Composyx is a linear algebra C++ library focused on composability. Its purpose is to allow the user to express a large pannel of algorithms using a high-level interface to range from laptop prototypes to many node supercomputer parallel computations.

PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. Numerical algorithms are implemented in single or double precision (real or complex) using LLt, LDLt and LU with static pivoting (for non symmetric matrices having a symmetric pattern). This solver also provides some low-rank compression methods to reduce the memory footprint and/or the time-to-solution.

Ginkgo is a high-performance numerical linear algebra library for many-core systems, with a focus on solution of sparse linear systems.

Chameleon is a dense linear algebra solver relying on sequential task-based algorithms where sub-tasks of the overall algorithms are submitted to a run-time system. Such a system is a layer between the application and the hardware which handles the scheduling and the effective execution of tasks on the processing units. A run-time system such as StarPU is able to manage automatically data transfers between not shared memory area (CPUs-GPUs, distributed nodes).

qr_mumps is a software package for the solution of sparse, linear systems on multicore computers based on the QR factorization of the input matrix. Therefore, it is suited to solving sparse least-squares problems and to computing the minimum-norm solution of sparse,underdetermined problems. It can obviously be used for solving square problems in which case the stability provided by the use of orthogonal transformations comes at the cost of a higher operation count with respect to solvers based on, e.g., the LU factorization. qr_mumps supports real and complex, single or double precision arithmetic. This is an experimental version of the package for distributed memory.

This software’s goal is to propose a parallel algebraic strategy to decompose a sparse linear system Ax=b, enabling its resolution by a domain decomposition solver. Up to now, Paddle is implemented for the MaPHyS linear solver.

Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain-specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.

The Blaze library offers:

• high performance through the integration of BLAS libraries and manually tuned HPC math kernels;

• vectorization by SSE, SSE2, SSE3, SSSE3, SSE4, AVX, AVX2, AVX-512, FMA, SVML, SLEEF, and XSIMD;

• parallel execution by OpenMP, HPX, C++11 threads and Boost threads;

• an intuitive and easy to use API of a domain specific language;

• unified arithmetic with dense and sparse vectors and matrices;

• thoroughly tested matrix and vector arithmetic;

• completely portable, high quality C++ source code.

PyLops is an open-source Python library focused on providing a backend-agnostic, idiomatic, matrix-free library of linear operators and related computations. It is inspired by the iconic MATLAB Spot – A Linear-Operator Toolbox project.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

Bazel is a build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

GPCNeT is a benchmark suite that includes simulated network congestion, allowing the benchmarking of network performance in closer-to-real-conditions in HPC networks.

The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive meshes, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes.

mpiGraph is a MPI benchmark to generate network bandwidth images.

The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive meshes, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes.

This is an R package which interfaces with the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

Key features of IQ-TREE:

• Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

• An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

• An ultrafast and automatic model selection (ModelFinder);

• A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

• Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 2.

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

This package provides a tool to download or view data in the cloud environments of ICGC.