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8 materials found

Target audience: postgrad  or software engineers 


Plant Phenotyping Data managment (MIAPPE)

This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners...

Scientific topics: Data management, Plant biology, Phenomics

Operations: Formatting, Annotation

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

Plant Phenotyping Data managment (MIAPPE) http://tess.elixir-uk.org/materials/plant-phenotyping-data-managment-miappe This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners will know how to use standards and ontologies, how to describe their measurment protocole and practices how to fill a template with their data and how to apply the standards concept in some data managment tools. Data management Plant biology Phenomics Plant Phenotyping, Data-format, data sharing Biologists geneticists plant researchers software engineers database managers
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
Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing

This course is available on FutureLearn and developed by St George's University of London. This postgraduate-level course will help you understand these new and established genetic technologies, and their application to clinical practice.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing http://tess.elixir-uk.org/materials/genomic-technologies-in-clinical-diagnostics-next-generation-sequencing This course is available on FutureLearn and developed by St George's University of London. This postgraduate-level course will help you understand these new and established genetic technologies, and their application to clinical practice. Rare diseases Rare Diseases & Research postgrad Scientists Healthcare
InterMine operator manual

Documentation on how to install, configure and operate an InterMine instance.

Keywords: Data integration, Data analysis, Data publishing, FAIR

Resource type: Documentation

InterMine operator manual http://tess.elixir-uk.org/materials/intermine-operator-manual Documentation on how to install, configure and operate an InterMine instance. Data integration, Data analysis, Data publishing, FAIR Bioinformaticians software engineers
Clinical Bioinformatics I - Tutor notes

Clinical Bioinformatics I is a 10 credit module of the new MSc in Clinical Bioinformatics, delivered by Nowgen/NGRL and the University of Manchester in the UK. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work...

Keywords: Clinical bioinformatics, Genomics, Introduction bioinformatics

Clinical Bioinformatics I - Tutor notes http://tess.elixir-uk.org/materials/clinical-bioinformatics-i-tutor-notes Clinical Bioinformatics I is a 10 credit module of the new MSc in Clinical Bioinformatics, delivered by Nowgen/NGRL and the University of Manchester in the UK. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work placement based training interspersed with academic teaching.  The tutor notes describe the content taught on each day of the 5 day course, and the approach used to teach the materials. Each day is divided into two parts, a series of lectures in the morning to introduce the topics, then the afternoon sessions present a series of case studies for the students to work through in a 'problem based learning (PBL) approach to reinforce the lecture content.  Clinical bioinformatics, Genomics, Introduction bioinformatics Life Science Researchers healthcare professionals postgrad 2013-11-28 2017-10-09
Bioinformatics: Gene-protein-structure-function

This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...

Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast

Bioinformatics: Gene-protein-structure-function http://tess.elixir-uk.org/materials/bioinformatics-gene-protein-structure-function This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The presentation concludes with an analysis of 'expert' systems and integrated approaches (GeneQuiz, MAGPIE, InterPro, etc.), and dispels the commonly held notion that one database and/or one analysis tool is best. Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
InterPro: An introduction

This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose. 

Keywords: Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis

InterPro: An introduction http://tess.elixir-uk.org/materials/interpro-an-introduction This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose.  Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
PRINTS: A protein family database with a difference

A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to...

Keywords: Functional diagnosis, Protein family characterisation, Protein sequence analysis

PRINTS: A protein family database with a difference http://tess.elixir-uk.org/materials/prints-a-protein-family-database-with-a-difference A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to demonstrate the importance of understanding how to interpret the results of different sequence analysis methods and, crucially, the differences between them, and the added value that fingerprints bring. Functional diagnosis, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09