Open-Omics-Acceleration-Framework

UMAP: Uniform Manifold Approximation and Projection UMAP: Uniform Manifold Approximation and Projection Reporting Security Issues STAR 2.7.11b — 2024/01/24 ::: Minor in one parameter.STAR 2.7.10a — 2022/01/14 ::: New features, behavior changes and bug fixes STARconsensus: mapping RNA-seq reads to consensus genome.STARsolo: mapping, demultiplexing and quantification for single cell RNA-seq AlphaFold v2.3.0 Security Policy Security Policy CP2K Open Source Molecular Dynamics LIBXSMM Service Functions Backend Compatibility Matrix Multiplication Performance Analysis Q&A LIBXSMM Samples Scripts Tensor Processing Primitives Customization Validation Security Policy Release 2.2.1 (17 March 2021)bwa-mem2 DeepVariant FAQ Building DeepTrio from sources DeepTrio training data DeepTrio Using DeepTrio for small variant calling from the trio sequenced with PacBio HiFi DeepTrio quick start DeepTrio whole genome sequencing case study Building DeepVariant from sources DeepVariant whole genome sequencing case study DeepVariant training data DeepVariant usage guide DeepVariant whole exome sequencing (WES) case study Getting Started with GCP DeepVariant Genomic VCF (gVCF) support Using the DeepVariant hybrid model for calling on PacBio and Illumina data together DeepVariant with Oxford Nanopore R10.4.1 Duplex reads DeepVariant with Oxford Nanopore R10.4.1 Simplex reads Using DeepVariant for small variant calling from PacBio HiFi reads DeepVariant quick start DeepVariant RNA-seq Case Study Advanced Case Study: Train a customized SNP and small indel variant caller for BGISEQ-500 data.VCF stats report DeepTrio runtime and accuracy metrics for all release models Runtime and accuracy metrics for all release models Runtime by region profiling for make_examples show_examples: Saving human-readable images from DeepVariant examples Best practices for multi-sample variant calling with DeepVariant (WES trio demonstration)HTSlib 64 bit reference positions Release 1.4.0: Februrary 2023 Thread pool tests Release 2.24-r1122 (26 December 2021)Table of Contents Open-Omics-Autodock-Vina Open-Omics-Autodock OpenOmics ProtGPT2 OpenOmics ProteinMPNN OpenOmics RFdiffusion STAR 2.7.11b AlphaFold2 optimized on Intel Xeon CPU AlphaFold Protein Structure Database Intel(R) Tensor Processing Primitives extension for PyTorch*We can accelerate the attention module in intel-alphafold2 codebase by replacing it with the optimized version from [tpp_pytorch_extension].Graph Neural Network Graph Attention Netowrk GraphSAGE LIBXSMM CP2K Artificial Benchmark 1D Dilated Convolutional Layer Elementwise correctness- and performance tests Hello LIBXSMM Magazine NEK Sample Collection SPECFEM Sample Matrix Transpose (TCOPY)Dispatch Scratch Memory Allocation (Microbenchmark)SMM Benchmark Wrapped DGEMM Scripts LIBXSMM Test Suite (INTERNAL)PARLOOPER : PARallel LOOP gEneratoR safestringlib Open-Omics-DeepVariant DeepTrio is under development.Documentation Open-Omics-ESM Htscodecs Reference implementation files RMI Trans-Omics Acceleration Library Instructions for ubuntu Create an Anaconda environment RMI safestringlib SIMD Everywhere µnit Getting Started Open-Omics-Moflow samtools Steps to use to reproduce benchmarking results of Open Omics Acceleration Framework v2.1 on AWS EC2 instances published in the AWS Intel blog Benchmarking of Open Omics Acceleration Framework on AWS Trans-Omics Acceleration Library Instructions for ubuntu Create an Anaconda environment RMI safestringlib Pipeline overview fq2vcf: OpenOmics Deepvariant based Variant Calling Pipeline fq2SortedBAM: OpenOmics’ Genomics Secondary Analysis Pipeline Pipeline overview

CP2K Open Source Molecular Dynamics

CP2K Open Source Molecular Dynamics

The CP2K recipe (PDF) has been incorporated into the XCONFIGURE project.

Open-Omics-Acceleration-Framework

Open-Omics-Acceleration-Framework

Intel lab's open sourced data science framework for accelerating digital biology