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Target audience: policy officer  or computational scientists 

BioExcel Building Blocks (BioBB) Training Material

BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR.

Keywords: molecular dynamics, Docking, Modeling, life sciences

Resource type: Jupyter notebook

BioExcel Building Blocks (BioBB) Training Material http://tess.elixir-uk.org/materials/bioexcel-building-blocks-biobb-training-material BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR. Josep Lluís Gelpí Stian Soiland-Reyes molecular dynamics, Docking, Modeling, life sciences PhD students computational scientists Computational biologists
Data Management Plans and Policies

PDF with slides of the course: - Data management definitions - RDM and DM policy - DMPs: content and competencies - DMPs for European and National funded projects

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, on-line, e-learning

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

Data Management Plans and Policies http://tess.elixir-uk.org/materials/data-management-plans-and-policies PDF with slides of the course: - Data management definitions - RDM and DM policy - DMPs: content and competencies - DMPs for European and National funded projects Data management FAIR data ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, on-line, e-learning project manager Researchers policy officer
Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica

PDF with slides of the course in Spanish - Data management definitions - DMP Objectives - DMP Content and structure - Competencies needed - Practical session: DMP content analysis and evaluation

Scientific topics: FAIR data, Data management

Keywords: ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish

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

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica http://tess.elixir-uk.org/materials/elaboracion-de-un-plan-de-gestion-de-datos-dmp-teoria-y-practica PDF with slides of the course in Spanish - Data management definitions - DMP Objectives - DMP Content and structure - Competencies needed - Practical session: DMP content analysis and evaluation FAIR data Data management ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish operational manager IT support data manager project manager policy officer
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics http://tess.elixir-uk.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
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
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
Next Generation Sequencing (NGS) wikibook

Next generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to...

Keywords: Bioinformatics, Next generation sequencing, Ngs

Next Generation Sequencing (NGS) wikibook http://tess.elixir-uk.org/materials/next-generation-sequencing-ngs-wikibook Next generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to foster novel discovery in biomedical research. However, as the quantities of sequence data increase exponentially, the analysis bottle-neck is yet to be solved. The current sources for NGS informatics are extremely fragmented. A novice could read review articles in various journals, follow discussion threads on forums such as Biostar[1] or SEQanswers [2], or sign up for courses organized by various institutes. Finding a centralized synthesis is much more difficult. Books are available, but the development of the field is so fast that book chapters risk being obsoleted by the time they are even printed. Moreover, cost for a handful of authors to continually update their text would presumably take up a lot of their schedule. Drawing from the obvious goodwill and community spirit displayed on discussion forums, and exploiting the collaborative tools made available by the Wikimedia foundation, we propose to initiate the editing of a collaborative WikiBook on NGS. Our plan is to collect a sufficient amount of text that people will be incentivized to contribute to it, essentially providing the same information as a forum but in a tidier form. Ultimately, our goal is to create a collective lab book that explains the key concepts and describes best practices in NGS. Parnell LD, Lindenbaum P, Shameer K et al. BioStar: an online question & answer resource for the bioinformatics community, PLoS Comput Biol 2011;7:e1002216. Li JW, Schmieder R, Ward RM et al. SEQanswers: an open access community for collaboratively decoding genomes, Bioinformatics 2012;28:1272-1273 Join this initiative now and contribute to further expand and improve the contents and case studies in the NGS wikibook! Read about this initiative and the nine rules for NGS data analysis here: The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability Bioinformatics, Next generation sequencing, Ngs Biologists bioinformaticians computational scientists 2013-07-15 2017-10-09