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Licence: MIT License 


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 https://tess.elixir-europe.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
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 https://tess.elixir-europe.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
BcForms tutorial

BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models...

Scientific topics: Systems biology, Protein modifications, Proteomics

Operations: Validation

Keywords: BiologicalMacromolecules, protein complex, macromolecular complex, crosslink, modification

Resource type: Jupyter notebook

BcForms tutorial https://tess.elixir-europe.org/materials/bcforms-tutorial BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models . BcForms includes a grammar for describing forms of macromolecular complexes composed of DNA, RNA, protein, and small molecular subunits and crosslinks between the subunits. The DNA, RNA, and protein subunits can be described using BpForms and the small molecule subunits can be described using SMILES. BcForms also includes four software tools for verifying descriptions of complexes and calculating physical properties of complexes such as their molecular structure, formula, molecular weight, and charge: this website, a JSON REST API, a command line interface, and a Python API. This tutorial provides an introduction to BcForms. Systems biology Protein modifications Proteomics BiologicalMacromolecules, protein complex, macromolecular complex, crosslink, modification genomics researchers computational biologists bioinformaticians systems biologists
BpForms tutorial

BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of...

Scientific topics: Systems biology, Protein modifications, Proteomics, Transcriptomics, Epigenomics

Operations: Validation

Keywords: RNA modification, protein modification, DNA repair, DNA damage, crosslink, nick

Resource type: Jupyter notebook

BpForms tutorial https://tess.elixir-europe.org/materials/bpforms-tutorial BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of biopolymers, BpForms aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. This tutorial provides an introduction to BpForms. Systems biology Protein modifications Proteomics Transcriptomics Epigenomics RNA modification, protein modification, DNA repair, DNA damage, crosslink, nick genomics researchers computational biologists bioinformaticians systems biologists
ObjTables Python tutorials

ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of...

Scientific topics: Data submission, annotation, and curation, Data quality management, Data integration and warehousing, Data management

Operations: Validation

Keywords: spreadsheet, schema, table, workbook, worksheet, XLSX, Excel, standard, reuse, compose, integrate, quality control

Resource type: Jupyter notebook

ObjTables Python tutorials https://tess.elixir-europe.org/materials/objtables-python-tutorials ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a markup format for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. ObjTables is ideal for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. The tutorials provide a brief introduction to the ObjTables format for schemas for spreadsheets, the ObjTables markup syntax for spreadsheets, and the ObjTables Python package for parsing, validating, querying, editing, comparing, merging, splitting, revisioning, migrating, and analyzing spreadsheets. Data submission, annotation, and curation Data quality management Data integration and warehousing Data management spreadsheet, schema, table, workbook, worksheet, XLSX, Excel, standard, reuse, compose, integrate, quality control Researchers Scientists Data scientists computational scientists
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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
NBIS Reproducible research course

The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker

Keywords: data management, Reproducibility, Data analysis

Resource type: Training materials

NBIS Reproducible research course https://tess.elixir-europe.org/materials/nbis-reproducible-research-course The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker Leif Wigge Rasmus Ågren John Sundh data management, Reproducibility, Data analysis bioinformaticians
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 https://tess.elixir-europe.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. https://tess.elixir-europe.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