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Commit 05e6fe8c authored by Laurent Heirendt's avatar Laurent Heirendt ✈
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Merge branch 'develop' into 'master' 

Regular merge of develop

See merge request R3/school/courses!67
parents a808e347 4ce8acbf
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2020/2020-02-17_IT101-DM/slides/reproducibility.md 0 → 100644
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# 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
* Intermediate and final data not generated by deterministic processes
</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">Excel 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>
<img src="slides/img/excel_data-sheet.png" height="350px">
</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="350px">
</div>
</div>
<div class="content-box fragment" style="width:70%;margin:0 auto;">
<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 Excel.
* 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="600px">
<div class="fragment" data-fragment-index="3" style="position:absolute">
<img src="slides/img/excel_analyses-sheet.jpeg" width="600px"><br>
</div>
<div class="fragment" data-fragment-index="4" style="position:relative">
<img src="slides/img/red-cross.png" width="600px"><br>
</div>
</div>
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# Storage set-up
* Download Anti-virus software
* Encrypt movable media
### Backup
* take care of your own backups!
* don't work on your backup copy!
* minimum is <b>3-2-1 backup rule</b>
<div class="fragment" style="display:inline-grid;grid-template-columns: repeat(3, 1fr);">
<div class="content-box">
<div class="box-title green">Personal research data</div>
<div class="content">
* Working documents on your laptop
* Online share (DropIt, OwnCloud)
* Copy on an external hard drive
</div>
</div>
<div class="content-box">
<div class="box-title blue">Group research data</div>
<div class="content">
* Research data generated in group
* Back-up by central IT
* Geo-resilient copy
</div>
</div>
</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>
# 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
* ...
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# 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:r3lab.core@uni.lu">r3lab.core@uni.lu</a>
</center>
Links:
HowTo cards: https://howto.lcsb.uni.lu/
HPC: https://hpc.uni.lu/
LCSB GitLab: https://git-r3lab.uni.lu/
Service Portal: https://service.uni.lu/sp
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# 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>
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# 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>
<aside class="notes">
Policy! - code in central repository
</aside>
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# 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 JíObj.z Ohře-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
# 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
* Handover data to a new responsible when leaving
</div>
<div style="position:relative;left:50%; width:40%">
<img src="slides/img/cleaning-table.jpg" height="450px">
</div>
# Data housekeeping
## End of project
* data should be kept as a single copy on server-side storage
* no copies on desktops and external devices
* non-proprietary formats
* minimal metadata:
* source
* context of generation
* data structure
* content
* 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
# 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
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# 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
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# 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>
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# 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>
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# LCSB How-Tos
<br>
https://howto.lcsb.uni.lu/
<center>
<iframe data-src="https://howto.lcsb.uni.lu/" height="600px" width="1200px"></iframe>
</center>