17136d973bc9a81e70687fa1934d0f5b4f9c5baf..5dbc2360d7b5b8d68580868e6431ce26e8746eb1 100644
--- a/2021/2021-04-20_IT101-DM/slides/list.json
+++ b/2021/2021-04-20_IT101-DM/slides/list.json
@@ -1,19 +1,17 @@
[
- { "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" }
-]
\ No newline at end of file
+ {"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"}
+]
diff --git a/2021/2021-04-20_IT101-DM/slides/reproducibility.md b/2021/2021-04-20_IT101-DM/slides/reproducibility.md
index b93079f25ad16151f5e2db41b3d55f4c8dd6cb54..a73310ceaf1031a2e79e0f55083319e52680f5cf 100644
--- a/2021/2021-04-20_IT101-DM/slides/reproducibility.md
+++ b/2021/2021-04-20_IT101-DM/slides/reproducibility.md
@@ -94,4 +94,3 @@
<img src="slides/img/red-cross.png" width="700px"><br>
</div>
</div>
-
diff --git a/2021/2021-04-20_IT101-DM/slides/storage_setup.md b/2021/2021-04-20_IT101-DM/slides/storage_setup.md
index d321b5ccd652709e969a2027cac2d7c3a7c69a6a..c4f5e9070cec562fe4ecf14589be1a07c99c647f 100644
--- a/2021/2021-04-20_IT101-DM/slides/storage_setup.md
+++ b/2021/2021-04-20_IT101-DM/slides/storage_setup.md
@@ -4,8 +4,12 @@
* Regularly update your SW/OS
* Encrypt movable media
+### Passwords
-<div class="fragment" >
+* Strong passwords
+* Password manager
+* Safe password exchange channels
+* Expiration time on password share
### Backup
* take care of your own backups!
@@ -20,35 +24,6 @@
<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
diff --git a/2021/2021-07-27_IT101-DM/slides/code_versioning.md b/2021/2021-07-27_IT101-DM/slides/code_versioning.md
deleted file mode 120000
index b5c7e06fec7c70db4c46438f42df5aada0c4e3b6..0000000000000000000000000000000000000000
--- a/2021/2021-07-27_IT101-DM/slides/code_versioning.md
+++ /dev/null
@@ -1 +0,0 @@
-../../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/code_versioning.md b/2021/2021-07-27_IT101-DM/slides/code_versioning.md
new file mode 100644
index 0000000000000000000000000000000000000000..eccd4a189300591de6be79ffbee91fcc987c631c
--- /dev/null
+++ b/2021/2021-07-27_IT101-DM/slides/code_versioning.md
@@ -0,0 +1,33 @@
+# Code versioning
+<div style="position:absolute; width:40%">
+
+**git**
+
+ * Current standard for code versioning
+ * Maintain versions of your code as it develops
+ * Local system, which does not require an online repository
+ * Repositories allow distributed development
+
+<img align="middle" height="300px" src="slides/img/Git-logo.png">
+</div>
+
+<div class="fragment" style="position:absolute; left:50%; width:40%"">
+
+**git@lcsb**
+* Recommended, supported repository
+* Allows tracking of issues
+* Ready for continous integration - code checked on commits to the repository.
+* [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
+
+
+ **Use at LCSB**
+
+ * All analyses code should be in a repository
+ * Minimally at submission of a manuscript
+ * Better daily
+ * Even better "analyses chunkwise"
+</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-07" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-07 Source Code Management Policy</a>
+</div>
diff --git a/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
deleted file mode 120000
index 6146c0087b6fb77fe25b41811ba800db5a2f6f45..0000000000000000000000000000000000000000
--- a/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
+++ /dev/null
@@ -1 +0,0 @@
-../../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-housekeeping.md b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
new file mode 100644
index 0000000000000000000000000000000000000000..ab2cca61ce38875fd70e9cd34ee325d0c4160b7a
--- /dev/null
+++ b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
@@ -0,0 +1,143 @@
+# Data housekeeping
+## File names
+<div style="display:flex; position:static; width:100%">
+<div class="fragment" data-fragment-index="0" style="position:static; width:30%">
+
+### General pricinples
+ * Machine readable
+ * Human readable
+ * Plays well with default ordering
+</div>
+<div class="fragment" data-fragment-index="1" style="position:absolute; left:33%; width:30%">
+
+### Separators
+ * No spaces
+ * Underscore to separate
+ * Hyphen to combine
+
+</div>
+<div class="fragment" data-fragment-index="2" style="position:absolute; left:66%; width:30%">
+
+### Date format follows **ISO 8601**<br>
+
+ 2018-12-03<br>
+ 2018-12-06_1700
+
+</div>
+</div>
+
+
+<div class="fragment" data-fragment-index="3" style="width:100%; position:static">
+<div style="position:absolute;width:55%">
+<b>Bad</b> names
+
+```bash
+ PhD-project-Jan19 alldata_final.foo
+ Finacial detailes BIocore 19/11/12.xls
+ ATACseq1Londonmapped.bam
+ Hlad.jez.M-L-průtoky JÃObj.z OhÅ™e-od 10-2011.xlsx
+```
+</div>
+<div style="position:relative;width:55%; bottom:20%; left:50%">
+<b>Good</b> names
+
+```bash
+Iris-setosa_samples_1927-05-12.csv
+PI102_Mouse12_EEG_2018-11-03_1245.tsv
+Bioinfiniti_FullProposal_2018-11-15_1655.do
+```
+</div>
+</div>
+<br>
+<br>
+<div class="fragment" data-fragment-index="3" style="width:100%;">
+From Jenny Bryan by CC-BY
+(https://speakerdeck.com/jennybc/how-to-name-files)
+</div>
+
+
+
+# Data housekeeping
+## File organization
+* Have folder organization conventions for your **group**
+ * Per Paper
+ * Per Study/Project
+ * Per Collaborator
+* Keep <b>readme files</b> for data
+ * Title
+ * Date of Creation/Receipt
+ * Instrument or software specific information
+ * People involved
+ * Relations between multiple files/folders
+
+* 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
+<div style="position:absolute">
+
+## When working
+ * Clarify and separate source and intermediate data
+ * Keep data copies to a **minimum**
+ * Cleanup post-analysis
+ * Cleanup copies created for presentations or for sharing
+</div>
+<div style="position:relative;left:50%; width:40%">
+<img src="slides/img/cleaning-table.jpg" height="450px">
+</div>
+
+
+
+# Data housekeeping
+## End of project
+ * handover data to a new responsible when leaving
+ * data should be kept as a single copy on server-side storage
+ * no copies on desktops and external devices
+ * non-proprietary formats
+ * minimal metadata
+ * sensitive data (e.g. whole genome) **must** be encrypted
+ <br/>
+ <br/>
+ * If not specified otherwise, data must be kept for **10 years** following project end for reproducibility purposes
+<aside class="notes">
+Note: sometimes it is hard to find/understand dataset 10 days old
+</aside>
+
+## In doubt on data archival?
+Contact R<sup>3</sup> for support on archival of datasets using tickets:
+ * https://service.uni.lu/sp
+ * Home > Catalog > LCSB > Biocore: Application services > Request for: Support
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
+<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-03" style="color:grey; font-size:0.8em;">Research Data Retention and Archival Policy</a>
+</div>
+
+
+
+# Data housekeeping - Summary
+## Server is your friend!
+ * Allows a consistent backup policy for your datasets
+ * Keeps number of copies to minimum
+ * Specification of clear access rights
+ * High accessibility
+ * Data are discoverable
+ * Server can't be stolen
+
+## General guidelines
+ * Use institutional media for storage of **all** data
+ * Research data (particularly sensitive data) should be in a single source location
+ * Enable encryption for data stored on movable media
+ * Clarify and separate source and intermediate data
+ * Disable write access to relevant source data (read-only)
+ * Backup research data!
+ * Download Anti-virus software
+ * Generate checksums
diff --git a/2021/2021-07-27_IT101-DM/slides/data-introduction.md b/2021/2021-07-27_IT101-DM/slides/data-introduction.md
deleted file mode 120000
index a38b5e87a9dad6508aabfeb86be6ee262cfe2dfc..0000000000000000000000000000000000000000
--- a/2021/2021-07-27_IT101-DM/slides/data-introduction.md
+++ /dev/null
@@ -1 +0,0 @@
-../../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-introduction.md b/2021/2021-07-27_IT101-DM/slides/data-introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..c269d80286a4bb458eec2d5640664eeb1e718713
--- /dev/null
+++ b/2021/2021-07-27_IT101-DM/slides/data-introduction.md
@@ -0,0 +1,86 @@
+# Data and metadata
+<div style="display:grid;grid-gap:100px;grid-template-columns: 40% 40%">
+<div >
+
+## Data
+ * "*information in digital form that can be transmitted or processed*"
+ <p align="right">-- Merriam-Webster dictionary</p>
+ * "*information in an electronic form that can be stored and processed by a computer*"
+ <p align="right">--Cambridge dictionary</p>
+
+</div>
+<div>
+
+## Metadata
+ * data describing other data
+ * information that is given to describe or help you use other information
+ * metadata are data
+ * can be processed and analyzed
+</div>
+</div>
+
+<div class="fragment">
+
+## Metadata examples:
+<div style="position:absolute">
+ <ul>
+ <li> LabBook </li>
+ <li> author/owner of the data</li>
+ <li> origin of the data
+ <li> data type
+ </ul>
+</div>
+<div style="position:absolute;left:25%">
+ <ul>
+ <li> description of content </li>
+ <li> modification date </li>
+ <li> description of modification </li>
+ <li> location </li>
+ </ul>
+</div>
+<div style="position:relative;left:50%;top:0.7em">
+ <ul>
+ <li> calibration readings</li>
+ <li> software/firmware version</li>
+ <li> data purpose</li>
+ <li> means of creation</li>
+ </ul>
+</div>
+</div>
+
+<div class="fragment">
+<br>
+</center>
+<center style="color:red">!Insufficient metadata make the data useless!</center>
+</div>
+<aside class="notes">
+Sometimes metadata collection takes more time than data collection
+</aside>
+
+
+
+# LCSB research data
+three categories:
+ * **Primary data**
+ * scientific data
+ * measurements, images, observations, notes, surveys, ...
+ * models, software codes, libraries, ...
+ * metadata directly describing the data
+ * data dictionaries
+ * format, version, coverage descriptions, ...
+
+ * **Research record**
+ * description of the research process, including experiment
+ * experiment set-up
+ * followed protocols
+ * ...
+
+ * **Project accompanying documentation**
+ * ethical approvals, information on the consent
+ * collaboration agreements
+ * intellectual property ownership
+ * other relevant documentation
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right;">
+<a href="https://howto.lcsb.uni.lu/internal/policies/LCSB-POL-BIC-03/" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-03 Research Data Retention and Archival Policy</a>
+</div>
\ 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
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index b7a2b3166efee639efba7cbf54e7f69b9d69f53f..0000000000000000000000000000000000000000
--- a/2021/2021-07-27_IT101-DM/slides/data_flow.md
+++ /dev/null
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-../../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_flow.md b/2021/2021-07-27_IT101-DM/slides/data_flow.md
new file mode 100644
index 0000000000000000000000000000000000000000..396c1ec70825f3695e46344ac94dc20617c71c2f
--- /dev/null
+++ b/2021/2021-07-27_IT101-DM/slides/data_flow.md
@@ -0,0 +1,106 @@
+# Typical flow of data
+
+<div style="display:grid;grid-gap:10px;grid-template-columns: 30% 20% 30%;
+ grid-auto-flow:column;grid-template-rows: repeat(4,auto);position:relative;left:8%">
+
+<div class="content-box fragment" data-fragment-index="1">
+ <div class="box-title red">Source data</div>
+ <div class="content">
+
+ * Experimental results
+ * Large data sets
+ * Manually collected data
+ * External
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="2">
+ <div class="box-title yellow">Intermediate</div>
+ <div class="content">
+
+ * Derived data
+ * Tidy data
+ * Curated sets
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="3">
+ <div class="box-title blue">Analyses</div>
+ <div class="content">
+
+ * Exploratory
+ * Model building
+ * Hypothesis testing
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="4">
+ <div class="box-title green">Dissemination</div>
+ <div class="content">
+
+ * Manuscript, report, presentation, ...
+
+ </div>
+</div>
+<center>
+<img src="slides/img/data-flow_sources.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_transformation.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_chart.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_paper.png" height=60%>
+</center>
+
+<div class="content-box fragment" data-fragment-index="5">
+<div class="box-title red">Preserve</div>
+ <div class="content">
+
+ * Version data sets
+ * Backup
+ * Protect
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="6">
+ <div class="box-title yellow">Reproduce</div>
+ <div class="content">
+
+ * Automate your builds
+ * Use workflow tools (e.g. Snakemake)
+
+ </div>
+</div>
+
+
+<div class="content-box fragment" data-fragment-index="7">
+<div class="box-title blue">Trace</div>
+ <div class="content">
+
+ * Multiple iterations.
+ * Code versioning (Git)
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="8">
+<div class="box-title green">Track</div>
+ <div class="content">
+
+ * Through multiple versions
+
+ </div>
+</div>
+
+</div>
+<aside class="notes">
+flow of the data is downstream (mostly), but you are going back and forth
+applies to all data (financial report, lab safety assessment)
+</aside>
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
index a1f1d84bd80a57b481a8c63d2aa70507731335e3..1b538d2e29fe326527e7b41394ff0258b0df2ce0 100644
--- a/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md
+++ b/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md
@@ -1,14 +1,14 @@
# Some practical recommandations
-* Plan your data walking along the data life cycle
+* Do your data processing according to the data life cycle steps
<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:
+* Use data management planning 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>
diff --git a/2021/2021-07-27_IT101-DM/slides/fair-principles.md b/2021/2021-07-27_IT101-DM/slides/fair-principles.md
deleted file mode 120000
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--- a/2021/2021-07-27_IT101-DM/slides/fair-principles.md
+++ /dev/null
@@ -1 +0,0 @@
-../../2021-04-20_IT101-DM/slides/fair-principles.md
\ No newline at end of file
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--- /dev/null
+++ b/2021/2021-07-27_IT101-DM/slides/fair-principles.md
@@ -0,0 +1,12 @@
+# FAIR (meta)data principles
+ * dates back to 2014
+ * well accepted by scientific community
+ * necessity in data driven science
+ * officially embraced by EU and G20
+ * required by funding agencies and journal publishers
+
+<center>
+<img src="slides/img/fair-principles.png" height="400px">
+</center>
+<br>
+<br>
diff --git a/2021/2021-07-27_IT101-DM/slides/howtos.md b/2021/2021-07-27_IT101-DM/slides/howtos.md
deleted file mode 120000
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--- a/2021/2021-07-27_IT101-DM/slides/howtos.md
+++ /dev/null
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-../../2021-04-20_IT101-DM/slides/howtos.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
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index 0000000000000000000000000000000000000000..34998e54e7604a3ee50213dfe9650785c9ced8ed
--- /dev/null
+++ b/2021/2021-07-27_IT101-DM/slides/howtos.md
@@ -0,0 +1,6 @@
+# LCSB How-Tos
+<br>
+https://howto.lcsb.uni.lu/
+<center>
+ <img src="slides/img/howtocard.png" width="50%">
+</center>
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+# Data housekeeping
+## Available data storage
+<div class='fragment' style="position:absolute">
+<img src="slides/img/LCSB_storages_full.png" height="750px">
+</div>
+
+<div class='fragment' style="position:relative">
+<img src="slides/img/LCSB_storages_personal-crossed.png" height="750px">
+
+<div style="position:absolute;left:65%;top:60%">
+
+* Unless consortium/project has formally agreed to use a secure commercial cloud
+
+</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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+</div>
+
+
+
+
+# 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">
+
+### Solution
+
+ * disable write access to the source data
+ * generate checksums!
+
+<div style="position:absolute;left:40%;top:30%">
+<img src="slides/img/checksum.png" width="500px">
+</div>
+</div>
+
+<div class="fragment" style="position:relative; left:0%">
+
+
+## When to generate checksums?
+* before data transfer
+ - new dataset from collaborator
+ - upload to remote repository
+
+* long term storage
+ - master version of dataset
+ - snapshot of data for publication
+</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/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'>
+
+* Guaranted confidentiality
+</div>
+<div class='fragment'>
+
+* Encryption key 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>
+
+
diff --git a/2021/2021-07-27_IT101-DM/slides/introduction.md b/2021/2021-07-27_IT101-DM/slides/introduction.md
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+# Introduction
+<div class="fragment" style="position:absolute">
+<img height="450px" src="slides/img/wordcloud.png"><br>
+
+## Learning objectives
+
+ * How to manage your data
+ * How to look and analyze your data
+ * Solving issues with computers
+ * Reproduciblity in the research data life cycle
+
+</div>
+<div class="fragment" style="position:relative;left:50%; width:40%">
+<div >
+<center>
+<img height="405px" src="slides/img/rudi_balling.jpg"><br>
+Prof. Dr. Rudi Balling, director
+</center>
+</div>
+
+## Pertains to practically all people at LCSB
+ * Scientists
+ * PhD candidates
+ * Technicians
+ * Administrators
+</div>
+
+
diff --git a/2021/2021-07-27_IT101-DM/slides/list.json b/2021/2021-07-27_IT101-DM/slides/list.json
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@@ -0,0 +1,19 @@
+[
+ { "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" }
+]
\ No newline at end of file
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@@ -0,0 +1,25 @@
+## Overview
+
+0. Introduction - learning objectives + targeted audience
+1. Data workflow
+1. Ingestion:
+ * receiving/sending/sharing data
+ * file naming
+ * checksums
+ * backup
+ 1. making data tidy
+ * what is table
+ *
+ 1. Learning to code workflows and analyses - excel files, coding
+ 1. Code versioning and reproducibility
+ 1. Visualization
+ * see the data
+ 1. problem solving
+ * guide
+ * rubberducking
+ * google for help
+ * oracle
+ 1. R3 team
+ 1. Acknowledgment
+
+ 1. data minimization
diff --git a/2021/2021-07-27_IT101-DM/slides/reproducibility.md b/2021/2021-07-27_IT101-DM/slides/reproducibility.md
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@@ -0,0 +1,97 @@
+# Reproducibility
+* ensures credibility
+* key requirement for follow-up and collaborative studies
+
+<div style="position:absolute">
+<img src="slides/img/reproducibility_nature.png" height="650px">
+</div>
+
+<div class="fragment" style="position:relative;left:50%">
+
+## Why is our workflow not reproducible?
+
+ Lack of provenance:
+ * Input data downloaded from “some websiteâ€
+ * Copy & paste operations
+ * Manual text entry
+ * Analysis not coded
+
+</div>
+
+
+
+# Reproducibility
+## Learning to code workflows and analyses
+<div style="display:inline-grid;grid-gap: 40px;grid-template-columns: auto auto;position:relative;left:12%">
+<div class="fragment">
+<div class="content-box">
+<div class="box-title red">Spreadsheets alone</div>
+<div class="content">
+
+ * Is great for looking at data.
+ * Data entry is fast.
+ * Analysis flow is hidden and not in focus.
+
+</div>
+</div>
+<div style="text-align:center">
+<img src="slides/img/excel_data-sheet.png" height="280px">
+</div>
+</div>
+
+<div class="fragment">
+<div class="content-box">
+<div class="box-title">Coding</div>
+<div class="content">
+
+ * Is great for controlling analysis
+ * Data is hidden.
+ * Flow is visible.
+</div>
+</div>
+<img src="slides/img/code-example.png" height="280px">
+</div>
+</div>
+
+<div class="content-box fragment" style="left:15%;width:60%;position:relative">
+<div class="box-title green">Develop data science skills</div>
+<div class="content">
+
+ * Develop good data management and analysis habits.
+ * Start coding your analysis within spreadsheets.
+ * Make yourself familiar with a statistics environment such as R, Python or Matlab
+ * No need to learn a high level programming language such as C++ or Java.
+
+</div>
+</div>
+
+</div>
+
+
+
+# Table
+<div style="position:absolute">
+"Tabular format of data"
+
+### Header
+
+ * one line!
+ * **good** names of columns
+
+### Rows
+ * represent observations/entities
+
+### Columns
+ * represent property of the observations
+ * one data type
+</div>
+<div style="left:50%; position:relative; top:-2em">
+<img src="slides/img/excel_data-sheet.png" width="700px">
+<div class="fragment" data-fragment-index="3" style="position:absolute">
+<img src="slides/img/excel_analyses-sheet.jpeg" width="700px"><br>
+</div>
+<div class="fragment" data-fragment-index="4" style="position:relative">
+<img src="slides/img/red-cross.png" width="700px"><br>
+</div>
+</div>
+
diff --git a/2021/2021-07-27_IT101-DM/slides/storage_setup.md b/2021/2021-07-27_IT101-DM/slides/storage_setup.md
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@@ -0,0 +1,79 @@
+# Storage set-up
+
+* Download Anti-virus software
+* Regularly update your SW/OS
+* Encrypt movable media
+
+
+<div class="fragment" >
+
+### 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>
+<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>
+
+</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
+## 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>
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@@ -0,0 +1,42 @@
+# Thank you.<sup> </sup>
+<center><img src="slides/img/r3-training-logo.png" height="200px"></center>
+<br>
+<br>
+<br>
+<br>
+<center>
+Contact us if you need help:
+
+<a href="mailto:lcsb-r3@uni.lu">lcsb-r3@uni.lu</a>
+</center>
+<div style="position:absolute">
+Links:
+
+HowTo Cards / Policies: https://howto.lcsb.uni.lu/
+
+Course Slides: https://courses.lcsb.uni.lu/
+
+Internal Presentations: https://presentations.lcsb.uni.lu/
+
+LCSB GitLab: https://gitlab.lcsb.uni.lu/
+
+HPC: https://hpc.uni.lu/
+
+Service Portal: https://service.uni.lu/sp
+
+LCSB intranet: https://intranet.uni.lux
+</div>
+<div style="position:relative;top:1.5em;left:55%;width:45%">
+Avalable SW and tools:
+<div style="margin-left: 20px;">
+SIU managed:
+
+  - Service Portal > All Catalogs > IT > Softwares
+</div>
+<div style="margin-left: 20px;">
+LCSB managed:
+
+  - Service Portal > Knowledge > FAQ - Corporate Software\
+  - LCSB intranet > Science tab > Tools
+</div>
+</div>
diff --git a/2021/2021-07-27_IT101-DM/slides/visualization.md b/2021/2021-07-27_IT101-DM/slides/visualization.md
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@@ -0,0 +1,21 @@
+# Visualization
+<center>
+
+**Plot your data!**
+<figure>
+ <img src="slides/img/DinoSequentialSmaller.gif" height="500px">
+ <blockquote>"never trust summary statistics alone; always visualize your data"</blockquote>
+ <figcaption>--Alberto Cairo</figcaption>
+</figure>
+</center>
+
+
+
+# Visualization
+<center>
+
+**Plot your data!**
+<figure>
+ <img src="slides/img/plot-data.png" height="800px">
+</figure>
+</center>