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104 materials found

Content provider: CSC - IT Center for Science  or European Bioinformatics Ins... 


Introduction to using containers - OpenShift, Kubernetes and Docker oriented view

This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez

Keywords: Containers, Kubernetes, Cloud computing

Introduction to using containers - OpenShift, Kubernetes and Docker oriented view http://tess.elixir-uk.org/materials/introduction-to-using-containers-openshift-kubernetes-and-docker-oriented-view This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez Containers, Kubernetes, Cloud computing Cloud users
Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science http://tess.elixir-uk.org/materials/introduction-to-research-data-management-data-management-planning-and-services-provided-by-csc-it-center-for-science Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project. Maria Lehtivaara DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE Researchers Life Science Researchers Undergraduate students Master students PhD candidates postdoctoral researchers Senior Researchers, Lab Managers, Postdocs and PhD Students with basic knowledge of DMPs. Participants in the "Introduction to Data Management Plans" workshop.
Discovering scientific evidence using Europe PMC SciLite annotation

For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find...

Keywords: Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer

Resource type: Life Sciences Literature Database

Discovering scientific evidence using Europe PMC SciLite annotation http://tess.elixir-uk.org/materials/discovering-scientific-evidence-using-europe-pmc-scilite-annotation For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find evidence in scientific literature. Who is this course for? This webinar is suitable for scientists, database curators or anyone who wishes to learn more about how to use annotations. Outcomes By the end of the webinar you will be able to: Explore Europe PubMed Central Use text mining for scientific literature searches Aravind Venkatesan Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer
Finding the data behind research publications with Europe PMC

This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints,...

Keywords: Biomedical Literature, Data links, databases, External links

Resource type: Life Sciences Literature Database

Finding the data behind research publications with Europe PMC http://tess.elixir-uk.org/materials/finding-the-data-behind-research-publications-with-europe-pmc This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more. Who is this course for? This webinar is aimed at scientists with an interest in learning more about the data-rich literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful. Michael Parkin Biomedical Literature, Data links, databases, External links
Using Europe PMC for effective literature research

This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex...

Keywords: Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID

Resource type: Life Science Literature Database, Life Sciences Literature Database

Using Europe PMC for effective literature research http://tess.elixir-uk.org/materials/using-europe-pmc-for-effective-literature-research This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries. Europe PMC (https://europepmc.org/) is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more. 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. Michael Parkin Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID
Searching and browsing scientific publications with the new Europe PMC

Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant...

Keywords: Literature search, Data links, preprints

Resource type: Life Sciences Literature Database

Searching and browsing scientific publications with the new Europe PMC http://tess.elixir-uk.org/materials/searching-and-browsing-scientific-publications-with-the-new-europe-pmc Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant and most cited articles in a topic of interest. Also, learn how to find and explore the enhanced content available in Europe PMC. This webinar is aimed at life science scientists who are interested in optimising their literature search skills. No prior knowledge of bioinformatics is required. Michael Parkin Literature search, Data links, preprints
MGnify quick tour

This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets.

Scientific topics: Metagenomics

Keywords: Metagenomics, Sequence analysis, MGnify, Microbiology

Resource type: Tutorial

MGnify quick tour http://tess.elixir-uk.org/materials/mgnify-quick-tour This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets. Ola Tarkowska Lorna Richardson Metagenomics Metagenomics, Sequence analysis, MGnify, Microbiology Life Scientists
Metagenomics Bioinformatics

Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis.

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Tutorial

Metagenomics Bioinformatics http://tess.elixir-uk.org/materials/metagenomics-bioinformatics Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis. Alex Mitchell Varsha Kale Rob Finn Guillermo Rangel Pineros Rebecca Campos Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
EBI Metagenomics: analysing and exploring metagenomics data

EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets...

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Webinar

EBI Metagenomics: analysing and exploring metagenomics data http://tess.elixir-uk.org/materials/ebi-metagenomics-analysing-and-exploring-metagenomics-data EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive. Alex Mitchell Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
Analysing and visualising microbiome-derived datasets using the MGnify Web API

MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available...

Analysing and visualising microbiome-derived datasets using the MGnify Web API http://tess.elixir-uk.org/materials/analysing-and-visualising-microbiome-derived-datasets-using-the-mgnify-web-api MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets drawn from the European Nucleotide Archive (ENA).
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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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
Tools for data management planning

Having a data management plan is essential if we're to make the most of our own data and share it with others. Just like planning an experiment, we should plan what we are going to do with our data and how we are going to do it to ensure that we (and others) can use and re-use the data. If you...

Scientific topics: Data management

Keywords: Data managment plan

Resource type: Video

Tools for data management planning http://tess.elixir-uk.org/materials/tools-for-data-management-planning Having a data management plan is essential if we're to make the most of our own data and share it with others. Just like planning an experiment, we should plan what we are going to do with our data and how we are going to do it to ensure that we (and others) can use and re-use the data. If you have never made a data management plan before the process may initially seem daunting, but fortunately there are many tools out there to help you think through the what, where, how, why and when of data management. In this webinar Sarah Jones from the Digital Curation Centre and Rob Hooft from ELIXIR Netherlands show us two tools - DMP online and the ELIXIR Data Stewardship Wizard - and explain how they can help you apply data management and FAIR data practices in your own research. Data management Data managment plan Life Science Researchers
Giving data context, structure and meaning

Metadata, standards and ontologies are common ways of providing data with context, structure and meaning. In this webinar Sira explores the idea of once data are ontologised (mapped to standard structured vocabulary), they become linkable to build a bigger infrastructure of knowledge network and...

Keywords: metadata, Ontologies

Giving data context, structure and meaning http://tess.elixir-uk.org/materials/giving-data-context-structure-and-meaning Metadata, standards and ontologies are common ways of providing data with context, structure and meaning. In this webinar Sira explores the idea of once data are ontologised (mapped to standard structured vocabulary), they become linkable to build a bigger infrastructure of knowledge network and provides a few scientific examples of how knowledge are drawn from linked data. She also provides a brief overview of tools that can be used to give data context, structure and meaning at different stages of the data lifecycle. metadata, Ontologies
What happens to your data?

This webinar focuses on what happens to your data after you submit it to a public repository and addresses the question of data ownership. Keeva and Nancy introduce the concepts of FAIR data, metadata and standards. They then show you where you can find an appropriate place to share your data...

Scientific topics: Data management

Keywords: metadata, ArrayExpress

Resource type: Video

What happens to your data? http://tess.elixir-uk.org/materials/what-happens-to-your-data This webinar focuses on what happens to your data after you submit it to a public repository and addresses the question of data ownership. Keeva and Nancy introduce the concepts of FAIR data, metadata and standards. They then show you where you can find an appropriate place to share your data and give examples of how metadata and standards are used when you submit data to Metabolights and ArrayExpress. They also answer a few frequently asked data submission-related questions. Data management metadata, ArrayExpress Life Science Researchers
Why share your data?

Presented in two parts, this webinar will explore the value of sharing your data from an institutional and researcher perspective. Our first speaker, Ewan Birney, is one of the directors of EMBL-EBI. He speaks about how the growth in data over the past decade has changed the way that we...

Scientific topics: Data management

Keywords: data sharing

Resource type: Video

Why share your data? http://tess.elixir-uk.org/materials/why-share-your-data Presented in two parts, this webinar will explore the value of sharing your data from an institutional and researcher perspective. Our first speaker, Ewan Birney, is one of the directors of EMBL-EBI. He speaks about how the growth in data over the past decade has changed the way that we approach biology and how EMBL-EBI provides some of the infrastructure to allow data sharing. He finishes up by highlighting the benefits of data sharing to the EMBL-EBI and shares his top four reasons for sharing data. Our second speaker, Elisabeth Busch, is the head of the Vertebrate Genetics and Genomics Group at the Wellcome Sanger Institute and the University of Cambridge. She tells us about her experiences in sharing her own research data, and the reasons that she felt compelled to share her data including the advantages for her own research. Elisabeth Busch Data management data sharing Life Science Researchers
Managing and making the most of your data

In this webinar Marta Teperek & Yasemin Türkyilmaz-van der Velden provide an overview of what data management is highlighting common misconceptions, pitfalls and best practice. They pose the questions 'Is there a reproducibility crisis in science'? and 'How much data would lose if your laptop...

Scientific topics: Data management

Resource type: Video

Managing and making the most of your data http://tess.elixir-uk.org/materials/managing-and-making-the-most-of-your-data In this webinar Marta Teperek & Yasemin Türkyilmaz-van der Velden provide an overview of what data management is highlighting common misconceptions, pitfalls and best practice. They pose the questions 'Is there a reproducibility crisis in science'? and 'How much data would lose if your laptop was stolen?'. This is followed up with an exploration of the selfish benefits of data management and a few hints, tips to get you started on your data management journey. Data management
Text mining: Key concepts and applications

EMBL-EBI presents this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the methods and available tools. The 2nd part looks at how to find articles on Europe PMC - a free literature resource for...

Keywords: Literature search, Text mining, Europe PMC, Biomedical Literature

Resource type: Webinar

Text mining: Key concepts and applications http://tess.elixir-uk.org/materials/text-mining-key-concepts-and-applications EMBL-EBI presents this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the methods and available tools. The 2nd part looks at how to find articles on Europe PMC - a free literature resource for biomedical and health researchers - and how to build your own text mining pipeline. The final part gives a nice case study showing how Europe PMC's pipeline was integrated into a new drug target validation platform called Open Targets (previously CTTV). Literature search, Text mining, Europe PMC, Biomedical Literature
Extracting research evidence from publications

Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature...

Keywords: Literature search, Biomedical Literature, Europe PMC, Text mining

Resource type: Webinar

Extracting research evidence from publications http://tess.elixir-uk.org/materials/extracting-research-evidence-from-publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation. Literature search, Biomedical Literature, Europe PMC, Text mining Wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically.
Europe PMC, programmatically

Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single...

Keywords: Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature

Resource type: Webinar

Europe PMC, programmatically http://tess.elixir-uk.org/materials/europe-pmc-programmatically Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single search. The mission of Europe PMC is to build open access, full-text scientific literature resources and deliver world-class literature services. This webinar will introduce the Europe PMC Articles RESTful API and show you how to access publications and related information, such as citations, data links, or text-mined terms, programmatically. Francesco Talo Yogmatee Rochun Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature
Europe PMC: get the most from literature searches

With Europe PMC, a free biomedical repository and partner in PubMed Central International, you can search worldwide, life-sciences literature, including articles, books, patents, and clinical guidelines. In this webinar, we will show how to use Europe PMC for effective literature research. We...

Keywords: Literature search, Life sciences publications, Europe PMC

Resource type: Webinar

Europe PMC: get the most from literature searches http://tess.elixir-uk.org/materials/europe-pmc-get-the-most-from-literature-searches With Europe PMC, a free biomedical repository and partner in PubMed Central International, you can search worldwide, life-sciences literature, including articles, books, patents, and clinical guidelines. In this webinar, we will show how to use Europe PMC for effective literature research. We will cover searches by topic and author, advanced search options for building complex queries, and setting alerts for your topic to stay on top of the published literature. Literature search, Life sciences publications, Europe PMC This webinar is aimed at scientists with an interest in learning more about the Europe PMC and optimising their literature searches.
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

Introduction to using cloud and containers for training - OpenStack and Docker oriented view http://tess.elixir-uk.org/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 storage. The original material was produced by Shubham Kapoor and Johan Guldmyr, and it was tailored for trainers by Jarno Laitinen. Eija Korpelainen Cloud computing, Containers Trainers
Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists