miRBooking simulates the stochiometric mode of action of miRNAs.

This page hosts the releases of the C implementation as well as some general information on running the program and interpreting its output.

To compile and install miRBooking, you’ll need Meson, Ninja and the development file of GLib suitable for your platform. For the 2.0 release series, you will need a sparse linear solver and fast fourier transform library; details are available in the README.md file.

It’s also possible to write programs that consumes its C API as-is or via GObject Introspection using Python, JavaScript and Vala.

The miRBooking-scan Web service is now available and propose the exploration of the microtargetome a few cell lines. You can also download the raw picomolar quantifications to run custom analysis from there.

Source code is available on GitHub and IRICs GitLab where the main development takes place.


  • mirbooking-2.4.2.tar.xz (sha256)
  • mirbooking-2.3.0.tar.xz (sha256)

    This release brings a very nice set of features that makes miRBooking more robust, efficient and convenient to use. We focused on providing dense linear solvers to address certain problem types.

    • add --version flag
    • locate the default score tables automatically
    • fold the seed with a mask and temperature
    • add gene_accession and gene_name to the output format
    • introduce a new detailed TSV format
    • add support for LAPACK and MKL LAPACK solvers with --sparse-solver=lapack
    • reintroduce SuperLU MT solver
    • select best available solver
    • move I/O facilities in the broker
    • add a blacklist filter system
    • add a new mirbooking-iterative script to solve the system gradually using the blacklist filter
  • mirbooking-2.2.3.tar.xz (sha256)

    This release contains mostly fixes backported from the upcoming 2.3 series.

  • mirbooking-2.2.2.tar.xz (sha256)

    Fix the footprint scope and an erroneous calculation in the Jacobian.

  • mirbooking-2.2.0.tar.xz (sha256)

    This release mainly bring a better interaction model with variable forward rates and catalytic rate based respectively on seed mismatches and mid-region binding probability. It also improve the convergence criteria by looking at error-to-tolerance ratio, avoiding useless work for high-concentration interactions.

  • mirbooking-2.1.2.tar.xz (sha256)

    Fix CUDA root issue by using the pkg-config dependency.

  • mirbooking-2.1.1.tar.xz (sha256)

    Use CBLAS to accelerate tight loops in the broker implementation.

  • mirbooking-2.1.0.tar.xz (sha256)

    The key feature of this release is joint factorization to calculate the true probability of a target interval to be unbound. It also accelerates and parallelize numerical integration with CBLAS.

  • mirbooking-2.0.3.tar.xz (sha256)

    Backport of CUDA root fix.

  • mirbooking-2.0.0.tar.xz (sha256)

    Initial reference implementation of the miRBooking 2.0 model.

  • mirbooking-1.2.5.tar.xz (sha256)

    Backport usage of new Meson Python module.

  • mirbooking-1.2.4.tar.xz (sha256)
  • mirbooking-1.2.3.tar.xz (sha256)

    This release bring some build convenience, a standardized floats format (6 digits) and introduce a permissive MIT license.

  • mirbooking-1.2.2.tar.xz (sha256)

    More efficient computation of sequence index and fix issues with variable-length seed.

  • mirbooking-1.2.1.tar.xz (sha256)

    Fix mirna_quantity column in the TSV output.

  • mirbooking-1.2.0.tar.xz (sha256)

    This release backport some changes from the trunk and stabilize the C/Python API.

    • Provide and reorganize a more detailed output with common names and vacancy.
    • Add Pandas-based helper to the Python API to manipulate the output as a dataframe.
    • Drop the mirbooking-aggregate tool considering that we now have a Pandas-friendly API.
  • mirbooking-1.1.0.tar.xz (sha256)

    Few memory and CPU time optimizations and add --seed-index and --seed-offset options.

  • mirbooking-1.0.0.tar.xz (sha256)

    Initial release with a identical reimplementation of the Java version.

Supplementary material (only for 1.0)

  • score table (sha256)
    This is passed via the --score-table flag and provides hybridization probabilities of all heptamer duplexes. It also possible to generate a custom table.

Cite us

If you use miRBooking 2.0:

Poirier-Morency, G. Modélisation des réseaux de régulation de l’expression des gènes par les microARN. (2021).

If you use miRBooking 1.0:

Weill, N, Lisi, V, Scott, N, Dallaire, P, Pelloux, J, Major, F. MiRBooking simulates the stoichiometric mode of action of microRNAs. Nucleic Acids Research 43, no. 14, 0305-1048, 1362-4962; 10.1093/nar/gkv619 (2015).