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49 materials found

Resource type: Jupyter notebook  or Slides 


BioExcel Building Blocks (BioBB) Training Material

BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR.

Keywords: molecular dynamics, Docking, Modeling, life sciences

Resource type: Jupyter notebook

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data governance, Data management

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

DSW Template Development Kit: The Tutorial

Data Stewardship Wizard is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines...

Scientific topics: Data management

Keywords: data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development

Resource type: Video, Slides, Webinar

FAIR data - Module 4 (share and publish data)

Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données

Scientific topics: Data management, Biology, Bioinformatics

Keywords: data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse

Resource type: Slides

FAIR data - Module 3 (Metadata)

Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données

Scientific topics: Data management, Biology, Bioinformatics

Operations: Data handling

Keywords: metadata, data annotation, life science standards, data sharing

Resource type: Slides

FAIR data - Module 2 (data life cycle)

La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données

Scientific topics: Bioinformatics, Biology, Data management

Operations: Data handling

Keywords: Data preserving, Data storage

Resource type: Slides

FAIR data - Module 1 (research data)

Research data and their centrality in the research process.
This material is mostly in French.

Keywords: metadata, Data Life Cycle, Reproducibility, Data management plan

Resource type: Slides

Slides DMP writing workshop for Researchers in Bergen online 21.04. - 22.04.2021

Slides DMP writing workshop for Researchers in Bergen online 21.04. - 22.04.2021

Scientific topics: Data management

Operations: Deposition, Data handling, Data retrieval

Keywords: Data management plan, data management

Resource type: Slides

Slides from DMP writing workshop, for Researchers in Aas, online 09.03.- 10.03.2021

Slides from DMP writing workshop, for Researchers in Aas, online 09.03.- 10.03.2021

Scientific topics: Data management

Operations: Data retrieval, Data handling, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Data Management Planning workshop for new Life Science Projects

Slides from Data Management Planning online workshop for Life Science Projects for researchers

Scientific topics: Data management

Operations: Data retrieval, Data handling, Deposition

Keywords: data management plan, NeLS, TSD, metadata, sensitive, data publication, data protection, storage, identifiers, DMP, licensing, Compliance, data life cycle - collect, data life cycle - reuse, data life cycle - analyse, data life cycle - process, data life cycle - preserve, data life cycle - share, data life cycle - plan

Resource type: Slides

Plant Phenotyping Data managment Webinar (MIAPPE)

The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking...

Scientific topics: Data submission, annotation, and curation, Data quality management, Phenomics, Plant biology

Operations: Standardisation and normalisation

Resource type: Video, Slides

Slides from Data Management Planning Workshop

Slides from Data Management Planning online workshop for Life Science Projects for researchers at UiO 2020-12-11

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop

Slides from Data Management Planning online workshop for Life Science Projects for researchers at NTNU 2020-12-01

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

DE-Sim examples, tutorials, and documentation

DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, Scipy,...

Scientific topics: Computational biology, Mathematics, Computer science, Simulation experiment

Operations: Visualisation, Modelling and simulation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Ås 11 March 2020

Scientific topics: Data management

Operations: Deposition, Data retrieval, Data handling

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Bergen 04 March 2020

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

WheatIS DataDiscovery webinar

The WheatIS project aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is...

Scientific topics: Data management

Keywords: wheat, information system, data discovery

Resource type: Webinar, Slides, Video

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data management, Data governance

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides

Helis Academy - FAIRify your data

FAIRify your data: FAIRification & Data modelling using linked data

Keywords: linked data, Wikidata, data management

Resource type: Slides

Literature Searching Skills and Tools

Training slides on literature searching skills and tools. Part of biocurators training for the Postgraduate Certificate in Biocuration, developed by the University of Cambridge and the European Bioinformatics Institute (EMBL-EBI).

Keywords: Medical publications, Curation strategy, PubMed search, Literature database search, Biocuration, Europe PMC

Resource type: Slides

Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Mascot training course

The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.

Scientific topics: Proteomics

Keywords: Protein identification, Protein Mass Spectrometry

Resource type: Slides, Video, Training materials

FAIRification & Data modelling

Wikidata
fairification

Keywords: FAIR, linked data, ontologies, metadata

Resource type: Slides

Helis Academy - Persistent identifiers and their use cases

Managing increasing numbers of data objects
Sharing data from different sourcesamongst researchers
Data needs to be (globally) identifiable and addressable to ensure reuse of data
Data citation
Linking data from different source

Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management

Resource type: Slides

Helis Academy - Data Sharing, publishing and archiving

Basic knowledge of:
o Know what a repository is
o Characteristics of Data Sharing, Archiving and Publishing
o Knowledge of major platforms for Sharing, Archiving and Publishing

Hands on experience:
o Dataverse possibilities for sharing and publishing
o Designing requirements digital...

Keywords: data sharing, Data publishing, data archiving, data repositories, data management

Resource type: Slides

Helis Academy - Data Management Plans, why and how?

Research Data Management
The organisation of data throughout the research project
everyday management of research data (storage, file naming, preservation)
how will data be preserved and shared after the project is completed?

Scientific topics: Data management

Keywords: Data managment plan, Data Life Cycle

Resource type: Slides, PDF

ELIXIR Beacons (at ISMB / ECCB)

Large cohorts, with potentially millions of participants, are needed to understand the genetic and molecular signatures of diseases, and they provide a cornerstone for the creation of personalised treatments. The ELIXIR::GA4GH Strategic Partnership will facilitate the responsible sharing of these...

Keywords: beacon

Resource type: Slides, Computer Software

FAIR Data Stewardship - Data sharing, archiving and publishing

In this workshop we focus on three aspects of FAIR data stewardship: Data sharing, publishing and archiving. Many scientists have an insufficient overview over data services, roles and their responsibilities towards safe data sharing, archiving and publishing. Shedding light on these roles helps...

Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

Resource type: Slides, Training materials

Introduction to using cloud and containers for training - OpenStack and Docker oriented view

This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object...

Keywords: Cloud computing, Containers

Resource type: Slides, course materials

How to install and deploy Beacon

This is an online tutorial where you can learn how to install the Beacon application and "light a beacon" (i.e. deploy the Beacon application) on your data.

The tutorial is hosted on the ELIXIR-SI eLearning Platform (EeLP). The main part of the tutorial are learning materials with...

Scientific topics: Genomics

Keywords: genomics, open access, eLearning, EeLP

Resource type: Video, Manual, Slides, Installation instructions