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Authors: Conradsen, Cara (orcid: 000...  or Doyle, Maria  or Liffers, Matthias (orcid: 0... 

WORKSHOP: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

 

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.   Event description Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: Spreadsheets, organising data and first steps with R Manipulating and analysing data with dplyr Data visualisation Summarized experiments and getting started with Bioconductor   This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): A breakdown of the topics and timings for the workshop Recommended resources (PDF): A list of resources recommended by trainers and participants Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere:   This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
23 (research data) Things

23 (research data) things is a set of training materials exploring research data management. Each of the 23 things offers a variety of learning opportunities with activities at three levels of complexity:

  • Getting started
  • Learn more
  • Challenge me

All resources used in the program are online...

Keywords: research data management, training material

23 (research data) Things https://dresa.org.au/materials/23-research-data-things-793872d2-c221-4cd6-91be-11a313c74b78 23 (research data) things is a set of training materials exploring research data management. Each of the 23 things offers a variety of learning opportunities with activities at three levels of complexity: * Getting started * Learn more * Challenge me All resources used in the program are online and free to use and reuse under a Creative Commons Attribution 4.0 International licence. You could use all of them as a self-paced course, or choose components to integrate into your own course. The 23 things are designed to build knowledge as the program progresses, so if you’re new to the world of research data management, we suggest you start with things 1-3 and then decide where you want to go from there. These materials supported an international community-based training program delivered in 2016 by the Australian National Data Service. This release migrates these materials to a GitHub repository for continued maintenance. Some updates were made to material that was outdated. We welcome contributions and suggestions via GitHub Issue or Pull Request. contact@ardc.edu.au research data management, training material
Software publishing, licensing and citation

This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research...

Keywords: software, code, Repositories, code sharing, training material

Software publishing, licensing and citation https://dresa.org.au/materials/software-publishing-licensing-and-citation-49097378-f296-44aa-b724-a57d22214d99 This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research vocabularies, persistent identifiers, data discovery catalogues, metadata issues, licensing, governance, underpinning infrastructure (e.g. Nectar Research Cloud) and more. ARDC can also connect projects to national and international communities and initiatives trying to solve common challenges and outline best practice. This session explained why and how to publish, licence and cite software. A video recording of this session can also be found on ARDC's YouTube channel: https://youtu.be/l2acLeuF_QE contact@ardc.edu.au software, code, Repositories, code sharing, training material
National skills ecosystem - call to action

In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4.

  • Skilled trainers / facilitators

  • National training registry

  • National training event calendar

  • Jointly developed training

  • Research...

Keywords: national skills initiatives, data skills, training, skills community, training material

National skills ecosystem - call to action https://dresa.org.au/materials/national-skills-ecosystem-call-to-action-ffd9b4ed-b557-496b-ac35-72467c03c71b In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4. - Skilled trainers / facilitators - National training registry - National training event calendar - Jointly developed training - Research support professionals: career/progression contact@ardc.edu.au national skills initiatives, data skills, training, skills community, training material
Software publishing, licensing, and citation

A short presentation for reuse includes speaker notes.

Making software citable using a code repository, an ORCID and a licence.

Keywords: Software citation, Software publishing, Software registries, Software Repositories, research Software, training material

Software publishing, licensing, and citation https://dresa.org.au/materials/software-publishing-licensing-and-citation-d222144f-380a-455d-b4aa-c56283afc23e A short presentation for reuse includes speaker notes. Making software citable using a code repository, an ORCID and a licence. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Software citation, Software publishing, Software registries, Software Repositories, research Software, training material
ARDC Guide to making software citable

A short guide to making software citable using a code repository, an ORCID and a licence.

Keywords: Software citation, Software publishing, Software registries, Software repositories, Research software, training material

ARDC Guide to making software citable https://dresa.org.au/materials/ardc-guide-to-making-software-citable-46d0f9e4-ef55-43b9-b237-3e52a9d1e141 A short guide to making software citable using a code repository, an ORCID and a licence. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Software citation, Software publishing, Software registries, Software repositories, Research software, training material
ARDC FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

The course structure was based on 'FAIR Data in the...

Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided-2d794a84-f0ff-4e11-a39c-fa8ea481e097 FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub. contact@ardc.edu.au training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
ARDC Datacite API Jupyter notebook

This Jupyter notebook presents a low-barrier entry to using the DataCite REST API to mint, update, publish, and deleted DOIs and their associated metadata.

It was designed specifically to not use any third-party libraries so that it can be reused in almost any Jupyter notebook environment

Code...

Keywords: jupyter, notebook, DataCite, api, python, metadata, DOI, training material

ARDC Datacite API Jupyter notebook https://dresa.org.au/materials/ardc-datacite-api-jupyter-notebook This Jupyter notebook presents a low-barrier entry to using the DataCite REST API to mint, update, publish, and deleted DOIs and their associated metadata. It was designed specifically to not use any third-party libraries so that it can be reused in almost any Jupyter notebook environment Code is presented alongside human readable comments that explain the use of each component of the notebook. contact@ardc.edu.au jupyter, notebook, DataCite, api, python, metadata, DOI, training material