omicX raises €2.6 million to upgrade the OMICtools platform

The French startup omicX, creator of the OMICtools platform dedicated to researchers and bioinformaticians, has signed a new €2.6 million fundraising agreement with a Swiss-based private investment bank, Normandie Participations and Bpifrance.

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The digital transformation of science has seen breakthrough innovations in biology and technology, generating ever-increasing volumes of data. The development of bioinformatics tools for storing, processing and sharing massive volumes of biological data is the fastest growing field in biomedical sciences.

Democratizing bioinformatics

Arnaud Desfeux, PhD in Neurosciences, founder and CEO of omicX, recognized early the need to make these tools more readily accessible for researchers, as well as the value of an interconnected and accessible community of bioinformaticians, tool developers, and researchers. “In today’s context of an exponential production of these essential research tools, locating, classifying and documenting them in a single location will solve a major challenge for users and experts alike”.

Launched in 2013, OMICtools is a continuously updated database with a proprietary classification designed by the team. It provides a single platform for finding new tools, encourages collaboration and promotes member expertise. In just a few guided clicks, users can find adapted computational answers to their biological questions. As the current leader in the domain of bioinformatics tools and the reference on the international biology scene, it offers more than 22,000 tools and is consulted by 1,300,000 visitors annually from leading universities and institutions worldwide.

Combining artificial intelligence and collective intelligence

After raising €1 million in 2016, omicX will use the €2.6 million round of fundraising from late 2017 to continue expanding the OMICtools platform. Funds will be funneled into creating a unique and innovative feature which provides a logical sequence of tools to answer complex biological questions. The project is based on algorithms fed by machine learning from OMICtools, and fine-tuned by user feedback. “Combining artificial intelligence with collective intelligence, the pipelines project foreshadows the future of omicX as a global bioinformatics leader” affirms Arnaud Desfeux.

Based in Rouen with nearly 30 employees, the company is currently hiring to reinforce its artificial intelligence capabilities to customize tools pathways.

About omicX

Since 2013, omicX, the French start-up founded by Arnaud Desfeux PhD, has been striving to democratize bioinformatics, by offering a practical work environment, dedicated to biological data analysis to assist life scientists identify the optimal tools for exploiting their omics data.

See the press folder

Consulter le dossier de presse

Write a review and go in the draw to win a tablet!

omictools contest review

Do you use bioinformatics to analyze your biological data? Give your feedback to the community and you can go in the draw to win a tablet! To participate, all you need to do is provide your opinion on the performance and ease of use of the tools which you routinely use. The competition is open until the 30 November.

How does it work?

  • Sign in to your account (or sign up for free if you aren’t already an omics community member).
  • Locate your favorite tools: use the search engine and filters to rapidly locate your tools.
  • Click on “write a review” to give it a rating and provide your feedback.

Why is your review important?

Reviews offer a double advantage. As a user, you can rapidly identify which tools can optimally fulfil your needs based on other users’ experience. As a reviewer, you can increase the visibility of your skills concerning a specific software and become known in the omics community as a scientific expert in your field.

To be useful, the reviews should discuss elements relative to the tool’s performance, ease of installation, and ease of use.  So make sure you highlight to a maximum the extent of the functionalities and their benefits. Also don’t forget to mention what you consider can be improved – the program developers will appreciate it!

The prize

The winners will be announced on 30 November 2017 by e-mail.

  • 1st prize: a tablet (Samsung Galaxy) worth 208.25 €
  • 2nd prize:  a speaker (Bose SoundLink) worth 115.83 €
  • 3rd prize: headphones (Beats by Dr. Dre) worth 82.50 €

 Prize draw

The prize will be drawn on a semi-random basis. All reviews made throughout the duration of the competition will be entered in the draw. So the more tools you review, the greater your chance of winning!

Review eligibility criteria

The OMICtools team will evaluate all reviews from a quality perspective. Before being entered in the draw, the reviews, which are anonymized throughout the selection phase of the draw, will be classified by order of quality. Only those presenting a true scientific interest for the scientific community will be eligible.

Data storage

The data collected during this project will be computer processed to ensure the competition is implemented fairly. Data will be saved in a computerized file from which the competition winners will be identified and contacted. Our marketing team will have the right to exploit the data throughout the duration of the competition. Each participant’s first name and surname will be recorded, along with the tool(s) evaluated, and the content and the date of submission of the review(s). Access to these data is password-protected.

Data will be kept for their scientific value and will be stored on our SI with restricted access (available only to individuals authorized to administer the website). We reserve the right to delete the entire contents of any reviews including any defamatory, racist or xenophobic text. In conformance with the French data protection act (“Informatique et Libertés”), you can exercise your right to access your data, and correct or delete your data electronically by contacting us at the following email address: desfeux.arnaud@omictools.com.

By participating in this game, you agree to the conditions of the game, including our data management processes.

OMICtools uses code versioning to enhance tool traceability

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Software tools on the Web evolve over time, with developers adding or removing features to improve their product, making code versioning an essential aspect of sustainable software development. Reliable code versioning allows developers to automatically track their work and revert to previous versions when needed.

Discover here how OMICtools can help you facilitate the traceability of your tool – and learn how to successfully upload your work in a community-controlled repository.

Benefits of version control

  • Provides a mechanism to keep track of code changes
  • Allows you to track the history of changes, work on the same code files, and merge code from different branches
  • Shows conflicts on code merges, allowing you to resolve them quickly

Following the FAIR data principles

The FAIR system provides recommendations for scientific data management and stewardship. OMICtools applies the FAIR guidelines to bioinformatics tools, by making them easily Findable, Accessible, Interoperable and Reusable.

  • Findability: Software and code versions are easy to find with the OMICtools advanced search engine. We continuously collect and update information from original articles, websites and repositories to make available the latest bioinformatics tools.
  • Accessibility: OMICtools ensures ongoing access to software tools, contributing to make knowledge and support available for users. Clear and accessible relevant information as well as a direct link to the original source are provided for each tool. We also provide metadata about the tool maintenance and use (name and email of the tool developer, forum and feedbacks from the biomedical community).
  • Interoperability: As far as possible, we record all tools which can be combined with other datasets by either users or computer systems. Maintainability of software is only one of the quality dimensions. Each tool on the OMICtools website also has a unique Research Resource Identifier (RRID), developed under the Resource Identification Initiative, which is transferred to the Neuroscience Information Framework (NIF) registry.
  • Reusability: OMICtools keeps a complete history of code versions so that they can be easily accessed and/or downloaded. This long-term software archive allows all users easy access to a previous version. 

Uploading and versioning your source code

If you want to version your source code, you can get started by finding your tool in the OMICtools repository using the search engine. Once you find it, click the upload version button and follow the instructions. All you need to do is indicate the version of the source code, the operating system and architecture, and add the publication  linked to the code. It’s as quick and easy as that – and of course you can contact us with any questions.

Once your code is uploaded, the programmatic access to DataCite’s API automatically generates the corresponding DOI. This unique identifier is defined by the International DOI Foundation and assigned by OMICtools to allow precision long-term preservation of your tool. If a DOI has already been attributed for your code version, you can let us know and it will be directly imported from the software platform you used. The DOI and files can’t be modified later.

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This control repository service is designed to facilitate the development, maintenance and follow-up of bioinformatic tools by the designers themselves.

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An overview of the variety of distribution channels of the tools

Remember that each published source code version is registered with a unique DOI which provides a permanent identification of your resource, even if material is moved or rearranged. Hence OMICtools, not only supports scientists in the analysis and understanding of biological datasets, but also improves the precision of citing bioinformatics methods used to produce and reproduce results, thereby promoting the quality of scientific publications in accordance with the FAIR guiding principles for scientific data management.

Want to share your thoughts? Offer your feedback. Tell us if you’re satisfied and what you think can be improved.