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NBIS Reproducible research course

The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker

Keywords: data management, Reproducibility, Data analysis

Resource type: Training materials

NBIS Reproducible research course https://tess.elixir-europe.org/materials/nbis-reproducible-research-course The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker Leif Wigge Rasmus Ågren John Sundh data management, Reproducibility, Data analysis bioinformaticians
Bioconductor updates

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioconductor updates https://tess.elixir-europe.org/materials/bioconductor-updates Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Helis Academy - FAIRify your data

FAIRify your data: FAIRification & Data modelling using linked data

Keywords: linked data, Wikidata, data management

Resource type: Slides

Helis Academy - FAIRify your data https://tess.elixir-europe.org/materials/helis-academy-fairify-your-data FAIRify your data: FAIRification & Data modelling using linked data linked data, Wikidata, data management bioinformaticians software developers, bioinformaticians Life Science Researchers
Online course 'Learn to write your Data Management Plan'

Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for...

Keywords: Data management plan, data management

Resource type: e-learning

Online course 'Learn to write your Data Management Plan' https://tess.elixir-europe.org/materials/online-course-learn-to-write-your-data-management-plan Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for you research project. While you are training, you can write your DMP in DMPonline. You can do the whole course or just parts of it. That is all up to you. Data management plan, data management Life Science Researchers
Improving findability of BioC packages

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Improving findability of BioC packages https://tess.elixir-europe.org/materials/improving-findability-of-bioc-packages Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Cancer Immuno-Oncology: Bioconductor and beyond

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Cancer Immuno-Oncology: Bioconductor and beyond https://tess.elixir-europe.org/materials/cancer-immuno-oncology-bioconductor-and-beyond Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Workshop
Ready For BioData Management?

"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.

Scientific topics: Data management

Keywords: Data managment plan

Resource type: course materials

Ready For BioData Management? https://tess.elixir-europe.org/materials/ready-for-biodata-management "Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences. Marta Silva Data management Data managment plan Life Science Researchers PhD students Master students Technicians
OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

OpenRiskNet: Ontology Walkthrough and Workshop https://tess.elixir-europe.org/materials/openrisknet-ontology-walkthrough-and-workshop Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Discussion: Guidelines for submitting data to ExperimentHub

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Discussion: Guidelines for submitting data to ExperimentHub https://tess.elixir-europe.org/materials/discussion-guidelines-for-submitting-data-to-experimenthub Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
ELIXIR Webinar: Requirements in data protection law and the upcoming General Data Protection Regulation (GDPR) implementation

Regina Becker (ELIXIR Luxembourg) will give an introduction into the upcoming General Data Protection Legislation (GDPR) that will come into force on 25 May 2018. The new regulation has considerable consequences for managing and storing personal data, imposing more responsibility on the data...

Keywords: GDPR

Resource type: Webinar

ELIXIR Webinar: Requirements in data protection law and the upcoming General Data Protection Regulation (GDPR) implementation https://tess.elixir-europe.org/materials/elixir-webinar-requirements-in-data-protection-law-and-the-upcoming-general-data-protection-regulation-gdpr-implementation Regina Becker (ELIXIR Luxembourg) will give an introduction into the upcoming General Data Protection Legislation (GDPR) that will come into force on 25 May 2018. The new regulation has considerable consequences for managing and storing personal data, imposing more responsibility on the data controllers and data processors. During the webinar, relevant parts of the legislation for research and data sharing will be highlighted. Practical consequences for research institutions and in particular ELIXIR Nodes will be explained, and measures outlined that should be implemented for compliance. In addition, challenges and open questions will be addressed and suggestions made on how to jointly tackle these challenges in ELIXIR. This webinar is of interest for data stewards, Technical Coordinators, and everyone interested in the requirements for processing data for research under the GDPR. GDPR
HCA Data Access

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCA Data Access https://tess.elixir-europe.org/materials/hca-data-access Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
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

Literature Searching Skills and Tools https://tess.elixir-europe.org/materials/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). Medical publications, Curation strategy, PubMed search, Literature database search, Biocuration, Europe PMC
BLAST and multiple sequence alignment (MSA) programs

Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: Blast, E learning, Multiple sequence alignment

BLAST and multiple sequence alignment (MSA) programs https://tess.elixir-europe.org/materials/blast-and-multiple-sequence-alignment-msa-programs-0b2b34d0-a157-49d4-a065-3dcad67ff99d Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search. The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics   Blast, E learning, Multiple sequence alignment Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
Phylogenetics of animal viral pathogens

Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: Animal pathogens, E learning, Phylogenetics

Phylogenetics of animal viral pathogens https://tess.elixir-europe.org/materials/phylogenetics-of-animal-viral-pathogens-428432a3-67ca-4284-8962-fefc2ade75db Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
Integrating publications into bioinformatics analysis

Overview Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as...

Keywords: Europe PMC, REST API, Bioinformatic analysis

Resource type: Webinar

Integrating publications into bioinformatics analysis https://tess.elixir-europe.org/materials/integrating-publications-into-bioinformatics-analysis Overview Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as genes and proteins, metabolites, species, mutations, phosphorylations, interactions, associations, and many more. This webinar will demonstrate how to access text-mined literature evidence programmatically, and how to supplement it with bibliographic information for advanced use cases. Two of such use cases, mapping of tropical disease research by author affiliation geoparsing and comparison of applicability of analytical chemistry techniques, will be introduced by invited speaker, Dr. Magnus Palmblad. This webinar was recorded on 2nd October 2019. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded below. Audience This webinar is aimed at individuals who wish to learn about accessing text-mined literature evidence programmatically. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful. See the EMBL-EBI training pages for a list of upcoming webinars. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful. Europe PMC, REST API, Bioinformatic analysis
Navigating the data-rich literature: finding evidence in biomedical publications

In the age of data‐driven science, discovering all the data associated with a study can be tricky. In this webinar, we will demonstrate how to locate primary data in a publication, find facts and evidence to support your hypothesis, and scan a paper for important biological concepts using tools...

Keywords: Europe PMC, Biomedical Literature, Literature search

Resource type: Webinar

Navigating the data-rich literature: finding evidence in biomedical publications https://tess.elixir-europe.org/materials/navigating-the-data-rich-literature-finding-evidence-in-biomedical-publications In the age of data‐driven science, discovering all the data associated with a study can be tricky. In this webinar, we will demonstrate how to locate primary data in a publication, find facts and evidence to support your hypothesis, and scan a paper for important biological concepts using tools provided by Europe PMC. This webinar was recorded on 4th October 2017. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded here. This webinar is aimed at scientists with an interest in learning more about the literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. If you would like to learn more about Europe PMC have a look at our other webinar on Europe PMC: get the most from literature searches and our Europe PMC: Quick tour. See the EMBL-EBI training pages for a list of upcoming webinars. Europe PMC, Biomedical Literature, Literature search
Preprint discovery 101: Tips & tricks for authors and readers

Preprints - research articles that are publicly posted before undergoing formal peer review - provide a rapid means to share research results. In this webinar, we will demonstrate how to follow hot-off-the-press research by incorporating preprints in your literature search routine using discovery...

Keywords: Europe PMC, Preprints

Resource type: Webinar

Preprint discovery 101: Tips & tricks for authors and readers https://tess.elixir-europe.org/materials/preprint-discovery-101-tips-tricks-for-authors-and-readers Preprints - research articles that are publicly posted before undergoing formal peer review - provide a rapid means to share research results. In this webinar, we will demonstrate how to follow hot-off-the-press research by incorporating preprints in your literature search routine using discovery tools developed by Europe PMC. We will also share some useful tips for those of you posting preprints, including how to claim a preprint to your ORCID or check if your preprint has been cited, reviewed or recommended by others. To learn more about using Europe PMC in your research try our Europe PMC: Quick tour or our webinar Effective Literature Research with Europe PMC. This webinar was recorded on 17 October 2018. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded below. See the EMBL-EBI training pages for a list of upcoming webinars. This webinar is aimed at biological researchers who wish to learn more about incorporating pre-prints into their research. No prior knowledge is required. Europe PMC, Preprints
How to Share Text Mining Results in Biology

Overview Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar, Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission...

Keywords: Europe PMC, Text mining, Literature search

Resource type: Webinar

How to Share Text Mining Results in Biology https://tess.elixir-europe.org/materials/how-to-share-text-mining-results-in-biology Overview Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar, Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission System allows text miners and curators in the field of life sciences to make their results available to the public. Annotated concepts can be browsed and searched for both on Europe PMC website as a part of SciLite tool and Advanced search, as well as via the Annotations API. This webinar was recorded on 9th of July 2019. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded below. Audience This webinar is aimed at individuals who wish to learn more about sharing and reusing results of biomedical text-mining. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful. See the EMBL-EBI training pages for a list of upcoming webinars. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. Europe PMC, Text mining, Literature search
Extracting gene-disease evidence from literature, genetics, genomics and more

Do you want to identify and prioritise new therapeutic targets? Are you looking for associations of your gene of interest with a specific disease? Do you work in the area of drug repurposing? Are you interested in disease biology? If you said yes to any of these questions, this webinar is for...

Keywords: Europe PMC, Open Targets, gene-disease relationship, Text mining

Resource type: Webinar

Extracting gene-disease evidence from literature, genetics, genomics and more https://tess.elixir-europe.org/materials/extracting-gene-disease-evidence-from-literature-genetics-genomics-and-more Do you want to identify and prioritise new therapeutic targets? Are you looking for associations of your gene of interest with a specific disease? Do you work in the area of drug repurposing? Are you interested in disease biology? If you said yes to any of these questions, this webinar is for you. Watch to explore gene-disease relations using freely available tools from Europe PMC and Open Targets. Maria and Denise will show you how to access evidence from research literature, genetics, genomics and chemical data to obtain information at drug targets and disease levels. This webinar was recorded on 7th June 2018. It is best viewed in full screen mode using Google Chrome. The slides from this webinar can be downloaded below. Europe PMC, Open Targets, gene-disease relationship, Text mining Scientists
Europe PMC: Services for academic authors

Researchers are often asked to maintain an up-to-date publication list, whether for job applications, tenure evaluations, or grant proposals. An easy way to do this is by using your ORCID iD and linking it to your published papers. An ORCID is a unique identifier - personalised number that is...

Keywords: Europe PMC, ORCID, Biomedical Literature

Resource type: Webinar

Europe PMC: Services for academic authors https://tess.elixir-europe.org/materials/europe-pmc-services-for-academic-authors Researchers are often asked to maintain an up-to-date publication list, whether for job applications, tenure evaluations, or grant proposals. An easy way to do this is by using your ORCID iD and linking it to your published papers. An ORCID is a unique identifier - personalised number that is assigned to you when you register. By using your ORCID in addition to your name you can make sure that you are easily distinguishable from other researchers with the same name, keep track of your work through name changes, and even pull together different kinds of achievements, like grant awards, training, etc. This video shows how you can register for an ORCID, add your publications in three easy steps to build your digital CV, and how to get a personal author profile page that showcases your publications and citations. This webinar was recorded on 7th of August 2017. It is best viewed in full-screen mode using Google Chrome. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. Europe PMC, ORCID, Biomedical Literature
Effective Literature Research with Europe PMC

Following the latest developments in your scientific field requires thorough and frequent literature research. In this webinar, we will show how to find and access relevant scientific literature using Europe PMC, an open biomedical literature database, part of PubMed Central International. We...

Keywords: Europe PMC, Biomedical Literature, Literature search

Resource type: Webinar

Effective Literature Research with Europe PMC https://tess.elixir-europe.org/materials/effective-literature-research-with-europe-pmc Following the latest developments in your scientific field requires thorough and frequent literature research. In this webinar, we will show how to find and access relevant scientific literature using Europe PMC, an open biomedical literature database, part of PubMed Central International. We will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries. This webinar was recorded on 30 May 2018. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded here. To learn more about searching grant information and on managing, exporting and saving searches you can watch our previous webinar Europe PMC: get the most from literature searches. You will find more information about Europe PMCs API service in our webinar Europe PMC, programmatically. You can also try our Europe PMC: Quick Tour. See the EMBL-EBI training pages for a list of upcoming webinars. This webinar is aimed at scientists who want to optimise their literature searches. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. Europe PMC, Biomedical Literature, Literature search Scientists who want to optimise their literature searches
Detecting differentially expressed genes with RNA-seq 11.9.2019

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and...

Scientific topics: RNA-Seq

Detecting differentially expressed genes with RNA-seq 11.9.2019 https://tess.elixir-europe.org/materials/detecting-differentially-expressed-genes-with-rna-seq This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the workshop is thus suitable for everybody. RNA-Seq
Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis. 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 of two samples. We use Seurat v3...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Single cell RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. 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 of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
Single cell updates

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Single cell updates https://tess.elixir-europe.org/materials/single-cell-updates Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Pitfalls and best practices for serializing Bioconductor objects

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Pitfalls and best practices for serializing Bioconductor objects https://tess.elixir-europe.org/materials/pitfalls-and-best-practices-for-serializing-bioconductor-objects Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Introduction to DataFrames and the impact of recent changes

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Introduction to DataFrames and the impact of recent changes https://tess.elixir-europe.org/materials/introduction-to-dataframes-and-the-impact-of-recent-changes Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Research Data Management and Sharing

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Resource type: e-learning

Research Data Management and Sharing https://tess.elixir-europe.org/materials/research-data-management-and-sharing This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management plans, and be familiar with best practices for working with data including the organization, documentation, and storage and security of data. Learners will also understand the impetus and importance of archiving and sharing data as well as how to assess the trustworthiness of repositories. Today, an increasing number of funding agencies, journals, and other stakeholders are requiring data producers to share, archive, and plan for the management of their data. In order to respond to these requirements, researchers and information professionals will need the data management and curation knowledge and skills that support the long-term preservation, access, and reuse of data. Effectively managing data can also help optimize research outputs, increase the impact of research, and support open scientific inquiry. After completing this course, learners will be better equipped to manage data throughout the entire research data lifecycle from project planning to the end of the project when data ideally are shared and made available within a trustworthy repository. This course was developed by the Curating Research Assets and Data Using Lifecycle Education (CRADLE) Project in collaboration with EDINA at the University of Edinburgh. This course was made possible in part by the Institute of Museum and Library Services under award #RE-06-13-0052-13. The views, findings, conclusions or recommendations expressed in this Research Data Management and Sharing MOOC do not necessarily represent those of the Institute of Museum and Library Services. Data management Life Science Researchers
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

Mascot training course https://tess.elixir-europe.org/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. Proteomics Protein identification, Protein Mass Spectrometry Biologists bioinformaticians Biochemists mass spectrometry
Surprises from scalable container and cloud-based R / Bioconductor deployments

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Surprises from scalable container and cloud-based R / Bioconductor deployments https://tess.elixir-europe.org/materials/surprises-from-scalable-container-and-cloud-based-r-bioconductor-deployments Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Introduction to Persistent Identifiers

Module also available as self-study material in data carpentry style

Scientific topics: Data management

Keywords: system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers

Resource type: course materials

Introduction to Persistent Identifiers https://tess.elixir-europe.org/materials/introduction-to-persistent-identifiers Module also available as self-study material in data carpentry style Data management system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers data stewards data managers bioinformaticians