OpenBio.eu

OpenBio.eu is an open collaborative workflow management system. It is focused (but not limited!) to the bioinformatics community.

Documentation

Here is an incomplete documentation

Discord

Join our discord server for questions, suggestions and comments.

Features

Main features include:

• No DSL (Domain Specific Language) required. Do you have a bash script that installs a tool (or dataset)? Just copy paste it!
• Completely web based. You do not have to install anything. Use openbio.eu for your everyday science tasks from your browser.
• Simple workflow structure. Drag'n'drop a tool (or dataset) to add it in a workflow. Do the same for a workflow! Workflows can contain other workflows indefinitely.
• Drag'n'drop a tool to another tool's dependency panel to add it as a dependency.
• Simple mental mondel. Tools have variables (think: environment variables). For example: installation_path=path/to/executable. Worfklows have input and output variables as well. For example input_data=path/to/data, results=path/to/results. Create your workflow steps according to the values of these variables.
• No DSL to describe workflow steps (and structure). Simply describe your steps in bash. Each workflow step is available as a bash function.
• You have absolutely no idea about bash? You don't have to. Reading environment variables (which is as simple as "$my_var") is all you need to know.
• Use python, or perl, or java or.. any language you like, to do your analysis. Call these tools the same way you would call them from the command line.
• Does it support iterations? conditional execution? Yes. In fact it supports anything bash supports (even recursion).
• What name should I use for my tool/dataset/workflow? Anything you like. Each tool/data is identified by a name (anything you want), a version (anything you want) and an id provided by the system. Similarly each workflow is identified by a name (anything you want) and an id provided by the system. The combination tool_name/tool_version/id and worfklow_name/id is quaranteed to by unique. The namespace is unique and global.
• Fork existing tools/workflows to create your own versions.
• Add markdown descriptions to these objects. Use t/tool_name/tool_version/id and w/worfklow_name/id to link to an object anywhere in the site.
• Each object has a Questions and Answers section.
• Add scientific references. Link with r/reference_name. Bored to add all bibliographic details for a paper? Just add the DOI. The system will get the rest.
• Execute workflows on your own enviroment. You do not have to share code or data with openbio.eu. Only the bash commands that install/download them. Monitor the execution, during runtime in a graphic interface.
• ...more to come

Directories

• OpenBio: The awesome OpenBio platform! This directory also contains:
  • app/ The Django application of the project
  • ExecutionEnvironment. The Execution Environment of openbio.eu . Use executor.py to execute a worfklow in json format that you downloaded from openbio.eu.
• deployment_notes.md: Some notes on how to deploy on an Ubuntu 16.04 server
• discourse-graph. A very experimental effort to add a discourse graph to the discussion of objects in openbio.eu.
• tests/. Selenium tests.

For Developers

We will be very happy to accept Pull Requests. The project does not have any active development or contribution guidelines at the moment.

Contributors

Main developer is Alexandros Kanterakis mail, twitter. For a complete list of current contributors see CONTRIBUTORS.md

Funding

This research has been co‐financed by the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH – CREATE – INNOVATE (project code: T1EDK - 05275)

Posters / Conferences / Papers

• Poster in BOSC2019, DOI: https://doi.org/10.7490/f1000research.1117273.1

More

• Twitter: https://twitter.com/openbioe/