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://github.com/KarrLab/de_sim
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*.
Jonathan Karr
Arthur Goldberg
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
How to use Common Workflow Language
**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**
Scientific topics: Workflows
Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP
Resource type: Installation instructions, Manual
How to use Common Workflow Language
https://elixir.mf.uni-lj.si/course/view.php?id=37
http://tess.elixir-uk.org/materials/how-to-use-common-workflow-language
**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**
Rob Finn
Michael Crusoe
Rob Finn
Michael Crusoe
Workflows
commonwl, common workflow language, CWL, Workflows, eLearning, EeLP
bioinformaticians
life scientists
programmers
Adding nanomaterial data
This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.
Scientific topics: Database management, Toxicology
Keywords: nanotoxicology, enanomapper, resource description framework, ontology
Resource type: Tutorial
Adding nanomaterial data
https://nanocommons.github.io/tutorials/enteringData/
http://tess.elixir-uk.org/materials/adding-nanomaterial-data
This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.
Egon Willighagen
Database management
Toxicology
nanotoxicology, enanomapper, resource description framework, ontology
programmers
data entering
Parsing data records using Python programming
This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list data structure. The...
Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing
Parsing data records using Python programming
https://www.mygoblet.org/training-portal/materials/parsing-data-records-using-python-programming
http://tess.elixir-uk.org/materials/parsing-data-records-using-python-programming
This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list data structure. The text of exercises is provided in a separate file.
allegra.via Via
Bioinformatics, Programming, Python, Python biologists, Record parsing
Biologists
beginner bioinformaticians
bioinformaticians
programmers
2013-07-05
2017-10-09
