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30 materials found

Difficulty level: Advanced 


Hands-on for 'Python - Multiprocessing' tutorial

The questions this addresses are:
- How can I parallelize code to make it run faster
- What code is, or is not, a prime target for parallelisation

The objectives are:
- Understanding how to paralellise code to make it run faster.
- Identifying how to decompose code into a parallel unit.

Keywords: data-science, jupyter-notebook

Resource type: hands-on tutorial

Spatial Omics Data Analysis

This is an international course hosted by the National Bioinformatics Infrastructure Sweden (ELIXIR-SE) in collaboration with the Human Developmental Cell Atlas (HDCA), the Royal Institute of Technology, Stockholm University, Karolinska Institutet, Uppsala University, Charité Clinical University...

Keywords: spatial, Multiomics, In situ sequencing, Spatial Transcriptomics, Single cell RNAseq

Resource type: FREE online course, course materials, online course

Hands-on for 'Genome annotation with Maker' tutorial

The questions this addresses are:
- How to annotate an eukaryotic genome?
- How to evaluate and visualize annotated genomic features?

The objectives are:
- Load genome into Galaxy
- Annotate genome with Maker
- Evaluate annotation quality with BUSCO
- View annotations in JBrowse

Keywords: genome-annotation, eukaryote

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein Quantification via Stable Isotope Labelling (SIL)' tutorial

The questions this addresses are:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?

The objectives are:
- MS1 feature quantitation and mapping of quantitations to peptide and...

Scientific topics: Proteomics

Keywords: proteomics, DDA, SILAC

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using OpenMS tools' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

The objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'dplyr & tidyverse for data processing' tutorial

The questions this addresses are:
- How can I load tabular data into R?
- How can I slice and dice the data to ask questions?

The objectives are:
- Read data with the built-in read.csv
- Read data with dplyr's read_csv
- Use dplyr and tidyverse functions to cleanup data.

Keywords: data-science, R, jupyter-notebook, rmarkdown-notebook

Resource type: hands-on tutorial

Hands-on for 'Rule Based Uploader: Advanced' tutorial

The questions this addresses are:
- How to use the rule based uploader to create complex collections

The objectives are:
- Learn even more about the Rule Based Uploader

Keywords: galaxy-interface, collections, tags

Resource type: hands-on tutorial

Hands-on for 'High Throughput Molecular Dynamics and Analysis' tutorial

The questions this addresses are:
- How are protein-ligand systems parameterized for molecular dynamics simulation?
- What kind of analysis can be carried out on molecular trajectories?
- How can high-throughput MD be used to study multiple ligands?

The objectives are:
- Learn about...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Educational webinars on rare endocrine conditions (ENDO-ERN)

The European Reference Network on rare endocrine conditions (Endo-ERN) aims to improve access to high-quality healthcare for patients with rare hormonal disorders.

Various webinar on rare endocrine conditions are proposed :
- Update on congenital adrenal hyperplasia
- Prophylactic...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Educational webinars on rare and complex epilepsies (EpiCARE ERN)

EpiCARE ERN (European Reference Network for rare and complex epilepsies) has launched a series of educational webinars presented by experts. The webinars are free to join from anywhere in the world, pre-registration is required.
Topics are related to epilepsy diagnostics and treatment and...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Postgraduate Curriculum in Rare Kidney Diseases developed by ERKNet

The European Reference Network for Rare Kidney Diseases (ERKNet), the European Society for Paediatric Nephrology (ESPN) and the International Pediatric Nephrology Association (IPNA) have since January 2020 launched a set of webinars.

They take place monthly on Tuesdays 4 pm CET (except summer...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Education and Training webinars on genetic tumor risk syndromes (ERN GENTURIS)

Target audience for the webinars are clinicians, genetic counsellors, clinical scientists and other genetics health professionals. The presentation itself lasts approximately 20-30 minutes, and viewers have the opportunity to send questions on the subject area which will be addressed in a...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Educational videos on rare and low prevalence complex diseases of the heart (ERN GUARD-Heart)

ERN GUARD-Heart (European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart) propose educational videos for experts on the following topics:
- CPVT: Diagnosis and Risk; Treatment; ICD therapy
- HCM: Definition, etiology and diagnostic work-up
- Sudden cardiac death:...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Video, e-learning

Educational webinars on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET)

ERN ReCONNET is the European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases. These include hereditary conditions, and systemic autoimmune diseases such as systemic sclerosis, mixed connective tissue diseases, inflammatory idiopathic myopathies,...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, Video, e-learning

DE-Sim examples, tutorials, and documentation

DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, Scipy,...

Scientific topics: Simulation experiment, Computer science, Mathematics, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

Jaqpot Hackathon - Training materials

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, attendees learned how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file.

Jaqpot is a computational platform for in silico...

Keywords: nanoinformatics, toxicity prediction, e-tools, Modeling, data FAIRness

Whole Genome Sequencing: Decoding the Language of Life and Health

Whole genome sequencing is a relatively new technology that allows us to ‘read’ a person’s or organism’s entire genetic code. But how does it work and what does it mean for all of us? How do scientists and clinicians begin to make sense of the vast amount of information that whole genome...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing

This course focuses on genomic sequencing.
Topics covered:
- The changing landscape of genomics: From Sanger sequencing to Next Generation Sequencing
- Overview of Next Generation Sequencing platforms and their methodology
- Targeted resequencing
- Alignment, variant calling and...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomic Technologies in Clinical Diagnostics: Molecular Techniques

This course focuses on molecular techniques. By the end, you will be able to demonstrate knowledge and applicability of the molecular principles behind:
- array comparative genomic hybridisation (array CGH);
- karyotyping;
- fluorescent in situ hybridisation (FISH);
- Southern blotting;
-...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

EATRIS Transmed Academy - course on translational medicine

Online course on the landscape of translational medicine
An online course for the next generation of translational scientists (PhDs, Postdocs and MDs) is touching upon key aspects of translational research and medicines development. You will learn more about target validation, predictive models,...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning, Webinar

Integrated DEsign and AnaLysis of clinical trials in small population group (IDeAl) resources

IDeAl Webinar Series, included introduction by Ralf-Dieter Hilgers, randomisation, clinical trials, extrapoling doseresponse inforation, biomarker surrogate endpoints, design studies, design of pharmacogenetic, genetic factors influencing the response to the therapy, decision analysis... in small...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning, Webinar

Webinars on rare neurological diseases (ERN-RND)

ERN-RND (European Reference Network for Rare Neurological Diseases (ERN- RND)) provides educational webinars on rare neurological and neuromuscular diseases - in collaboration with the European Reference Network for Rare Neuromuscular Diseases (EURO-NMD) and the European Academy of Neurology...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Webinars on rare neuromuscular diseases (EURO-NMD)

EURO-NMD provides educational webinars on a monthly basis to increase the knowledge around different specialist areas related to the neuromuscular field. Each webinar lasts approximately one hour with the opportunity for viewers to ask questions on the subject area. The recordings and slides will...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

RD-Connect Webinars

As part of a close working relationship between EURO-NMD (European Reference Network for the thematic grouping of rare neuromuscular diseases (NMDs)) and RD-Connect three informative webinars were organised for those researchers involved in ERNs :
1. Genomic analysis quick and easy: RD-Connect...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Genomics in Healthcare

3 online courses with academic credential to gain a deep insight into the potential of genomics in healthcare, and the clinical applications of molecular genetic techniques and next generation sequencing (NGS) technologies.
1. The Genomics Era: the Future of Genetics in Medicine
2. Genomic...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Adding ontology terms

This tutorial describes how terms can be added to the eNanoMapper ontology.

Keywords: enanomapper, ontologies

Resource type: Tutorial

Adding ontology terms

This tutorial describes how terms can be added to the eNanoMapper ontology.

Keywords: enanomapper, ontologies

Phylogenetics & Phylogeography (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography (lecture-part 1)

  2. Phylogenetics & Phylogeography (lecture-part 2)

  3. Phylogenetics & Phylogeography (lecture-part 3)

  4. Phylogenetics & Phylogeography (lecture-part 4)

  5. Phylogenetics & Phylogeography (lecture-part 5)

6....

Keywords: Phylogenetics, Roslin Institute

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography Practical - Overview

  2. Phylogenetics & Phylogeography Practical 1

  3. Phylogenetics & Phylogeography Practical 2 - Part 1

  4. Phylogenetics & Phylogeography Practical 2 - Part 2

  5. Phylogenetics & Phylogeography Practical 3

6....

Keywords: Phylogenetics, Phylogeography, Roslin Institute

Advanced R

This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and...

Keywords: R programming, Babraham Institute