Getting Started with the Pipeline Generator

As a biologist, you probably know that the key to good data analysis is the selection and use of appropriate software. Owing to the increasing complexity of biological data, the number of tools typically required to perform an analysis is constantly growing, rendering the selection of software even more difficult. Indeed, finding the best series of tools that match your analysis criteria is challenging.

 

A pipeline is a series of software presented in a logical order. With your data as a starting point, a pipeline shows you the right pathway of tools to perform your analysis.

 

Until now, finding the optimal workflow was very challenging because pipelines are difficult to decipher or remain buried in the masses of biomedical texts. To face this big challenge, we’ve combined powerful capabilities with AI to engineer a unique Pipeline Generator to help you find (or create) a wide range of pipelines for effective bioinformatics analyses.

 

Access pipelines in an easy way

 

Depending on the scope of your research, you can find two kinds of pipelines on OMICtools.

 

  • Pipelines extracted from the literature: we scan all free-access biomedical publications with text-mining to decipher analyses and integrate them in a pipeline corpus you can explore and browse in a rich way.

 

How it is useful: getting an overview of the start of the art in the field of bioinformatics analyses. With extracted pipelines, you broaden your knowledge and have a unique place to find the best solutions.

 

  • Pipelines generated by artificial intelligence: we analyze the pipeline corpus to deliver you, in real time, tailored pipelines you can rearrange, by adding analytical steps and tools.

 

How it is useful: getting the most optimal and efficient combination of tools among the 11,000 pipelines of the corpus. With generated pipelines, you save time and ensure to solve complex analyses.

 

Visualize and customize pipelines

 

The Pipeline Generator provides many options to edit pipelines that are generated or extracted from the literature. The editor is the simplest way for anyone to get started with creating pipelines. It’s also a great way for less tech savvy-researchers to customize existing bioinformatics analyses without needing to code.

 
 

Each analysis step in the pipeline is represented by a graphical icon and associated with at least two software tools. The basic mode is activated by default as you run the app. This mode generates the best fitted pipeline you can customize (but not modify) with the best tool for each analysis step.

 

Getting specifications

 

Clicking on the question mark next to the tool’s name opens an information box about the tool. If you want to learn more, click on the tool’s name (in blue) to reach the tool’s full page.

 

Setting actions with the toolbox

 

After a pipeline is generated, you can use the toolbox to adjust several parameters of the interface:

 

 

  • Adding the pipeline to your favorites
  • Undo previous action
  • Redo previous action
  • Saving as an high-quality image for future publication
  • Zooming out
  • Zooming to fit screen size
  • Zooming in

 

Modifying the tools of a pipeline

 

With the basic mode, you can also customize your pipeline using the tools you like and save it for future analyses. Filters can help you improve your selection by filtering choices by licenses, software type, interface, and much more.

 

By default, the optimal tool for each step is automatically selected. To unselect it, click on the “X” mark. After doing so, 3 tools are proposed for each step. To select a tool, click on the “+” mark.

 

If your favorite tools isn’t on the list, you can set specific filters to change the list of 3 tools provided. You can also click “see more tools” to display a complete list of tools matching the category and filtering criteria, and select the tool you prefer.

 

 

Adding optional categories

 

To add an optional category to your pipeline, simply drag and drop the icon to the pipeline. The interface will indicate the proper emplacement of the optional category, and a new tool will be automatically selected. Optional categories don’t  impact the sequence of analyses.

Design pipelines from scratch

 

Unlike the basic mode, the edit mode lets you change all the parameters of the pipeline including the sequence of analytical steps, or even start a new pipeline from scratch! If your pipeline needs to be changed again, the Pipeline Generator makes it easy to jump back in into the visual editor to modify it at any time.

 

Starting the editor

 

To create your own pipeline from scratch, start by entering the edit mode and click on “New pipeline” in the toolbox. This will generate a blank page. If you want to go back to the pipeline that was first generated in the advanced mode, click the reset button:

 

 

From a blank page, start by adding an analytical step:

 

 

Type the name of the step, or a part of it, and the interface will propose one or several corresponding steps. Drag and drop the icon to the blank space.

 

 

Continue by adding an input file format. Click the icon of the step and choose an INPUT file in the left menu.

 

 

To add a next or a previous step, click on the icon to select it and choose among the proposed pipeline categories:

 

 

Then drag and drop the icon to your pipeline. Placeholders will automatically indicate where you can drop the icon.

 

Modifying steps of a pipeline

 

In the edit mode, you can create branches to your pipeline tree, for example if you want your analysis to take different paths:

 

 

Analytical steps will automatically display branches if possible. You can manage connection with previous or next steps with the “CONNECTION” menu on the left:

 

Sharing a pipeline

 

In the edit mode, you can save your pipeline for further use/modification.

 

 

After naming your project, you can choose to make it private (default) or public.

 

 

Your pipeline will then be stored in your profile page.

 

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