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 0000000000000000000000000000000000000000..14cff81ab4fd0cf697050da35347ab2d42c6ef48 --- /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 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> 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 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 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..1b538d2e29fe326527e7b41394ff0258b0df2ce0 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md @@ -0,0 +1,23 @@ + +# Some practical recommandations + +* 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 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> + <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 100644 index 0000000000000000000000000000000000000000..be70f11a6f0b941a0e7f7b86b990a1c098096282 --- /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 new file mode 100644 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> diff --git a/2021/2021-07-27_IT101-DM/slides/img/3pillars-full.png b/2021/2021-07-27_IT101-DM/slides/img/3pillars-full.png new file mode 100644 index 0000000000000000000000000000000000000000..20484db55a5c781fdaa1d8600fa99bf10fe2410f Binary files /dev/null and b/2021/2021-07-27_IT101-DM/slides/img/3pillars-full.png differ diff --git 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b/2021/2021-07-27_IT101-DM/slides/img/scripts/ggplot_visualization.R new file mode 100644 index 0000000000000000000000000000000000000000..ac48ba28f1d937174ba5acdc0260e41321a201fc --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/img/scripts/ggplot_visualization.R @@ -0,0 +1,22 @@ + +library(ggplot2) +library(data.table) +library(ggpubr) +data(iris) +iris <- data.table(iris) +iris <- iris[c(1:103)] + +g1 <- ggplot(iris, aes(x = Species, y = Sepal.Length))+ + geom_bar(aes(fill = Species),stat="summary", fun.y="mean" ) +guides(fill = F)+ + ylim(c(0,8)) + ylab("Mean Sepal Lenght ") + +g2 <- ggplot(iris, aes(x = Species, y = Sepal.Length))+ + geom_boxplot(aes(fill = Species))+ + ylim(c(0,8))+guides(fill = F)+ylab("Sepal Length") + +g3 <- ggplot(iris, aes(x = Species, y = Sepal.Length))+ + geom_boxplot(aes(fill = Species))+ + ylim(c(0,8))+ geom_point( position="jitter")+ + guides(fill = F)+ylab("Sepal Length") + +ggarrange(g1, g2, g3, nrow = 1)+ggsave(filename = "../plot-data.png", device = "png", width =12, height = 6) diff --git a/2021/2021-07-27_IT101-DM/slides/img/undraw_secure_server_s9u8.png b/2021/2021-07-27_IT101-DM/slides/img/undraw_secure_server_s9u8.png new file mode 100644 index 0000000000000000000000000000000000000000..a38b9ed82faa9520a719c68c94d84ec6410ba0f1 Binary files /dev/null and b/2021/2021-07-27_IT101-DM/slides/img/undraw_secure_server_s9u8.png differ diff --git a/2021/2021-07-27_IT101-DM/slides/img/wordcloud.png b/2021/2021-07-27_IT101-DM/slides/img/wordcloud.png new file mode 100644 index 0000000000000000000000000000000000000000..7fb00a8005204df151fc4ebb151c9e86214bfc80 Binary files /dev/null and b/2021/2021-07-27_IT101-DM/slides/img/wordcloud.png differ 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 0000000000000000000000000000000000000000..6ac2ae378a2a442174b519beb7bd186a70419b24 --- /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 100644 index 0000000000000000000000000000000000000000..383467f0027ee1671425311aa48254ff9207ea4d --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/ingestion.md @@ -0,0 +1,90 @@ +# 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 new file mode 100644 index 0000000000000000000000000000000000000000..fed0b0971b7d1f868f2fd8213461c724834da16a --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/introduction.md @@ -0,0 +1,28 @@ +# 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 new file mode 100644 index 0000000000000000000000000000000000000000..17136d973bc9a81e70687fa1934d0f5b4f9c5baf --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/list.json @@ -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 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 100644 index 0000000000000000000000000000000000000000..6f9143c7c64fa539eb44c3ea5ff9eec076701879 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/overview.md @@ -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/problem_solving.md b/2021/2021-07-27_IT101-DM/slides/problem_solving.md new file mode 100644 index 0000000000000000000000000000000000000000..f34e0a2bc914e35010f492936be5a9506c8ecf27 --- /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 0000000000000000000000000000000000000000..723e779d6d42bf3a7bfd8d1203d712b8d58e3f58 --- /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"> + + * 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> 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 100644 index 0000000000000000000000000000000000000000..a21df4faf8d6981a4911ac5060a78717c2656b53 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/reproducibility.md @@ -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 website†+ * 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 new file mode 100644 index 0000000000000000000000000000000000000000..d321b5ccd652709e969a2027cac2d7c3a7c69a6a --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/storage_setup.md @@ -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> 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 100644 index 0000000000000000000000000000000000000000..0db75ff6af3e6c451f3171b3faf2c558d7392f61 --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/thanks.md @@ -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 new file mode 100644 index 0000000000000000000000000000000000000000..78847e73a297f77e3753623d7e546dcf499d4e2f --- /dev/null +++ b/2021/2021-07-27_IT101-DM/slides/visualization.md @@ -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>