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BioDT School_Open Access

Section outline

Select section BioDT School

BioDT School

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Select section Introduction

Introduction
- Select activity Information Booklet
  
  Information Booklet File
- Select activity BioDT Project Final Event
  
  BioDT Project Final Event File

Select section Day 1

Day 1

Trainers:

Gabriela Zuquim, BioDT Scientific coordinator, CSC - IT Center for Science

Desalegn Chala Gelete, Crop wild relatives pDT leader, Natural History Museum, University of Oslo

Dag Endresen, Data Scientist, University of Oslo, Natural History Museum, GBIF Norway

Taimur Khan, Data Scientist, UFZ

Select activity Agenda ...

Agenda

09:30 – 09:45	Welcome
09:45 – 10:00	Overview of the School programme
10:00 – 10:20	Participants' Introductions
10:20 – 11:00	1. Introduction to BioDT and the digital twin tool
11:00 – 11:30	Coffee Break
11:30 – 13:00	2. Presenting the digital twin tool (TwinEco)
13:00 – 14:00	Lunch Break
14:00 – 15:30	3. Conceptual design of digital twin (group exercise)
15:30 – 16:00	Coffee Break
16:00 – 17:00	4. Technical tools and platforms
17:00 – 17:30	Self-evaluation questionnaire

Select activity Welcome and Introduction

Welcome and Introduction File
Select activity Session 1

Session 1
Select activity Introduction to BioDT and the digital twin tool

Introduction to BioDT and the digital twin tool File
Select activity Session 2 and 3

Session 2 and 3
Select activity Conceptual design of DTs

Conceptual design of DTs File
Select activity Session 4

Session 4
Select activity Technical Tools and Platforms (GBIF, LUMI, LEXIS)

Technical Tools and Platforms (GBIF, LUMI, LEXIS) File
Select activity Getting started with NaaVRE

Getting started with NaaVRE File
Select activity Saving files in NaaVRE workflows with MinIO

Saving files in NaaVRE workflows with MinIO
Select activity Create GBIF user account, www.gbif.org --> Login

Create GBIF user account, www.gbif.org --> Login URL

To create a GBIF user account go to www.gbif.org, select Login in top right corner, choose login with ORCID, GitHub, Google, or with your email adress.

Select section Day 2

Day 2

Trainers:

Tomas Martinovic, Senior Researcher, IT4Innovations National Supercomputing Center

Jan Dick, Cultural ecosystem services pDT leader, UKCEH

Simon Rolph, Data Scientist, UKCEH

Dmitry Schigel, Data Scientist, GBIF Secretariate

Dag Endresen, Data Scientist, University of Oslo, GBIF Norway

Select activity Agenda ...

Agenda

09:30 – 11:00	1. Turning research/scientific questions: the Cultural Ecosystem Services journey
11:00 – 11:30	Coffee Break
11:30 – 13:00	2. Innovative solutions for digital twin challenges
13:00 – 14:00	Lunch Break
14:00 – 15:30	3. DOI data citation and data papers
15:30 – 16:00	Coffee Break
16:00 – 17:30	4. Use of data APIs and bioRIs

Select activity Session 1 (copy)

Session 1
Select activity Cultural Ecosystem Services background and biodiversity model

Cultural Ecosystem Services background and biodiversity model File
Select activity Cultural Ecosystem Services Information Booklet

Cultural Ecosystem Services Information Booklet File
Select activity Session 2 (copy)

Session 2
Select activity Innovative solutions for digital twin challenges - Session plan

Innovative solutions for digital twin challenges - Session plan File
Select activity Innovative solutions for digital twin challenges - Slides

Innovative solutions for digital twin challenges - Slides File
Select activity Session 3 - Part One

Session 3 - Part One
Click on GBIF demo (UAT) Derived Dataset Tool to open the resource.
Select activity Data papers (Dmitry Schigel, GBIF) - Slides

Data papers (Dmitry Schigel, GBIF) - Slides File
Select activity Data Citation (Dmitry Schigel, GBIF) - Slides

Data Citation (Dmitry Schigel, GBIF) - Slides File
Select activity Open data, data papers, and data citation (Dag Endresen, UiO) - Slides

Open data, data papers, and data citation (Dag Endresen, UiO) - Slides File
Select activity Session 3 - Part Two

Session 3 - Part Two
Select activity Exercise - GBIF Derived Dataset

Exercise - GBIF Derived Dataset File
Select activity Exercise dataset for creating a Derived Dataset

Exercise dataset for creating a Derived Dataset File
Select activity Session 4

Session 4
Select activity Use of data APIs and bioRIs

Use of data APIs and bioRIs File
Select activity Exercise - Using Darwin Core

Exercise - Using Darwin Core URL
Select activity Exercise - Programmatic access to GBIF-mediated data

Exercise - Programmatic access to GBIF-mediated data URL
Select activity Review your learning outcome

Review your learning outcome URL

Select section Day 3

Day 3

Trainers:

Tuomas Rossi, Senior Application Scientist, CSC - IT Center for Science

Tomas Martinovic, Senior Researcher, IT4Innovations National Supercomputing Center

Julian Lopez Gordillo, Data Specialist, Naturalis Biodiversity Center

Select activity Agenda ...

Agenda

09:30 – 11:00	1. Introduction to High-Performance Computing - Scaling up biodiversity models from laptops to supercomputers
11:00 – 11:30	Coffee Break
11:30 – 13:00	2. Hands-on LUMI, using LUMI web interface and Jupyter notebooks
13:00 – 14:00	Lunch Break
14:00 – 15:30	3. Introduction to Open Science
15:30 – 16:00	Coffee Break
16:00 – 17:30	4. Tools and practical steps

Select activity Session 1 (copy)

Session 1
Select activity Introduction to High-Performance Computing

Introduction to High-Performance Computing File
Select activity Session 2

Session 2
Select activity Model Optimisation with Cultural Ecosystem Services pDT

Model Optimisation with Cultural Ecosystem Services pDT File
Select activity Session 3

Session 3
Select activity FAIR and Open Science: from general principles to practical implementations

FAIR and Open Science: from general principles to practical implementations File
Select activity Games of Horror for Open Science Training

Games of Horror for Open Science Training URL
Select activity Session 4 (copy)

Session 4
Select activity Five Recommendations for Research Software

Five Recommendations for Research Software URL
Select activity The Turing Way

The Turing Way URL
Select activity RDMkit

RDMkit URL
Select activity The FAIR Cookbook

The FAIR Cookbook URL
Select activity RO-Crate - Introduction

RO-Crate - Introduction URL
Select activity RO-Crate in Python

RO-Crate in Python URL
Select activity Workflow Run RO-Crate Introduction

Workflow Run RO-Crate Introduction URL
Select activity BioDT FAIR pDT

BioDT FAIR pDT File

Select section Day 4

Day 4

Trainers:

Tomas Martinovic, Senior Researcher, IT4Innovations National Supercomputing Center

Marcella Rydmark, Research Coordinator, Natural History Museum, University of Oslo

Taimur Khan, Data Scientist, UFZ

Desalegn Chala Gelete, Crop wild relatives pDT leader, Natural History Museum, University of Oslo

Jürgen Groenveld, Pollinators pDT leader, UFZ

Select activity Agenda ...

Agenda

09:30 – 11:00	1. Introducing LEXIS and LEXIS API
11:00 – 11:30	Coffee Break
11:30 – 13:00	2. GUI development and Building Blocks/reusable parts
13:00 – 14:00	Lunch Break
14:00 – 15:30	3. BioDT pDTs presentation: Use cases, practical tips, and lesson's learned
15:30 – 16:00	Coffee Break
16:00 – 17:30	4. Presenting the Hackathon and the tasks
20:00	Social Dinner

Select activity Session 1 (copy)

Session 1
Select activity LEXIS Platform

LEXIS Platform File
Select activity Session 2 (copy) (copy)

Session 2
Select activity Development of Graphical User Interface for Interaction with Digital Twins

Development of Graphical User Interface for Interaction with Digital Twins File
Select activity Session 3

Session 3
Select activity Invasive Alien Plant Species Digital Twin
Invasive Alien Plant Species Digital Twin File
Checklist of IAS : https://floraveg.eu
IASDT dashboard : https://allantsouza.shinyapps.io/IAS-pDT-BioDT-web-app/
IASDT data server : http://opendap.biodt.eu/ias-pdt/0/outputs/
Jupyter noteebook for working with the server : https://github.com/BioDT/Hackathon25/blob/main/04-pDTs/IASDT/IASDT-outputs.ipynb
IASDT workflows for input data download and model fitting: https://github.com/BioDT/uc-ias-workflows/tree/lumi
Select activity Invasive Alien Plant Species Data Streaming Jupyter Notebook

Invasive Alien Plant Species Data Streaming Jupyter Notebook URL

Jupyter notebook for streaming data from the IASDT OPeNDAP server.
Select activity Crop Wild Relatives DT-GUI

Crop Wild Relatives DT-GUI File

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Data retention summary

Section outline

BioDT School

Introduction

Day 1

Trainers:

Agenda

Session 1

Session 2 and 3

Session 4

Day 2

Trainers:

Agenda

Session 1

Session 2

Session 3 - Part One

Session 3 - Part Two

Session 4

Day 3

Trainers:

Agenda

Session 1

Session 2

Session 3

Session 4

Day 4

Trainers:

Agenda

Session 1

Session 2

Session 3