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Introduction to Galaxy Analyses

Introduction to Galaxy Analyses

WikiPathways Academy

Pathways explain how the cells in our bodies work. Like a wiring diagram, pathways show the flow of interactions and reactions among molecules that perform all the functions of Life. There are pathways for the metabolism of sugars and the development of the heart. There are also pathways for...

Scientific topics: Systems biology, Biology

Keywords: Pathway

Compartición, análisis y almacenamiento de datos genómicos con RD-Connect GPAP y EGA

El Centro Nacional de Análisis Genómico (CNAG-CRG) y la European Genome-Phenome Archive (EGA) organizan un curso práctico sobre el uso de herramientas para compartir y analizar datos genómicos en el marco del proyecto VEIS - Valorización de EGA para la Industria y la Sociedad.

En el primer...

Scientific topics: Data integration and warehousing, Database management, Genomics

Resource type: Video

Making sense of genomic data: COVID-19 web-based bioinformatics

Develop your understanding of bioinformatics and SARS-CoV-2 data analysis:
Although testing and sequencing capacity has improved, in low-and-middle-income countries (LMICs) bioinformatics analyses still represent a bottleneck in the implementation of effective viral surveillance...

Keywords: bioinformatics, NGS bioinformatics, Next generation sequencing data analysis, covid-19, sars-cov-2, coronavirus, data-analysis, data visualization, genomics, Genomic data, pipelines, Galaxy, nexstrain

Resource type: FREE online course

From Swab to Server: Testing, Sequencing, and Sharing During a Pandemic

Discover how sample strategies can affect scientific research and results:
Sampling is a critical part of research in any field. In studying a disease such as Covid-19, it’s imperative that your sample and sampling methods are best-suited to reflect accurate results.

Supported by expert...

Keywords: metadata, Sequencing, genomics, Genomic data, data quality, scientific quality assurance, data sharing, ethics, data ethics, public health, coronavirus, sars-cov-2, covid-19, data linkage

Resource type: FREE online course

The Power of Genomics to Understand the COVID-19 Pandemic

Explore genome sequencing and the SARS-CoV-2 genome:
The course starts with a review of how viruses cause diseases and pandemics, examining the factors that can lead to a public health emergency.

You’ll also get a comprehensive introduction to the SARS-CoV-2 genome structure, and learn...

Keywords: coronavirus, covid-19, sars-cov-2, mutations, Variant calling, Sequencing, pandemic, surveillance, genomics, public health, Genomic data

Resource type: FREE online course

Introduction to using containers - OpenShift, Kubernetes and Docker oriented view

This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez

Keywords: Containers, Kubernetes, Cloud computing

Cellosaurus : A resource on cell lines

No description provided.

PSLS22 Practical Statistics for the Life Sciences

The concepts and methods are exclusively introduced via case-studies in the life sciences. For every study we elaborate on a concrete research question and then provide a study design, which is followed by data exploration. Next, we will focus on how to model the data and elaborate on the link...

Schema.org, what and why?

In this tutorial you will get an idea on what Schema.org is and how it is useful

Keywords: schemaorg, markup, structured data, schemaorg, markup, structured data

Bioschemas, what and why?

In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are

Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas

Schema.org markup examples

With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup

Keywords: schemaorg, markup, structured data, example, schemaorg, markup, structured data, example

How to select the right profile for your resource

In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources

Keywords: schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile

How to update a profile

In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll.

Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile

How to create a new Bioschemas profile

In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile.

Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile

How to check your Bioschemas deployment

This guide will show you how to check your deployed markup, both locally and what is retrieved by external services.

Keywords: schemaorg, JSON-LD, bioschemas

How to mark up your own resource with Bioschemas

In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile

Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas

Adding Schema.org to a GitHub Pages site

This guide will show you how to do add Schema.org markup to a GitHub Pages site.

Keywords: schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages

Tutorial on developing Building Blocks

This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.

Scientific topics: Personalised medicine, Workflows, Bioinformatics

Keywords: HPC, building blocks

Resource type: Tutorial

SARS-CoV-2 : Studying a new virus

No description provided.

neXtProt : Exploring human proteins

No description provided.

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

ELIXIR AAI Engagement Meetings Materials

ELIXIR AAI is an ELIXIR Compute Platform service that other services can use to authenticate their users and manage their access rights.
In the ELIXIR AAI Tas, we are preparing regular Community engagement meetings where we would like to share and discuss together new AAI needs,...

Scientific topics: Computer science

Keywords: AAI, IAM, Authentication, authorisation

Resource type: Documentation, Presentation

Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research

At the lowest scale, PhysiCell uses BioFVM solver to simulate the chemical microenvironment using partial differential equations which model the diffusion, uptake and secretion of substrates and signalling molecules. At the cell scale, PhysiCell uses mechanical equations to model individual cell...

Scientific topics: Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, cell simulations

Resource type: Webinar

Introduction to qualitative modelling with MaBoSS

Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the...

Scientific topics: Statistics and probability, Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, cell simulations, Boolean

Resource type: Webinar

Analysis of huge metabolic models with COBREXA.jl

COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base...

Scientific topics: Simulation experiment

Keywords: cell-level simulations, HPC, Biomodelling

Resource type: Webinar