How to use omicX protocols like a pro

We previously discussed all the cool things you can do with the omicX search engine. Here, we’ll uncover our latest and most exciting feature, omicX protocols, so you can analyze your big biodata like a pro.

What it a computational protocol


We know that the number of publications in biology is skyrocketing, and it’s becoming more and more difficult for scientists to identify the latest trends, analysis methods and tools in their field.


Searching through publications to benchmark or identify the best combination of tools for your analysis can take hours. For this reason, we developed a new feature that automatically extracts and recreates protocols (logical series of bioinformatics tools designed to perform an analysis task) from free biomedical texts. In one-click, you can access a thousand published protocols and edit them by choosing among our collection of 30,000+ tools to make your own, tailored protocol.


There are two types of protocols on omicX:


  • Corpus protocols

Using a handful of steps, we extract and transcribe bioinformatics protocols from scientific publications into actionable knowledge:

– Protocols are recognized using a context-aware dictionary containing keywords and synonyms, and terms are matched with our ontology of analytical steps and biological applications.

– Protocols are reconstructed using specific rules to order tools in a logical and application manner.

– Protocols are contextualized by collecting additional information about bio-entities such as diseases, species, genes, genetic variant, chemicals, cell types and tissues.


  • Generated protocols

A corpus-trained machine-learning algorithm that automatically proposes the best protocol to your question.

Based on our structured data, we can propose new protocols associated to a specific biological context, a particular user’s query or containing a specific tool.


Finding protocols

There are several entry points to access protocols on omicX.


Search engine


Whether you ask a question or search a tool, the search engine will return results classified in the following sections: Software, database, user, and protocols. In the protocol section, you will find corpus protocols related to your query, as well as access to generated protocols.


search engine for protocols


Tool page


We’ve added protocols in tool’s pages so you can have an insight of how is the tool used by your peers in publications.


Limma computational protocol


Filtering tools in protocols


Corpus protocols come with a bunch of filters to help you narrow down your search. You can choose to display protocols by application (i.e RNA-sequencing), analysis step, tool, technology, computer skill, and so on.


Once in the edit mode of a generated or corpus protocol, a new set of filters will help you decide what tools are best for each analysis step. For example, setting programming language to “C++” will change every tool of the protocol to their counterpart written in C++ (if there are any).


protocols editor


Comparing protocols with statistics


omicX gathers hundreds of protocols, and while filters are a great way to narrow down your research, it is difficult to compare the handful solutions you’ve found.


Now, after you’ve identified a protocol of interest, you can directly compare with similar pipelines to find the perfect one in a heartbeat. Color-coded dots representing tools and keywords make it very easy to find the protocol that best fits your needs.


Similar protocols