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Authors: Aidan Budd  or Christine Staiger 

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 http://tess.elixir-uk.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
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 - Persistent identifiers and their use cases http://tess.elixir-uk.org/materials/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 Referencing data and code, Findability of data and code, Identifying data and code, data management data stewards Life Science Researchers bioinformaticians
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 Sharing, publishing and archiving http://tess.elixir-uk.org/materials/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 archives o Finding your ideal archive data sharing, Data publishing, data archiving, data repositories, data management
Introduction to FAIR data stewardship

FAIR data Stewardship: How to improve the reuse of nanosafety data

Scientific topics: Data management

Keywords: FAIR

Introduction to FAIR data stewardship http://tess.elixir-uk.org/materials/introduction-to-fair-data-stewardship FAIR data Stewardship: How to improve the reuse of nanosafety data Data management FAIR Life Science Researchers
FAIR Data Stewardship - Data sharing, archiving and publishing

The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities...

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

Resource type: Slides, Training materials

FAIR Data Stewardship - Data sharing, archiving and publishing http://tess.elixir-uk.org/materials/fair-data-stewardship-data-sharing-archiving-and-publishing The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities towards data are distributed. The course does not require any prior knowledge. Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication General Interest Scientists Researchers data stewards
Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies http://tess.elixir-uk.org/materials/introduction-to-multiple-sequence-alignments-msas-and-phylogenies Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
Summarising sets of phylogenies

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics

Summarising sets of phylogenies http://tess.elixir-uk.org/materials/summarising-sets-of-phylogenies A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes examples of applications of these tools, along with introducing ideas of tree topology and some terminology associated with it. Designed for remote training. Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics Bench biologists 2013-10-23 2017-10-09
Introduction to Multiple Sequence Alignment

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

Keywords: Multiple sequence analysis, Protein structure, Sequence analysis

Introduction to Multiple Sequence Alignment http://tess.elixir-uk.org/materials/introduction-to-multiple-sequence-alignment An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of alignmetns (structural and evolutionary), and ways of building manual and automatic alignments, and an introduction to JalView Multiple sequence analysis, Protein structure, Sequence analysis Bench biologists 2013-10-23 2017-10-09
Introduction to Bioinformatics

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Keywords: Introduction bioinformatics

Introduction to Bioinformatics http://tess.elixir-uk.org/materials/introduction-to-bioinformatics An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could be wrong, and what we can do to spot it. Introduction bioinformatics Bench biologists 2013-10-23 2017-10-09
Interpreting Phylogenies

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: Molecular evolution, Phylogenetics

Interpreting Phylogenies http://tess.elixir-uk.org/materials/interpreting-phylogenies Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic trees. Includes exercises on visulaising and manipulating trees using Dendroscope and NJplot to reinforce some of these ideas, while also providing a very basic overview of steps involved in a generic phylogenetic analysis. Molecular evolution, Phylogenetics experimeintal biologist researchers field biologist researchers 2013-09-13 2017-10-09