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Helis Academy course FAIR data stewardship 2021, Day 6, FAIR Data

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021

Scientific topics: FAIR data, Data management

Operations: Data handling

Keywords: FAIR data, Data management planning, Metadata

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 6, FAIR Data http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-6-fair-data This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021 FAIR data Data management FAIR data, Data management planning, Metadata PhD candidates
Research Data Management Introduction for researchers

Short summary of the previous session 1.Scope of the DM 2.DMP Content and structure Practical activities 3.Planning the DM of a simple project 4.DMP evaluation

Scientific topics: Data management, FAIR data

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, DMP evaluation, evaluation, on-line, e-learning

Resource type: PDF, e-learning, slideck/ presentation

Research Data Management Introduction for researchers http://tess.elixir-uk.org/materials/research-data-management-introduction-for-researchers Short summary of the previous session 1.Scope of the DM 2.DMP Content and structure Practical activities 3.Planning the DM of a simple project 4.DMP evaluation Data management FAIR data ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, DMP evaluation, evaluation, on-line, e-learning Researchers PhD students
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](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html),...

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

Operations: Visualisation, Modelling and simulation

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

DE-Sim examples, tutorials, and documentation http://tess.elixir-uk.org/materials/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](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html), [pandas](https://pandas.pydata.org/), and [SQLAlchemy](https://www.sqlalchemy.org/) to build and simulate complex computational models. Similar to [Simula](http://www.simula67.info/), *DE-Sim* models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time. This website provides examples, tutorials, and documentation for *DE-Sim*. Computational biology Mathematics Computer science Simulation experiment data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science computational scientists Computational biologists bioinformaticians software engineers programmers
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

Jaqpot Hackathon - Training materials http://tess.elixir-uk.org/materials/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 modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot. Attached you find the following presentations: 1. Intro to NanoCommons by Martin Himly, PLUS 2. Electronic Lab Notebooks by Iseult Lynch, UoB 3. NanoCommons Knowledgebase by Dieter Maier, Biomax 4. Jaqpot Suite by Philip Doganis, NTUA Lee Walker, UKCEH Christine Balmer, UKCEH Irini Liampa, NTUA Pantelis Karatzas, NTUA Beatriz Alfaro Serrano, BNN Harry Sarimveis, NTUA nanoinformatics, toxicity prediction, e-tools, Modeling, data FAIRness
BioSimulations tutorial and help

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...

Scientific topics: Simulation experiment, Systems biology, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE

Resource type: Documentation

BioSimulations tutorial and help http://tess.elixir-uk.org/materials/biosimulations-help BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface. Simulation experiment Systems biology Computational biology SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE Life Science Researchers Computational biologists modelers
Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial

Datanator tutorial http://tess.elixir-uk.org/materials/datanator-tutorial Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. This tutorial provides a brief introduction to the Datanator database and web application. The tutorial illustrates how to search the Datanator database and obtain and refine clouds of data about specific metabolites, RNA, proteins, and reactions of interest. Omics Bioinformatics Systems biology Cell biology Molecular biology genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis mololecular cell biologists systems biologists bioinformaticians Computational biologists modelers
Introduction to GitHub

The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub

Keywords: GitHub, Reproducibility

Resource type: Training materials

Introduction to GitHub http://tess.elixir-uk.org/materials/introduction-to-github The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub Gabriella Rustici GitHub, Reproducibility Senior Managers
Beginners introduction to Git and GitHub

__Morning session__ (Sergio and Mark) https://tinyurl.com/git-intro-zoology: - Background and motivation - What is version control? What is Git? What is GitHub? - How can you use Git and GitHub? How can they be useful for you? - Practical session: working with Git and GitHub __Afternoon...

Keywords: Git, GitHub, control version, Reproducibility

Resource type: Training materials

Beginners introduction to Git and GitHub http://tess.elixir-uk.org/materials/beginners-introduction-to-git-and-github __Morning session__ (Sergio and Mark) https://tinyurl.com/git-intro-zoology: - Background and motivation - What is version control? What is Git? What is GitHub? - How can you use Git and GitHub? How can they be useful for you? - Practical session: working with Git and GitHub __Afternoon session__ (Mark and Anne) https://tinyurl.com/git-course: markdown, pages and wikis; creating good README files; issue tracking; sofware licenses Mark Fernandes pajanne Git, GitHub, control version, Reproducibility Researchers
Ready For BioData Management?

"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.

Scientific topics: Data management

Keywords: Data managment plan

Resource type: course materials

Ready For BioData Management? http://tess.elixir-uk.org/materials/ready-for-biodata-management "Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences. Marta Silva Data management Data managment plan Life Science Researchers PhD students Master students Technicians
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Biology, Bioinformatics, Computer science

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences http://tess.elixir-uk.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Biology Bioinformatics Computer science High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
Open Science MOOC: Module 5, Open Research Software and Open Source

Software and technology underpin modern science. There is an increasing demand for more sophisticated open source software, matched by an increasing willingness for researchers to openly collaborate on new tools. These developments come with a specific ethical, legal and economic challenges that...

Keywords: open source

Open Science MOOC: Module 5, Open Research Software and Open Source http://tess.elixir-uk.org/materials/open-science-mooc-module-5-open-research-software-and-open-source Software and technology underpin modern science. There is an increasing demand for more sophisticated open source software, matched by an increasing willingness for researchers to openly collaborate on new tools. These developments come with a specific ethical, legal and economic challenges that impact upon research workflows. This module will introduce the necessary tools required for transforming software into something that can be openly accessed and re-used by others. open source
Introductory image processing on biological images using python.

A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.

Resource type: Jupyter notebook, PDF

Introductory image processing on biological images using python. http://tess.elixir-uk.org/materials/introductory-image-processing-on-biological-images-using-python A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples. Anatole Chessel Volker Baecker Bioimage Analysts Image Analysts Computer Vision scientists bioinformaticians computational scientists Biophysicists Biologists Microscopists Python for Biologists PhD students
R Basics Quiz

No description provided.

R Basics Quiz http://tess.elixir-uk.org/materials/r-basics No description provided.
UNIX Fundamentals

No description provided.

UNIX Fundamentals http://tess.elixir-uk.org/materials/unix-fundamentals No description provided. 2014-01-13