Make research workflows repeatable by expressing repetition, decisions, parameters, and dependencies explicitly. Explore configurable commands, workflow tools, reproducible environments, data provenance, and checks that help collaborators inspect and rerun an analysis.
Expected and helpful background knowledge for joining an event on this topic.
Scientific analyses often involve repeating operations across files, choosing steps based on metadata, and running calculations in a particular order. As a project grows, expressing repetition, decisions, and dependencies explicitly helps an analysis remain understandable and repeatable.
A research workflow contains knowledge that can easily remain implicit: which files belong together, which parameters were used, which steps must run first, and how a result was produced. Making these decisions explicit reduces reliance on memory and manual coordination, helping both you and your collaborators understand and repeat the analysis.
Automation makes checks especially valuable because the same operation may run across many datasets. Defined expectations, reviewed reference outputs, and recorded provenance help you notice unexpected changes and investigate their causes. Together, these practices make workflows easier to inspect, update, and reuse.
For this approach, familiarity with Python and Jupyter notebooks is required. Consult the event page for its specific setup and requirements.
Using practical research examples, you will process files with loops and conditionals, extract metadata from filenames, and turn analysis steps into configurable commands. You will organize environments and tasks with Pixi, connect steps visually with Xircuits, and coordinate scripts and notebooks using Snakemake and other automation tools. DataLad will help connect results to versioned data and recorded commands, while acceptance and approval testing provide ways to check workflow behavior and outputs.
Explore upcoming dates and details from previous events.
This four-week online course shows how to turn scientific analyses into explicit, reproducible workflows. Participants will separate code from configuration, track data and …
Supporting high school students with data analysis workshops and research mentoring for Germany's premier neuroscience competition.
An introduction to Notebook-Driven Development using Jupyter Notebooks
It is becoming critical to make neuroscience analysis workflows robust, reproducible, and scalable. In this workshop, we will use Snakemake to develop complex data analysis …
Our view of the tools and practices relevant to this topic. Recommendation and teaching availability are separate.
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Distributed version control system for tracking changes in source code
Tools & platforms · Teaching
5 topics with recorded teaching · 20 recorded and scheduled offerings
Git is the industry standard for version control, enabling researchers to track changes, collaborate effectively, and maintain a complete history of their work. It's essential for reproducible research and collaboration.
Recorded in topic offerings; consult the dated event links for availability.
19 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsDeveloper EnvironmentRobust and Reusable SoftwareWebsite Development
Lightweight text-based format for storing and exchanging structured data with nested hierarchies
Data formats · Not currently taught
0 topics with recorded teaching · 0 recorded and scheduled offerings
JSON is the standard for structured data exchange on the web and in APIs. Its human-readable format with support for nested structures makes it perfect for configuration files, metadata, and hierarchical data that doesn't fit in CSV.
Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.
0 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Programming and Data AcquisitionAutomating Research WorkflowsDataframes and Statistics
Interactive computing environment combining code, visualizations, and narrative text
Tools & platforms · Teaching
6 topics with recorded teaching · 17 recorded and scheduled offerings
Jupyter notebooks allow you to combine code, results, and explanations in a single document. This makes them perfect for exploratory data analysis, teaching, and creating reproducible research workflows. You can iterate quickly, visualize results inline, and document your thought process as you work.
Recorded in topic offerings; consult the dated event links for availability.
15 past offerings · 2 upcoming offerings
Related themes: Scientific Computing
Related topics: Arrays and Numerical ComputingAutomating Research WorkflowsDataframes and StatisticsDeveloper EnvironmentMachine LearningRobust and Reusable SoftwareWebsite Development
Powerful data analysis and manipulation library for Python
Libraries · Teaching
5 topics with recorded teaching · 16 recorded and scheduled offerings
Pandas provides intuitive data structures (DataFrames) for working with tabular data, making it easy to clean, analyze, and visualize datasets. It's the go-to tool for exploratory data analysis and handling experimental results in research.
Recorded in topic offerings; consult the dated event links for availability.
14 past offerings · 2 upcoming offerings
Related themes: Neural Data AnalysisScientific Computing
Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsDataframes and StatisticsLocal Field Potential (LFP) AnalysisNeural Spike Analysis
Python standard-library module for working with filesystem paths as objects.
Libraries · Not currently taught
0 topics with recorded teaching · 0 recorded and scheduled offerings
pathlib makes path handling more readable and portable than manually joining path strings.
Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.
0 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Arrays and Numerical ComputingAutomating Research Workflows
Modern, fast package manager built on conda-forge
Tools & platforms · Teaching
2 topics with recorded teaching · 10 recorded and scheduled offerings
The repository already uses Pixi to manage its toolchain. Project dependency declarations, lock files, and tasks make it a practical candidate for reproducible research environments.
Recorded in topic offerings; consult the dated event links for availability.
9 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsDeveloper Environment
Python testing framework for writing simple and scalable test cases
Libraries · Teaching
3 topics with recorded teaching · 5 recorded and scheduled offerings
pytest makes it easy to write tests for research code, catching errors before they affect results. Its simple syntax and powerful features help ensure reproducibility and build confidence when refactoring analysis pipelines.
Recorded in topic offerings; consult the dated event links for availability.
3 past offerings · 2 upcoming offerings
Related themes: Scientific Computing
Related topics: AI-Assisted Software DevelopmentAutomating Research WorkflowsDeveloper EnvironmentRobust and Reusable Software
General-purpose programming language widely used for scientific computing and research software.
Languages & frameworks · Teaching
10 topics with recorded teaching · 33 recorded and scheduled offerings
Python combines a readable language with a mature scientific ecosystem, making it a practical default for research data analysis, automation, and teaching.
Recorded in topic offerings; consult the dated event links for availability.
26 past offerings · 7 upcoming offerings
Related themes: Neural Data AnalysisScientific Computing
Related topics: Programming and Data AcquisitionAI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsCalcium Imaging AnalysisDataframes and StatisticsDeveloper EnvironmentLocal Field Potential (LFP) AnalysisMachine Learning(M)EEG AnalysisNeural Spike AnalysisRobust and Reusable Software
Record and reproduce the software environment used for an analysis or application.
Practices · Teaching
0 topics with recorded teaching · 0 recorded and scheduled offerings
Declared dependencies and lock files help collaborators rerun analyses and distinguish environment changes from changes in scientific results.
Covered through our computing environment and research workflow topics; individual offerings are not yet attributed to this practice.
0 past offerings · 0 upcoming offerings
Related themes: Neural Data AnalysisScientific Computing
Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsCalcium Imaging AnalysisDataframes and StatisticsDeveloper EnvironmentLocal Field Potential (LFP) AnalysisMachine LearningRobust and Reusable Software
Container runtime for packaging Linux research software in portable, reproducible environments.
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
Apptainer makes it practical to move complex scientific software between laptops, workstations, and high-performance computing systems without asking researchers to rebuild every dependency by hand.
Recorded in topic offerings; consult the dated event links for availability.
0 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research Workflows
Package and environment manager for Python and scientific software
Tools & platforms · Teaching
2 topics with recorded teaching · 11 recorded and scheduled offerings
Useful for existing conda-based workflows and scientific package compatibility. Compare it with Pixi when designing new reproducible project environments; the group should review which approach to teach as its default.
Recorded in topic offerings; consult the dated event links for availability.
11 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsDeveloper Environment
Tool for versioning, publishing, and sharing research datasets and analysis workflows.
Tools & platforms · Teaching
2 topics with recorded teaching · 2 recorded and scheduled offerings
DataLad helps research groups keep data, code, and provenance connected while collaborating across machines and institutions.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsRobust and Reusable Software
Data and model versioning tool for machine learning and reproducible data pipelines.
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
DVC gives Git-like workflows for files that are too large or too changeable to store directly in Git repositories.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsDeveloper Environment
Unified filesystem interface for Python providing consistent API across local and remote storage
Libraries · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
fsspec provides a single, consistent interface for working with files whether they're on your local disk, in the cloud, or on GitHub. This means you can write code once and access data from multiple sources without changing your file operations.
Recorded in topic offerings; consult the dated event links for availability.
0 past offerings · 1 upcoming offerings
Related themes: Neural Data AnalysisScientific Computing
Related topics: Automating Research WorkflowsCalcium Imaging AnalysisDataframes and Statistics
Version control platform for research data
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
GIN combines Git-like version control with storage optimized for large research datasets. It's specifically designed for neuroscience and other data-intensive fields where you need both version control and efficient handling of large files.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsRobust and Reusable Software
Web-based platform for hosting and collaborating on Git repositories
Tools & platforms · Teaching
5 topics with recorded teaching · 18 recorded and scheduled offerings
GitHub is the de facto standard for sharing and collaborating on code. It provides excellent tools for code review, issue tracking, and project management. Most scientific software is hosted on GitHub, making it essential for reproducible research.
Recorded in topic offerings; consult the dated event links for availability.
18 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: AI-Assisted Software DevelopmentArrays and Numerical ComputingAutomating Research WorkflowsDeveloper EnvironmentRobust and Reusable SoftwareWebsite Development
Automation platform for running tests, checks, and deployment workflows from GitHub repositories.
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
GitHub Actions lets research teams automate repetitive checks so shared code remains easier to trust and maintain.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsRobust and Reusable Software
Git-based collaboration platform for repositories, issues, reviews, project boards, and automation.
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
GitLab combines code hosting, project coordination, and CI/CD in one place, making it useful for research groups that need transparent collaboration around shared software.
Recorded in topic offerings; consult the dated event links for availability.
0 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsDeveloper EnvironmentRobust and Reusable SoftwareWebsite Development
GitLab's built-in automation system for running tests, checks, builds, and deployments from repository changes.
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
GitLab CI/CD turns project expectations into repeatable checks, helping research teams catch broken tests, missing dependencies, and packaging problems before changes are merged.
Recorded in topic offerings; consult the dated event links for availability.
0 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsRobust and Reusable Software
Python tool for measuring memory usage line by line or over time.
Libraries · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
memory-profiler helps researchers see where an analysis allocates memory, which is often the first step toward making large-data workflows reliable.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Arrays and Numerical ComputingAutomating Research WorkflowsRobust and Reusable Software
Platform for open and reproducible research project management
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
OSF provides a comprehensive platform for managing research projects openly. It supports preregistration, data sharing, and connects with many other tools (GitHub, figshare, Dropbox). It's designed specifically for research workflows and promotes transparency.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsRobust and Reusable Software
Open-source file sync and share platform, used via Sciebo at German universities
Tools & platforms · Not currently taught
0 topics with recorded teaching · 0 recorded and scheduled offerings
OwnCloud (via Sciebo) provides secure cloud storage that's hosted by German universities, ensuring GDPR compliance and data sovereignty. The Python client makes it easy to automate dataset downloads and share data with collaborators.
Relevant to the topic landscape; no explicit recorded offering is currently attributed to this item.
0 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research Workflows
Tool for parameterizing and executing Jupyter notebooks programmatically
Tools & platforms · Teaching
2 topics with recorded teaching · 3 recorded and scheduled offerings
Papermill lets you run the same analysis notebook with different parameters, making it easy to process multiple subjects, conditions, or datasets. It's perfect for batch processing while keeping your analysis in the familiar Jupyter format.
Recorded in topic offerings; consult the dated event links for availability.
2 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsDeveloper Environment
Python task automation tool for defining and executing task dependencies
Tools & platforms · Teaching
1 topics with recorded teaching · 2 recorded and scheduled offerings
Pydoit brings make-style build automation to Python with a simple, Pythonic interface. It's perfect for automating repetitive analysis tasks, managing data processing pipelines, and ensuring your analysis steps run in the correct order.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research Workflows
Secure cloud storage for research data in German universities
Tools & platforms · Teaching
2 topics with recorded teaching · 10 recorded and scheduled offerings
Sciebo provides GDPR-compliant cloud storage hosted in Germany, specifically designed for academic use. It offers generous storage quotas and integrates well with university authentication systems, making it ideal for storing and sharing research data.
Recorded in topic offerings; consult the dated event links for availability.
10 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Arrays and Numerical ComputingAutomating Research WorkflowsDeveloper Environment
Python-based workflow management system for creating reproducible and scalable data analyses
Tools & platforms · Teaching
1 topics with recorded teaching · 3 recorded and scheduled offerings
Snakemake helps you build reproducible analysis pipelines that track dependencies automatically. It ensures your analyses run in the correct order, reruns only what's necessary when data changes, and scales from your laptop to compute clusters.
Recorded in topic offerings; consult the dated event links for availability.
2 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research Workflows
Python standard-library module for measuring execution time of small code snippets.
Libraries · Teaching
1 topics with recorded teaching · 2 recorded and scheduled offerings
timeit gives researchers a simple, repeatable way to compare small implementation choices before investing in heavier profiling or optimization work.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Arrays and Numerical ComputingAutomating Research WorkflowsRobust and Reusable Software
Microsoft-supported way to run Linux command-line environments directly on Windows.
Tools & platforms · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
WSL helps Windows users participate in Linux-oriented research workflows without needing a separate machine, making command-line tools, package managers, and pipeline software easier to use.
Recorded in topic offerings; consult the dated event links for availability.
0 past offerings · 1 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsDeveloper Environment
High-level plotting API providing interactive visualizations for pandas, xarray, and other data structures
Libraries · Teaching
1 topics with recorded teaching · 1 recorded and scheduled offerings
Assess whether this fits the group’s research and teaching workflows. hvPlot makes creating interactive visualizations as easy as using pandas' built-in plotting, but with interactivity out of the box. It's perfect for exploratory data analysis, allowing you to zoom, pan, and hover over data points without writing complex plotting code.
Recorded in topic offerings; consult the dated event links for availability.
1 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research Workflows
Framework for building tested, documented Python packages from Jupyter notebooks.
Languages & frameworks · Teaching
0 topics with recorded teaching · 0 recorded and scheduled offerings
Assess whether this fits the group’s research and teaching workflows. nbdev can help notebook-heavy projects become importable, documented, and tested packages while preserving an exploratory authoring workflow.
Recorded in topic offerings; consult the dated event links for availability.
0 past offerings · 0 upcoming offerings
Related themes: Scientific Computing
Related topics: Automating Research WorkflowsRobust and Reusable Software
For tutoring, collaboration, or follow-up support, contact the team. We are happy to help you connect workshop ideas with your own research practice.
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