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BioNT

BioNT provides training in digital skills relevant to the biotech and biomed sectors, while also fostering a community in these fields, engaging experienced learners and trainers. These self-paced learning courses cover topics from introductions to bioinformatics to machine learning, which you can use to learn these skills at your own pace.

The Space team has made the following datasets and collections publicly available. You must be a logged-in member of the Space to access all the datasets and collections.

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[theme_config]{"iconurl":"https://i.ibb.co/XkP34wk/BioNT.png","bgurl":"https://i.ibb.co/bKhTPQV/Whats-App-Image-2024-03-06-at-09-44-51-9c69ad6f.jpg","color1":"#2D849E","color2":"#802450","accent":"#CCE66F","website":"https://biont-training.eu/","collectionOrder":["6926b556e4b021481f76f6eb","661d1e94e4b08465bc30cbc9","6928aca1e4b021481f77237a","66a9fff9e4b08465347f32d8"],"footerText":"BioNT project is co-funded by the EU Digital Europe program, grant agreement number 101100604. Views and opinions expressed on this page are however, those of the author(s) only and do not necessarily reflect those of the European Union or European Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","footerImage":"https://biont-training.eu/images/eu_funded.png","breadcrumbMode":"extended"}[endtheme_config]

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Thumbnail of Data Management: FAIR Principles & Reproducible Analysis

Data Management: FAIR Principles & Reproducible Analysis

A practical overview of FAIR data principles, file organization and versioning, electronic lab notebooks, and reproducible research workflows.

*For each of the sections covered in this course, please visit and follow along with the linked training materials.
Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning 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Thumbnail of Reference-based RNA-Seq data Analysis: Differential Gene Expression analysis, Visualization and GO and KEGG pathway analysis

Reference-based RNA-Seq data Analysis: Differential Gene Expression analysis, Visualization and GO and KEGG pathway analysis

Learn how to interpret DESeq2 output, annotate and visualize differentially expressed genes, and conduct gene ontology and KEGG pathway enrichment analyses.

*For each of the sections covered in this course, please visit and follow along with the linked training materials. Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning 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Thumbnail of Data Management: Foundations & Planning

Data Management: Foundations & Planning

This video gives a concise introduction to data management covering FAIR principles, data protection (GDPR), good computing practices, and data governance across research and industry.

*For each of the sections covered in this course, please visit and follow along with the linked training materials.
Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning 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Thumbnail of Reference-based RNA-Seq data analysis: Counting using RNASTAR

Reference-based RNA-Seq data analysis: Counting using RNASTAR

Learn how to quantify RNA-Seq reads mapped to a reference genome using RNASTAR in a step-by-step workflow.

*For each of the sections covered in this course, please visit and follow along with the linked training materials. Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning experience.*[slides][{"0":"00:00:00.000","1":"00:00:23.920","2":"696dc911e4b0e8ba829fae41","3":"0.0","isRemoved":false},{"0":"00:00:23.920","1":"00:02:03.160","2":"696dc911e4b0e8ba829fae43","3":"23.92","isRemoved":false},{"0":"00:02:03.160","1":"00:02:46.400","2":"696dc911e4b0e8ba829fae49","3":"123.16000000000001","isRemoved":false},{"0":"00:02:46.400","1":"00:03:41.680","2":"696dc911e4b0e8ba829fae4b","3":"166.4","isRemoved":false},{"0":"00:03:41.680","1":"00:04:11.160","2":"696dc911e4b0e8ba829fae4d","3":"221.68","isRemoved":false},{"0":"00:04:11.160","1":"00:04:44.920","2":"696dc911e4b0e8ba829fae4f","3":"251.16000000000003","isRemoved":false},{"0":"00:04:44.920","1":"00:05:06.840","2":"696dc911e4b0e8ba829fae51","3":"284.92","isRemoved":false},{"0":"00:05:06.840","1":"00:05:26.800","2":"696dc911e4b0e8ba829fae53","3":"306.84000000000003","isRemoved":false}][endslides]

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Thumbnail of Reference-based RNA-Seq data analysis: Counting using FeatureCounts

Reference-based RNA-Seq data analysis: Counting using FeatureCounts

This video covers RNA-Seq quantification using FeatureCounts, showing how to count reads mapped to a reference genome.

*For each of the sections covered in this course, please visit and follow along with the linked training materials. Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning experience.*[slides][{"0":"00:00:00.000","1":"00:01:17.120","2":"696dc486e4b0e8ba829fadc0","3":"0.0","isRemoved":false},{"0":"00:01:17.120","1":"00:01:55.280","2":"696dc486e4b0e8ba829fadc2","3":"77.12","isRemoved":false},{"0":"00:01:55.280","1":"00:02:35.400","2":"696dc486e4b0e8ba829fadc4","3":"115.28000000000002","isRemoved":false},{"0":"00:02:35.400","1":"00:03:08.240","2":"696dc486e4b0e8ba829fadc6","3":"155.4","isRemoved":false},{"0":"00:03:08.240","1":"00:04:14.720","2":"696dc486e4b0e8ba829fadc8","3":"188.24","isRemoved":false},{"0":"00:04:14.720","1":"00:04:54.200","2":"696dc486e4b0e8ba829fadca","3":"254.72000000000003","isRemoved":false},{"0":"00:04:54.200","1":"00:05:14.160","2":"696dc486e4b0e8ba829fadcc","3":"294.20000000000005","isRemoved":false}][endslides]

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Thumbnail of Reference-based RNA-Seq data Analysis: First setups until mapping

Reference-based RNA-Seq data Analysis: First setups until mapping

This tutorial demonstrates RNA-Seq mapping workflows, from interpreting MultiQC/Falco reports to choosing a mapper and evaluating the resulting alignments.

*For each of the sections covered in this course, please visit and follow along with the linked training materials. Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning 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Thumbnail of Introduction to transcriptomics presentation

Introduction to transcriptomics presentation

Here we introduce the transcriptomics workflow, guiding you through RNA concepts, quantification, mapping, differential expression, and data visualization.

*For each of the sections covered in this course, please visit and follow along with the linked training materials. Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning experience.*[slides][{"0":"00:00:00.000","1":"00:01:01.033","2":"69270831e4b021481f770394","3":"0.0","isRemoved":false},{"0":"00:01:01.033","1":"00:02:39.900","2":"69270831e4b021481f770396","3":"61.03333333333333","isRemoved":false},{"0":"00:02:39.900","1":"00:03:42.633","2":"69270831e4b021481f770398","3":"159.9","isRemoved":false},{"0":"00:03:42.633","1":"00:04:19.900","2":"69270831e4b021481f77039a","3":"222.63333333333333","isRemoved":false},{"0":"00:04:19.900","1":"00:05:57.033","2":"69270831e4b021481f77039c","3":"259.9","isRemoved":false},{"0":"00:05:57.033","1":"00:07:15.033","2":"69270831e4b021481f77039e","3":"357.0333333333333","isRemoved":false},{"0":"00:07:15.033","1":"00:07:54.433","2":"69270831e4b021481f7703a0","3":"435.0333333333333","isRemoved":false},{"0":"00:07:54.433","1":"00:10:55.100","2":"69270831e4b021481f7703a2","3":"474.43333333333334","isRemoved":false},{"0":"00:10:55.100","1":"00:12:32.033","2":"69270831e4b021481f7703a4","3":"655.1","isRemoved":false},{"0":"00:12:32.033","1":"00:13:19.633","2":"69270831e4b021481f7703a6","3":"752.0333333333333","isRemoved":false},{"0":"00:13:19.633","1":"00:15:14.300","2":"69270831e4b021481f7703a8","3":"799.6333333333333","isRemoved":false},{"0":"00:15:14.300","1":"00:17:23.433","2":"69270831e4b021481f7703aa","3":"914.3","isRemoved":false},{"0":"00:17:23.433","1":"00:18:16.033","2":"69270831e4b021481f7703ac","3":"1043.4333333333334","isRemoved":false},{"0":"00:18:16.033","1":"00:21:49.900","2":"69270831e4b021481f7703ae","3":"1096.0333333333333","isRemoved":false},{"0":"00:21:49.900","1":"00:22:45.433","2":"69270831e4b021481f7703b0","3":"1309.9","isRemoved":false},{"0":"00:22:45.433","1":"00:23:45.300","2":"69270831e4b021481f7703b2","3":"1365.4333333333334","isRemoved":false},{"0":"00:23:45.300","1":"00:24:18.100","2":"69270831e4b021481f7703b4","3":"1425.3","isRemoved":false},{"0":"00:24:18.100","1":"00:25:54.100","2":"69270831e4b021481f7703b6","3":"1458.1","isRemoved":false},{"0":"00:25:54.100","1":"00:27:34.733","2":"69270831e4b021481f7703b8","3":"1554.1","isRemoved":false}][endslides]

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Thumbnail of Mapping hands-on

Mapping hands-on

A step-by-step tutorial on aligning reads to a reference genome, examining BAM file contents, and exploring results in a genome browser.

*For each of the sections covered in this course, please visit and follow along with the linked training materials. Additionally, you will find below a link to the history pad used during the live version of this course. Feel free to refer to it for exercises and Q&A, which might improve your learning experience.*[slides][{"0":"00:00:00.000","1":"00:01:54.160","2":"696cf3ece4b0e8ba829f9dec","3":"0.0","isRemoved":false},{"0":"00:01:54.160","1":"00:02:32.120","2":"696cf3ece4b0e8ba829f9dee","3":"114.16000000000001","isRemoved":false},{"0":"00:02:32.120","1":"00:03:22.240","2":"696cf3ece4b0e8ba829f9df0","3":"152.12","isRemoved":false},{"0":"00:03:22.240","1":"00:03:43.920","2":"696cf3ece4b0e8ba829f9df2","3":"202.24","isRemoved":false},{"0":"00:03:43.920","1":"00:07:35.960","2":"696cf3ece4b0e8ba829f9df4","3":"223.92000000000002","isRemoved":false},{"0":"00:07:35.960","1":"00:08:41.160","2":"696cf3ece4b0e8ba829f9dfc","3":"455.96000000000004","isRemoved":false},{"0":"00:08:41.160","1":"00:09:04.960","2":"696cf3ece4b0e8ba829f9dfe","3":"521.1600000000001","isRemoved":false},{"0":"00:09:04.960","1":"00:09:38.240","2":"696cf3ece4b0e8ba829f9e00","3":"544.96","isRemoved":false},{"0":"00:09:38.240","1":"00:10:04.840","2":"696cf3ece4b0e8ba829f9e02","3":"578.24","isRemoved":false},{"0":"00:10:04.840","1":"00:10:35.640","2":"696cf3ece4b0e8ba829f9e04","3":"604.84","isRemoved":false},{"0":"00:10:35.640","1":"00:11:08.680","2":"696cf3ece4b0e8ba829f9e06","3":"635.6400000000001","isRemoved":false},{"0":"00:11:08.680","1":"00:14:56.320","2":"696cf3ece4b0e8ba829f9e08","3":"668.6800000000001","isRemoved":false},{"0":"00:14:56.320","1":"00:15:31.840","2":"696cf3ede4b0e8ba829f9e0a","3":"896.32","isRemoved":false},{"0":"00:15:31.840","1":"00:18:08.040","2":"696cf3ede4b0e8ba829f9e0c","3":"931.84","isRemoved":false},{"0":"00:18:08.040","1":"00:18:39.280","2":"696cf3ede4b0e8ba829f9e0e","3":"1088.0400000000002","isRemoved":false},{"0":"00:18:39.280","1":"00:19:09.280","2":"696cf3ede4b0e8ba829f9e10","3":"1119.2800000000002","isRemoved":false},{"0":"00:19:09.280","1":"00:19:47.280","2":"696cf3ede4b0e8ba829f9e12","3":"1149.2800000000002","isRemoved":false},{"0":"00:19:47.280","1":"00:20:18.200","2":"696cf3ede4b0e8ba829f9e14","3":"1187.2800000000002","isRemoved":false},{"0":"00:20:18.200","1":"00:20:40.680","2":"696cf3ede4b0e8ba829f9e16","3":"1218.2","isRemoved":false},{"0":"00:20:40.680","1":"00:22:05.120","2":"696cf3ede4b0e8ba829f9e18","3":"1240.68","isRemoved":false},{"0":"00:22:05.120","1":"00:22:45.280","2":"696cf3ede4b0e8ba829f9e1a","3":"1325.1200000000003","isRemoved":false},{"0":"00:22:45.280","1":"00:24:02.560","2":"696cf3ede4b0e8ba829f9e1c","3":"1365.2800000000002","isRemoved":false},{"0":"00:24:02.560","1":"00:24:37.480","2":"696cf3ede4b0e8ba829f9e1e","3":"1442.5600000000002","isRemoved":false},{"0":"00:24:37.480","1":"00:27:02.720","2":"696cf3ede4b0e8ba829f9e20","3":"1477.48","isRemoved":false},{"0":"00:27:02.720","1":"00:27:27.000","2":"696cf3ede4b0e8ba829f9e22","3":"1622.72","isRemoved":false},{"0":"00:27:27.000","1":"00:27:56.640","2":"696cf3ede4b0e8ba829f9e24","3":"1647.0000000000002","isRemoved":false},{"0":"00:27:56.640","1":"00:28:37.720","2":"696cf3ede4b0e8ba829f9e26","3":"1676.64","isRemoved":false},{"0":"00:28:37.720","1":"00:29:07.120","2":"696cf3ede4b0e8ba829f9e28","3":"1717.72","isRemoved":false},{"0":"00:29:07.120","1":"00:29:42.720","2":"696cf3ede4b0e8ba829f9e2a","3":"1747.1200000000003","isRemoved":false},{"0":"00:29:42.720","1":"00:30:11.400","2":"696cf3ede4b0e8ba829f9e2c","3":"1782.7200000000003","isRemoved":false},{"0":"00:30:11.400","1":"00:31:28.920","2":"696cf3ede4b0e8ba829f9e2e","3":"1811.4","isRemoved":false},{"0":"00:31:28.920","1":"00:32:25.240","2":"696cf3ede4b0e8ba829f9e30","3":"1888.92","isRemoved":false},{"0":"00:32:25.240","1":"00:33:09.160","2":"696cf3ede4b0e8ba829f9e32","3":"1945.2400000000002","isRemoved":false},{"0":"00:33:09.160","1":"00:33:38.720","2":"696cf3ede4b0e8ba829f9e50","3":"1989.16","isRemoved":false},{"0":"00:33:38.720","1":"00:34:04.200","2":"696cf3ede4b0e8ba829f9e52","3":"2018.7200000000003","isRemoved":false},{"0":"00:34:04.200","1":"00:34:57.960","2":"696cf3ede4b0e8ba829f9e54","3":"2044.2000000000003","isRemoved":false},{"0":"00:34:57.960","1":"00:35:29.920","2":"696cf3ede4b0e8ba829f9e56","3":"2097.96","isRemoved":false},{"0":"00:35:29.920","1":"00:36:36.480","2":"696cf3ede4b0e8ba829f9e58","3":"2129.92","isRemoved":false},{"0":"00:36:36.480","1":"00:36:57.240","2":"696cf3ede4b0e8ba829f9e5a","3":"2196.48","isRemoved":false}][endslides]

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Thumbnail of Awareness in Data Management and Analysis for Industry and Research

Awareness in Data Management and Analysis for Industry and Research

This workshop covers essential research data management skills. The first part introduces data management fundamentals, best practices, European data spaces, and Data Management Plan creation. The second part focuses on practical implementation: data organisation, FAIR principles, Electronic Lab Notebooks, and reproducible data analysis using tools like Git, Zenodo, and Conda. Interactive exercises throughout help participants apply concepts to real-world research scenarios.

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Thumbnail of A practical introduction to bioinformatics and RNA-seq using Galaxy

A practical introduction to bioinformatics and RNA-seq using Galaxy

This course provides a comprehensive introduction to RNA-sequencing (RNA-seq) data analysis using the Galaxy platform. Galaxy offers an accessible, user-friendly, and FAIR environment that empowers researchers without programming experience to perform complex bioinformatics analyses. The course begins with an introduction to Galaxy, followed by tutorials on sequencing quality control and read mapping. Participants will then learn both the foundational and advanced steps of RNA-seq data analysis, including quantification and differential expression. The course concludes with an overview of relevant data types, databases, and resources to support further exploration and interpretation of RNA-seq results.

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BioNT Community Event & CarpentryConnect Heidelberg 2024

[ordering]manual[endordering][collection_order]["6744a8c8e4b0846534895a56","6744a8d8e4b0846534895a5b"][endcollection_order]

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Thumbnail of An introduction to High Performance Computing

An introduction to High Performance Computing

This course provides a comprehensive introduction to high-performance computing (HPC), covering fundamental concepts such as accessing and navigating HPC clusters using the Unix shell, transferring files, submitting and managing jobs through a scheduler, and understanding the benefits and limitations of parallel execution. The materials also introduce HPC workflow management with Snakemake, enabling learners to construct reliable, scalable, and reproducible scientific workflows suitable for both academic and industrial environments, particularly relevant for artificial intelligence applications requiring large-scale or specialised computation.

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From zero to hero with Python

This practical introduction to programming languages will cover all basic concepts needed to program in Python3 while also demonstrating how to showcase code and its results on a website. Thanks to its simple syntaxes and its wide range of usages, the programming language Python is considered an excellent candidate to begin a programming journey[ordering]manual[endordering]

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