## 4 Working with OpenBio.eu
### Importing ROs in OpenBio.eu  
The OpenBio.eu platform is organized around four basic building-blocks (Figure 3): (a) the RO repository, which is equipped with free-text search operations to locate the TDW object most relevant to the task at hand, workflow execution reports, references, and (potential) query-answering discourse sessions (upper-left); (b) a module to define/describe a TDW (lower-left); (c) the platform's core module where the installation (with validation) \begin{table}
\begin{tabular}{p{142.3 pt} p{142.3 pt}} \hline \hline \multicolumn{1}{c}{**Characteristic**} & \multicolumn{1}{c}{**Action**} \\ \hline Completely web-based; you do not have to install anything. & Use OpenBio.eu for your everyday science tasks from your browser. \\ No DSL (Domain Specific Language) required. & Simply describe your steps in BASH. Each workflow step is available as a BASH function. Do you have a BASH script that installs a TDW object (tool, dataset, or workflow)? Just copy/paste it! \\ Use Python, Perl, Java, or any language you like to conduct your analysis. & Call these tools the same way you would call them from the command line. \\ Fork existing tools/workflows to create your own versions. & Press the “Fork” button in the UI of any tool/data or workflow entry. OpenBio.eu offers a simple GUI, just drag-and-drop an already imported TDW object to add it into a workflow and/or create dependencies between tools. Do the same for a workflow! Workflows can contain other workflows indefinitely. \\ Simple mental model. & Tools have variables (i.e., environment variables) such as: installation\_path = path/to/executable. Workflows have input and output variables as well, such as: input\_data = path/to/data, results = path/to/results. \\ Does it support iterations or conditional execution? & Yes. In fact, it supports anything that BASH supports (even recursion). Anything you like. Each TDW object is identified by a name (anything you want), a version (anything you want), and an ID provided by the system. The namespace is unique and global. \\ Add markdown descriptions for the objects. & Use t/tool\_name/tool\_version/id and w/ workflow\_name/id to link to an object anywhere on the site. \\ Each object has a Questions and Answers section. & Navigate on the Discussion section of an RO. Contains a typical forum-like interface. \\ Add scientific references. & Link with r/reference\_name. If you do not want to manually add all bibliographic details for a paper, just add the DOI; the system will do the rest. \\ Execute workflows in your own environment. & You do not have to share code or data with OpenBio.eu, only the BASH commands that install and run workflows. Monitor the execution during runtime via the provided graphical interface. \\ \hline \hline \end{tabular}
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Table 5: Basic characteristics of OpenBio.eu and actions to perform. of TDW objects takes place, along with the definition of their dependencies (arrows between objects), as well as the composition of workflows (a GUI is provided to drag-and-drop the needed ROs); and (d) the module to define the execution environment and the actual execution of workflows (i.e., the Airflow execution manager that operates on CWL forms of workflows) accompanied by a resource manager (serviced by netdata) to monitor the execution process. OpenBio.eu users can create a TDW RO by simply importing the commands to install it. These commands are the same as those that install the tool on any computer that provides a BASH shell terminal. The same TDW object can have many versions. Different users can import TDWs that have the same name and version. Apart from the BASH commands, a TDW can be accompanied with rich-format text in markdown. In OpenBio.eu, users can define dependencies between TDWs with a simple drag-and-drop. TDW objects can be in the \"Draft\" or \"Finalized\" stage. Objects in the \"Draft\" stage may be edited in the future. Once users are confident that an imported object does not need any further refinements, they can choose to \"Finalize\" it.