Tip: You can sort the table by themed collections within the table, or via the navigation bar on the left of the page.
| Resource | Description | Topic(s) | Format | Provider |
|---|---|---|---|---|
| AlphaFold2, OpenFold, Protein Language Models and Beyond | Nazim Bouatta | Detailed and lucid talk on understanding the machine learning concepts behind AI protein structure prediction methods | Short Video | Community member | |
| A Brief Introduction to the Carpentries Pedagogic Model | A short version and resources that align with The Carpentries. | learning, teaching skills, assessment, feedback, live-coding | Blog | Paula Andrea Martinez (Author) |
| A guide to organising data associated to a publication using BioStudies | A webinar covering processes of data retrieval and submission to BioStudies. | Data sharing | Webinar | EMBL-EBI |
| AlphaFold 5 minute explainer - Medical Journal | Overview of the AlphaFold pipeline by the New England Journal of Medicine | Short Video | NEJM | |
| AlphaFold2 How-to Guide | Step-by-step guide to help you to understand how the AlphaFold2 algorithm works and how to interpret the output data. | Structure prediction | Guide | Australian Structural Biology Community |
| AlphaFold3 explainer | A visual walkthrough of the AlphaFold3 architecture, with more details and diagrams than you were probably looking for. | Structure prediction | Guide | Community member |
| Amber tutorial | Molecular Dynamics simulation tutorials | Molecular dynamics | Guide | Community member |
| An Introduction to Accessing NCBI Resources on the Command Line using EDirect for Biologists | A workshop teaching biological researchers how to use the command line to search and fetch NCBI data, focusing on creating bash commands to download and organize files and constructing search queries with the EDirect toolkit | Data collection, data reuse | Workshop | NCBI |
| An Introduction to NCBI Cloud Computing for Biologists | A workshop covering how to use AWS services like Athena to mine metadata from the NCBI SRA database for dataset selection, perform sequence alignment analysis with MagicBlast, and visualize aligned data in the NCBI Genome Data Viewer browser application. | Data collection, Data reuse, Data analysis, Genomics | Workshop | NCBI |
| An NCBI Guide to Finding and Analyzing Metagenomic Data | A workshop covering how to search and retrieve and perform analysis on metagenomic sequencing data from NCBI | Data analysis, Data reuse, Metagenomics | Workshop | NCBI |
| ArrayExpress in BioStudies | A tutorial introducing ArrayExpress and describing Annotare tool and MAGE-TAB spreadsheet method for data submission. | Data sharing | Online tutorial | EMBL-EBI |
| Best practices for presenting and sharing AlphaFold models in a paper | A guide to help new-comers get up to speed on presenting and sharing AlphaFold models in papers. | Structure prediction | Guide | Australian Structural Biology Community |
| Biomolecular Structure Prediction Tools | Lists state-of-the-art and emerging tools for Biomolecular Structure Prediction. | Structure prediction | Guide | Community member |
| BioSamples Quick tour | A tutorial introducing the BioSamples database and the concept of a biosample. It also provides website navigation tips, and directs users to more information on accessing and downloading data from BioSamples. | Data sharing | Online tutorial | EMBL-EBI |
| BLAST tutorial | Short how-to guide on using BLAST from the command line | Guide | tinybio | |
| Boston Protein Design and Modeling Club | ~1hr talks by method developers on recent breakthroughs in protein modelling | Webinar | Community member | |
| Brady Johnston Blender tutorials | Blender tutorials for protein animations | Short Video | Community member | |
| Bringing data to life, Data management for the biomolecular sciences | A tutorial encompassing concepts of data management e.g. the data management cycle, data management tools (DMPonline and Data stewardship wizard), FAIRness vs Openness, benefits/challenges of data sharing, and ontologies/standards (e.g. The Ontology Lookup Service (OLS) and The Experimental Factor Ontology (EFO)) to be used to describe/annotate data. | Online tutorial | EMBL-EBI | |
| Building a DSL2 pipeline in Nextflow | This blog post describes how to build analytical pipelines using version 2 of the DSL (domain specific language) that the Nextflow workflow manager implements. | nf-core, DSL-2 | blog post | Anthony Underwood (Author) |
| ChimeraX cavity visualisation | ChimeraX how-to | Guide | Community member | |
| ChimeraX outline selected area | ChimeraX how-to | Guide | Community member | |
| ChimeraX recipes | Protein visualisation guides for UCSF ChimeraX | Protein visualisation | Guide | Community member |
| ChimeraX tutorials | Playlist of tutorials on how to use ChimeraX with command lines | Short Video | Community member | |
| ColabDesign notebooks | Google Colab notebooks for running protein design | Guide | Community member | |
| ColabFold tutorial | Three short tutorials for running ColabFold | Structure prediction | Guide | Community member |
| Data publishing and archival | These slides focus on topics such as discipline-specific repositories, generalist repositories, the FAIRDOM platform, and reproducible models in FAIRDOM. | Data planning, Genomics | Slides | ELIXIR Luxembourg |
| Describing data consistently | What metadata is and why it is important to keep track of this information in biological experiments. | Data planning, Data sharing | Short Video | EMBL-EBI |
| DSL2 and Modules - Nextflow Workshop 2022 | Recording focused on Nextflow DSL2, explaining how to use modules to build more scalable, maintainable, and reusable bioinformatics workflows. It covers key DSL2 concepts, structuring pipelines with modules, and best practices for workflow development using nf-core standards. | DSL-2, nextflow, nf-core | YouTube video | Nextflow |
| DSL2: Pipeline Structure Walkthrough | A detailed walkthrough of the pipeline code structure for the new DSL2 template in Nextflow. | DSL-2, nextflow | YouTube video | nf-core |
| EMBL-EBI AlphaFold Guide | The best way to get up to competency with using an interpreting AlphaFold. Should be done by all grad students using AF | Structure prediction | Online tutorial | EMBL-EBI |
| European Centre of Excellence for Computational Biomolecular Research | Talks focused on molecular dynamics simulations and computational chemistry | Short Video | Community member | |
| Functional Genomics - Submitting data | A tutorial covering the importance of data submission, metadata templates like MIAME and MINSEQE, submission timelines, and submission locations for functional genomics data (e.g. ArrayExpress and GEO). It also discusses secondary databases like Expression Atlas. | Data sharing, Genomics | Online tutorial | EMBL-EBI |
| Getting Started with NCBI Data in Python | A workshop demonstrating effective use of python programming, BioPython package and Jupyter notebooks to facilitate download, analysis and visualisation of data in a reproducible fashion. | Data collection, Data reuse, Data analysis | Workshop | NCBI |
| GROMACS tutorials | Molecular Dynamics simulation tutorials | Molecular dynamics | Guide | Community member |
| GROMACS tutorials | Molecular Dynamics simulation tutorials | Molecular dynamics | Guide | Community member |
| Hello Nextflow (Nextflow) | This is a workshop for those who are completely new to Nextflow | nextflow | self-paced tutorial | Nextflow |
| Hello Nextflow (SIH) | This workshop will provide you with the foundational knowledge required to build Nextflow workflows. | nextflow pipelines, nextflow workflows | self-paced tutorial and workshop | Sydney Informatics Hub (SIH) |
| HH-suite tutorial | User guide for running Hiden Markov Models of protein sequences on the command line | Guide | Community member | |
| HMMER tutorial | User guide for running HMMER on the command line | Guide | Community member | |
| Introduction to Bioinformatics workflows with Nextflow and nf-core | A lesson that motivates the use of Nextflow and nf-core as development tools for building and sharing reproducible data science workflows. | nextflow, nf-core | self-paced tutorial | The Carpentries |
| Introduction to DSL2 in Nextflow | Discussion about the advancements in Nextflow’s Domain Specific Language version 2 (DSL2). It covers topics such as the modularization of workflows, enhanced code reusability, and the integration of community-driven modules, aiming to provide viewers with a comprehensive understanding of DSL2’s capabilities and its application in building complex, maintainable bioinformatics pipelines. | DSL-2, nextflow | YouTube video | nf-core |
| Introduction to exploring genome-phenome data with EGA | A webinar offering an overview of EGA, discussing its controlled access data, the process for gaining access through the Data Access Committee, the use of DUO ontology for tagging data, and a live demo of pyEGA3 for downloading permitted data. | Data planning, Genomics | Webinar | EMBL-EBI |
| Introduction to Nextflow for Data Intensive Pipelines: Part 1 | A video to provide HPC users with an overview on how to develop new and redevelop existing workflows using not only Nextflow but also industry accepted best practices, including code modularity and reuse, rapid prototyping and deployment, and platform independence. | nextflow | YouTube video | Pawsey Supercomputing Research Centre |
| LAMMPS tutorials | Molecular Dynamics simulation tutorials | Molecular dynamics | Guide | Community member |
| Luminous Lab Blender tutorials | Blender tutorials for protein animations | Short Video | Community member | |
| Metabolights - Quick Tour | A tutorial offering an introduction to Metabolights, a summary of data submission and retrieval processes, along with additional support resources. | Data sharing, Metabolomics | Online tutorial | EMBL-EBI |
| MetaboLights: the home for metabolomics experiments and derived information | A webinar introducing MetaboLights, metabolomics, and the Metabolomics Standards Initiative (MSI), demonstrating how to navigate the MetaboLights site to explore study information and providing a brief overview of study submission. | Data sharing, Metabolomics | Webinar | EMBL-EBI |
| MGnify portal - Submitting metagenomics data to the European Nucleotide Archive | A tutorial with a detailed walkthrough for submitting metagenomics data to ENA for analysis by MGnify, highlighting metadata standardization, the use of templates like GSC MIxS for contextual information, and submission methods through ENA or the MGnify browser | Data sharing, Metagenomics | Online tutorial | EMBL-EBI |
| MMseqs2 tutorial | User guide for running MMseqs from the command line | Guide | Community member | |
| NeuroSnap protein design videos | 100 second videos on how to use various protein tools. Guides are with their clean proprietary interface | Short Video | Community member | |
| Nextflow community training portal | A collection of learning resources and Nextflow tutorials. | nextflow training | self-paced tutorial, interactive exercises | Nextflow |
| Nextflow Docs | Get started by installing Nextflow, setting up a development environment with the Nextflow VS Code extension, and running your first script. | getting started, running and developing pipelines, software dependencies, compute and storage | Documentation | Nextflow |
| Nextflow Homepage | Nextflow webpage | documentation, training, resources and Forums | Webpage | Nextflow |
| Nextflow Patterns | This page collects some recurring implementation patterns used in Nextflow applications. | nextflow implementation patterns | self-paced tutorial | Nextflow |
| Nextflow Training | Introductory training on Nextflow | workflows, pipelines, best practices | self-paced tutorial | Curtin Institute of Radio Astronomy (CIRA), The Carpentries |
| Nextflow YouTube channel | Nextflow YouTube channel | videos and podcasts | YouTube channel | YouTube |
| nf-core Homepage | A global community effort to collect a curated set of open‑source analysis pipelines built using Nextflow. | nf-core | Webpage | nf-core |
| nf-core NCI Gadi HPC Configuration | Launch an nf-core pipeline on Gadi | nf-core, HPC configuration | self-paced tutorial | nf-core |
| nf-core Pawsey Setonix HPC Configuration | Launch an nf-core pipeline on Setonix | nf-core, HPC configuration | self-paced tutorial | nf-core |
| nfcamp-tutorial | This tutorial shows how convert the basic rnaseq-nf pipeline to Nextflow DSL-2. | nf-core, DSL-2 | self-paced tutorial | GitHub |
| Nucleotide sequencing data submission and retrieval at the ENA | A webinar introducing the background of the European Nucleotide Archive (ENA), data and metadata models, submission and retrieval processes, submission methods, and tools for data download. | Data collection, Data reuse, Data sharing, Genomics | Webinar | EMBL-EBI |
| Open access: Data sharing and submission | A webinar with discussion regarding importance of sharing research data and infrastructure available at EMBL-EBI to support sharing. It also describes data submission process to IntAct and ComplexPortal. | Data sharing | Webinar | EMBL-EBI |
| Open with purpose: How and why to make your data open | A webinar about open access data, examples of making BioSamples submissions FAIR, open data at IntAct database and how PMC Europe is promoting open access publicationg | Data planning | Webinar | EMBL-EBI |
| PRIDE - Quick tour | A tutorial with an overview of PRoteomics IDEntification (PRIDE) database, how to search and download datasets from PRIDE and an introduction of PRIDE tools: Proteome Xchange Submission Tool and PRIDE Inspector (to assess the quality of a dataset). | Proteomics, Data sharing | Online tutorial | EMBL-EBI |
| PRIDE database: Proteomics data submission, access and visualisation | A webinar covering proteomics data submission process including a demo for Proteome Xchange Submission Tool. | Data sharing, Proteomics | Webinar | EMBL-EBI |
| Pyrosetta tutorials | Collection of how-to guides for protein design | Guide | Community member | |
| Reproducible workflows with nf-core | This workshop will provide you with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. | nf-core | self-paced tutorial and workshop | Sydney Informatics Hub (SIH) |
| RFDiffusion | Walkthrough guide on running RFDiffusion | Guide | Community member | |
| Rosetta tutorial | User guide on protein design with Rosetta | Guide | Community member | |
| Running ColabFold notebook on a HPC | Covers basics of ssh and jupyter notebooks on a HPC | Guide | Community member | |
| Structural Biology Grid Consortium Talk Series | Talks focused on CryoEM but also computational structural biology and protein design | Short Video | Community member | |
| Submitting metagenomic data to ENA | A webinar with an introduction of ENA, INSDC agreement, the ENA data and metadata model, how to structure a metagenomic study and submit metagenomics data to ENA. | Data sharing, Metagenomics | Webinar | EMBL-EBI |
| Submitting your genome wide association study data to the GWAS Catalog | A webinar offering a detailed guide on submitting data to the GWAS Catalog, including user account setup, data format conversion, metadata provision, and validation using a command-line tool, with an emphasis on explaining metadata columns. | Data sharing, Genomics | Webinar | EMBL-EBI |
| Teaching Tech Together | How to create and deliver lessons that work and build a teaching community around them | teaching skills, lesson design, individual learning, community of practice, outreach | Book | Greg Wilson (Author) |
| Template-nf user guide | An How-To Guide to aid beginners in developing their own Nextflow workflows from a template-nf. | nextflow template | How-to Guide | Sydney Informatics Hub (SIH) |
| The Australian Nextflow Seqera Service | The Australian BioCommons Seqera Nextflow Service webpage, providing an overview of the service, its features, benefits, access information, and relevant resources for researchers interested in using Nextflow for bioinformatics workflows. | seqera, nexftlow | Webpage | Australian BioCommons |
| The Carpentries Instructor training | Learn about strategies to teach coding and data workshops, the basics of educational psychology and evidence-based teaching practices | teaching skills, inclusive and accessible learning, live coding, real-time feedback, concept maps | Online course, live | The Carpentries |
| The Open Science Blog | A section of Seqera Labs’ blog dedicated to articles about Nextflow, a platform to share updates, tutorials, community stories, and advancements related to Nextflow. | seqera, nexftlow | Blog | Seqera |
| Tips for Teaching Online from The Carpentries Community | Experiences in teaching and learning online from members of The Carpentries community | online teaching | Blog | The Carpentries |
| Tips on managing and sharing data | Basic tips on managing and sharing data to maximise its re-use in the future. | Data planning | Guide | EMBL-EBI |
| Train the Trainer: Design Genomics and Bioinformatics Training | Discover how to plan and design engaging learning for those wanting to generate and analyse genomic data | course design and development, evaluation, andragogy, outcome-driven training, active learning, online learning | Online course, self-paced | Future Learn |
| Understanding Proteomes | A webinar with an introduction to the proteomes and how to find and download relevant protein datasets. It also includes a UniProt demonstration to find proteomic data with user queries. | Data collection, Data reuse, Proteomics | Webinar | EMBL-EBI |
| Using Publicly available data | A tutorial about publicly available data and importance of licenses to make the data open. Topics covered include data formats, controlled vocabularies, ontologies, reporting guidelines, minimum reporting checklists and importance of unique identifiers for data artefacts. | Data collection, data reuse | Online tutorial | EMBL-EBI |
| Variant submission and data access at the European Variation Archive | A webinar providing an overview of the European Variation Archive (EVA) and its integration with other EBI resources, a live demo of the EVA interface for accessing data via web, FTP, or API, and clarification on using SS and RS IDs for variant access/reference. | Data sharing, Data reuse | Webinar | EMBL-EBI |