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.

omictools-platform-fundraising

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

OMICtools uses code versioning to enhance tool traceability

versioning-feature-omictools

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.

omictools-versioning-and-DOI

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

omictools-distribution
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.

Community members: your publication on arXiv.org!

Community experts, we’re pleased to inform you that you’re co-authors of the article titled OMICtools: a community-driven search engine for biological data analysis. The preprint version of this article has been assigned the permanent arXiv identifier 1707.03659 and is available on arXiv.org.

This publication gives us the opportunity to thank all the OMICtools biocurators and users for their helpful collaboration in providing high-quality and updated information on bioinformatics tools.

omictools-features-publication

Overview of the collaborative functionality offers on the OMICtools platform

Here’s the abstract: with high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational biology, in order to maximize the potential of their data.

OMICtools is designed to meet this need with its open-access search engine offering an easy means of locating the right tools corresponding to each researcher and their specific biological data analyses. The OMICtools website centralizes more than 18,500 software tools and databases, manually classified, by a team of biocurators including many scientific experts. Key information, a direct link, and access to discussions and evaluations by the biomedical community are provided for each tool. Anyone can join the OMICtools community and create a profile page, to share their expertise and comment on tools. In addition, developers can directly upload their code versions which are registered for identification and citation in scientific publications, improving research traceability.

The OMICtools community links thousands of life scientists and developers worldwide, who use this bioinformatics platform to accelerate their projects and biological data analyses.