Virtual Environment for Research Data and Analysis (VERDA)
-Jens Krüger, Halima Saker, Stephan Hachinger and Mukund Biradar
AGENDA
Introduction to research data management
Work plan
Centralised login, communication and collaboration tool(cf. https://gitlab.plantmicrobe.de/plantmicrobe-documentation/matrix-element)
Data handling through Gitlab
Interoperation
Conclusions
Introduction
Research Data Management
Research Context
ISA Tab
Annotated Research Context
Why ordered data and annotations are necessary;
Worst case scenario:
Measurements,Conditions, Values comments, All mixed
no automatic readability
all in one table
color marking instead of properly writing down problems
Why such folder structures are necessary
Keep your data ordered and systematic, otherwise you and your colleagues will only solve stupid riddles all day.
Instead of different names in one folder, create different consistent states (datasets / versions).
Raw data
Processed data
Processed and error-corrected data
… and so on
What it means for you (1)
I.Order your investigation (one ore more - big research project(s) you have in TRR) in your mind: What are your:
studies and
assays (where you have to remember what assays belong to each study)
II.Have one main folder for your investigation, with subfolders
"studies"
"assays"
("workflows, runs") [workflow descriptions and run results]
III.Have one folder for each study (e.g studies/my-cool-study) and one for each assay (e.g. assays/plant-n454312-lab2), and inside
one "protocols" folder with protocols
one "resources" folder (studies) /one "datasets" folder (assays) with other data
Element is a communication and collaboration tool designed to facilitate seamless and secure interactions between individuals and teams.
Element focuses on ensuring privacy and security, offering end-to-end encryption for all communication channels.
Provide a range of features for real-time messaging, file sharing, voice and video calls, and project management.
Secure Messaging
Element Chat ensures the privacy and security of your conversations through end-to-end encryption, which means only the intended recipients can access the messages. This feature protects your sensitive information from unauthorized access.
Cross-Platform Compatibility
Element Chat is available on various platforms
Element Login
Rooms and Communities
Group Chat and Direct Messaging
For Reference
File and Media Sharing
For Reference
Emojis, Reactions, and Formatting
user-friendly interface and customization options
Features to integrate
Matrix bridging services
Data Handling
Gitlab
Why TRR Gitlab and not (only) your disk
> Store your data securely
No worries about broken hard disks-redundant
Track and see old versions
Manage your data permissions
> Share your data
Fulfil FAIR principles
Fulfil Nagoya protocol
> Have your data ready for processing at both sites(Tübingen/Munich)
> What is Gitlab?
Web platform to collaborate and track changes in projects
Version control - see and revert to old versions
Basic unit of Gitlab is a git Repository ("more than a folder")
Logging in
Creating a group
Creating a Project
Editing a File
Making a Directory Structure
Uploading a File
Downloading the Entire Repo
Commit History: Single File
Interfacing
first steps/ideas
Features to offer - work with data
Features to integrate - systems interplay (a first idea)
Receive events in Element rooms for issues and merge requests
Collaborate on an issue from Element
Create issues
Close issues
Conclusion
> We like to empower you to
work collaboratively
process data flexibly and manage it
keep order and stay on track
Matrix/Element will be your social chat within TRR
> Gitlab (work in progress) will enable you to
publish data with your papers (or also without)
fulfil the FAIR principles and share/get data
> First Gitlab workshop coming soon!
put your data in nice structures already :)
Thanks for your attention, and remember: always keep your data management journey filled with smile!
Virtual Environment for Research Data and Analysis (VERDA)
