10x Genomics Git

EMA uses a latent variable model to align barcoded short-reads (such as those produced by 10x Genomics' sequencing platform). Separate processing prior to the batch correction step is more convenient, scalable and (on occasion) more reliable. samples: A character vector containing one or more directory names, each corresponding to a 10X sample. 10x Genomics: Culture of Collaboration And A New Product Engine | Jun 04, 2020 Intel, Penn Medicine Launch Federated Learning Model For Brain Tumors | May 28, 2020 Buying GitHub Would Take Microsoft Back To Its Roots. 00: The Crux mass spectrometry. Pathologic evaluation demonstrated follicular center site which stained. Cell Ranger, printed on 08/28/2020. scriptome data by the combination of 10x Genomics and. txt), PDF File (. We are working on projects in the areas of genomics, transcriptomics, antibiotics discovery and computational mass spectrometry. The Spark connector for SQL Server and Azure SQL Database also supports Azure Active Directory (Azure AD) authentication, enabling you to connect securely to your Azure SQL databases from Databricks using your Azure AD account. Watch how you can get new insights on the inner workings of biology with 10x Genomics. The motivation for this is that I recently stumbled over the GLM-PCA approach from Rafael Irizarry's lab (links see on the bottom of the post) which made me dive into the literature. Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. HDF5 Feature Barcode Matrix Format. Specifying Input FASTQ Files for 10x Pipelines. The Investor Relations website contains information about 10x Genomics's business for stockholders, potential investors, and financial analysts. 10x Genomics Chromium Single Cell Gene Expression. 10x Genomics Selects First 45 Members for Visium Clinical Translational Research Network. The cellranger pipeline requires FASTQ files as input, which typically come from running cellranger mkfastq, a 10x-aware convenience wrapper for bcl2fastq. Disruptions in GIT microbiome composition have been. what is bitcoin all time high - Bitcoin's price has rebounded, partly on the news of a long position held by Peter Thiel's Founders Fund. For patient DSN09, both 10x Genomics and SMART-seq2 methods were applied in parallel, giving us the opportunity to evaluate the power of integrated analysis on two types of datasets. This includes standard Smart-seq2 and protocols requiring capped mRNA like the TeloPrime protocol (Lexogen) for bulk sample analysis. User Guide. 00: API and toolkit for reading, writing, and manipulating BAM (genome alignment) files. Cell capture rate depends on several variables, including input cell number and viability. The 10X pipeline also computes the phase and IGV can separate the reads and color them by haplotype tag (HP) if present in the data file. , present ARCS, the Assembly Round-up by Chromium Scaffolding algorithm. Its small genome size, fully sequenced in the year 2000, chromosome number, fast growth cycle (from seed germination to set in. This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2. (2010) SNP discovery by high-throughput sequencing in soybean. All protocols were performed following the manufacturer’s instructions. Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. We invest in the world’s most ambitious people and then we invest in the companies they build. What’s version control? Version control is a system that records changes to a file or a set of files over time so that you can recall specific versions later. 05 −e 30000 −v 1 −m 20–4000 −z 500 and LINKS v1. We are a Talent Investor. Honours and postgraduate* projects are available to work on the assembly and annotation. 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells; 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells. Project Management: Git, Jenkins, NSIS OS: Windows, Linux, MAC-OS, VMWare Senior Software Engineer in Test at 10X Genomics. Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. R toolkit for single cell genomics Developed by the Satija lab at NY Genome Center “Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. 267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer. I can’t figure out the file format for the binary implementations of t-SNE? The format is described in the User’s guide. 25 mM Na2H. bam ch1这几天遇到了10x genomics的bam结果,发现单细胞的reads全包含在一个bam文件里,用barcode进行区分,因此. Cell Ranger4. This is complimented by existing PacBio data. In the case of the de novo assemblies, the chain files had to be produced from a BLAT [ 41 ] alignment between the de novo assembly and hg19 with the UCSC tool set [ 42 ]. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e. Brynn Claypoole, Software Engineer at 10x Genomics; Kyle Stewart Frantz, Content Developer at Udacity; Abe Feinberg, Content Developer at Udacity; Other Udacity Contributors: Dane Hammer, Robin Robin, James Bibby, Pradeep Uppala, Brok Bucholtz, Cezanne Camacho, Alan Anderson, Peiyan, David Harris, Stephen Welch, and Chris Gearhart. Official binary distributions of the Martian toolchain are available for Linux. How do I convert a 10X scRNA-seq bam file to fastq with dsub? Python How do I quantify 10X scRNA-seq gene expression with Kallisto and BUStools? Python How do I do Nearest Centroid Classification using BigQuery? Python: R *. Available for use only with the Chromium Controller (Part Numbers 120223 and 120246) or the Chromium Single Cell Controller (Part Numbers 120263 and 120212). I am looking for opinions (hands-on based experience) towards your favourit feature selection method for 10x scRNA-seq data. 10x Genomics Reports Second Quarter 2020 Financial Results. We adapt tips and tricks from the developer community to help you become a more proficient data scientist loved by team members and stakeholders. Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample. At 10x Genomics, we want ambitious, talented software engineers to join us in building revolutionary DNA sequencing technology. The cellranger pipeline requires FASTQ files as input, which typically come from running cellranger mkfastq, a 10x-aware convenience wrapper for bcl2fastq. The genomic and transcriptomic platform was set up in 2017 to coordinate NGS CPTP analyses coming from RNAseq, ChIPseq and ATACseq experiments. The company was formerly known as 10X Technologies, Inc. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e. Bioconductor version: Release (3. Compare this with all the ways a Genbank flatfile can be botched (I see this complaint routinely on Twitter), in part because Genbank files (and I think PDB; haven't munged one in a while) retain the mainframe-era penchant for the lateral position of text being. Its headquarters are located in Pleasanton, California. 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells; 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells. The kmer coverage value produced by SPAdes is half the read coverage, so a contig with 10X kmer coverage from SPAdes actually has 20X read coverage. , BMC Genomics, 2014)いいかも、とか。 乳酸菌RNA-seqデータの. During the latest edition of Microsoft Build, Microsoft’s. Getting Started Installing Martian. I just could not find it. So, they do have an offering around this. A few years later, I wiped my Windows installation from. sparQ DNA Frag & Library Prep Kit generates high quality DNA libraries with minimal duplication artifacts. PLEASANTON, Calif. show that hPSC-derived venous endothelial cells are better able to upregulate markers of LSECs in vitro and in vivo compared to arterial cells. 10x Genomics Biotechnology Pleasanton, California 53,753 followers Building tools for scientific discovery that reveal and address the true complexities of biology and disease. 0 (latest), printed on 09/03/2020. We started with a small number of cells in the first sample for inDrop and 10x Genomics technologies, which recovered 344 cells and 256 cells, respectively. 10x Genomics Single Cell Gene Expression. More information is available in our paper. Epidemiology is the basic science of public health genomics, concerned with understanding how human and pathogen genomic variation affects the distribution of disease in populations. If you are looking to improve your skills in data structures and algorithms -- to prepare for the technical portion of job interviews, to improve your software engineering skills, etc. Roadmap project. - More than 7 years of experience in plant genomics research and project coordination. As noted in the Encyclopedia of life: Arabidopsis thaliana is the most widely used model organism in plant biology. Details to follow. Breast, Thoracic, Gastrointestinal tract (GIT) and Genito-urinary tract (GUT) were included in this evaluation. iosonofabio: cerbero-profiler: crux-toolkit-git: r3149. , BMC Genomics, 2014)いいかも、とか。 乳酸菌RNA-seqデータの. HDF5 Feature Barcode Matrix Format. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Waterston_400_minutes 25875 # 400 minute synchronized embryos Waterston_300_minutes 17168 # 300 minute synchronized embryos Murray_b01 12129 # mixed time point. See full list on support. 00: The Crux mass spectrometry. Step 5: Quality Check. 10x Genomics First Quarter 2020 Earnings Conference Call. Long read assembly workshop. I wrote a post for 2018 here. A successful library preparation will have a broad peak with an average size between 400-1000 bp. EMA is faster and more accurate than current aligners, and produces not only the final alignments but interpretable per-alignment probabilities. I am not the only one who has impostor syndrome :) It is important to celebrate your small successes/achievements by writing them down. Use the HS DNA5000 or HS DNA1000 tape and appropriate reagent buffer. benwbooth: bcm2079x-i2c: 1-1: 0: 0. Watch how you can get new insights on the inner workings of biology with 10x Genomics. The 10x Genomics’ analysis pipeline, cellranger (version 2. BMC Genomics 14:137 pmid:23445355. Maintain Data Carpentry cloud computing for genomics lesson, coordinating the contributions of the community. Cases of four organ systems i. A 65-year-old gentleman presented with left groin swelling over the course of two months. SS2 and 10X are two frequently used scRNA-seq platforms with their unique strengths and weaknesses. We are using a combination of Illumina (HiSeq X and NovaSeq) short read sequencing, PacBio (RS II) long read and sequence and 10x Genomics Chromium linked reads. 1, HDF5, YAML is the nightmare of parsing bad formats is eliminated; there are real standards here. How To Become a 10x Data Scientist, part 1 - Sep 18, 2017. It then quickly builds trees using the GY94 model and, using these fixed topologies, estimates HLP19 model parameters. 2008) encoding, this XML-based format is more useful to programmers than to end users submitting data. TENxPBMCData PBMC data from 10X Genomics. benwbooth: bcm2079x-i2c: 1-1: 0: 0. In contrast to bulk RNA-seq, scRNA-seq provides quantitative measurements of the expression of every gene in a single cell. The Spark connector for SQL Server and Azure SQL Database also supports Azure Active Directory (Azure AD) authentication, enabling you to connect securely to your Azure SQL databases from Databricks using your Azure AD account. Here, we describe a brief analysis of the peripheral blood mononuclear cell (PBMC) dataset from 10X Genomics (Zheng et al. 00: API and toolkit for reading, writing, and manipulating BAM (genome alignment) files. what is bitcoin all time high - Bitcoin's price has rebounded, partly on the news of a long position held by Peter Thiel's Founders Fund. SS2 is a plate-based full-length approach with high transcriptome coverage per cell and greater sensitivity10, whereas the microfluidic droplet-based method, 10X, generally has lower coverage per cell and a higher. Hank's (Final): 9. August 6, 2020 10x Genomics to Participate in the UBS Genomics 2. Cell Ranger, printed on 08/28/2020. Project Management: Git, Jenkins, NSIS OS: Windows, Linux, MAC-OS, VMWare Senior Software Engineer in Test at 10X Genomics. Data sharing with external collaborators. g4b19ea8-1: 0: 0. Data was subsequently analyzed to determine how cryopreservation impacted the cellular composition of the tumor microenvironment. Senior Optical Engineer at 10x Genomics, 🔬+ 🧬 As a small startup I wore many other hats such as: developing our data analysis pipeline, introducing the use of Git and GitHub, helping set. Vor 3 Tagen gepostet. 2010; Croucher et al. May 11, 2020 at 1:30 PM PDT Listen to Webcast. Separate processing prior to the batch correction step is more convenient, scalable and (on occasion) more reliable. We started with a small number of cells in the first sample for inDrop and 10x Genomics technologies, which recovered 344 cells and 256 cells, respectively. [Udacity] Data Structures & Algorithms v1. We present Sparse Project VCF (spVCF), an evolution of VCF with judicious entropy reduction and run-length encoding, delivering ~10X size reduction for modern studies with practically. NET Core is the future of. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen. -- then this Nanodegree program will provide you with extensive practice with defined and open-ended problems so that you learn how to implement the appropriate solution based on your design choices. was founded in 2012 and is headquartered in Pleasanton. Getting Started; Selecting the Correct Single Cell Gene Expression User Guide; Technical Note. 10x Genomics has filed an amended up-to-$362. JoVE publishes peer-reviewed scientific video protocols to accelerate biological, medical, chemical and physical research. 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells; 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells. Insertions made up a smaller proportion of the total called errors ( Figure 3B), and required a lower coverage for complete correction ( Figure 3C). Mar 3, 2020 at 10. The genomic and transcriptomic platform was set up in 2017 to coordinate NGS CPTP analyses coming from RNAseq, ChIPseq and ATACseq experiments. SS2 is a plate-based full-length approach with high transcriptome coverage per cell and greater sensitivity10, whereas the microfluidic droplet-based method, 10X, generally has lower coverage per cell and a higher. Hiring: Senior Product Manager, Bioinformatics at 10x Genomics I'm hiring a Senior Software Product Manager, Bioinformatics to lead the delivery of on-market and new bioinformatics single cell analysis pipelines (including cellranger ) at 10x Genomics. Pathologic evaluation demonstrated follicular center site which stained. Background Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. 1 COURSE OVERVIEW. Git is a distributed version control and source code management (SCM) system with an emphasis on speed. txt), PDF File (. Apply to Scientist, Research Scientist, Data Scientist and more!. 0 (latest), printed on 09/03/2020. 10x Chromium Single Cell 3' Solution V2 and V3. 1) was first used to demultiplex and produce a gene-cell matrix. Focused panels contain a select set of genes or gene regions that have known or suspected associations with the disease or phenotype under study. 10x Genomics has filed an amended up-to-$362. This uses STAR to align reads to the reference genome and then counts the number of unique UMIs mapped to each gene. Hiring: Senior Product Manager, Bioinformatics at 10x Genomics I'm hiring a Senior Software Product Manager, Bioinformatics to lead the delivery of on-market and new bioinformatics single cell analysis pipelines (including cellranger ) at 10x Genomics. Git for Teams: DataLab: Data Science and Informatics: 10X Genomics, Pac Bio, Oxford Nanopore and Hi-C ] Bioinformatics Core: Oct 26, 2018 Phase Genomics Lunch and. EMA is an alignment tool for barcoded short-read sequencing data, such as those produced by 10x Genomics' Chromium platform. Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. AST’s address is 6201 15th Avenue, Brooklyn, New York 11219. Institute, is an open source genomics analysis package that contains all variant tools for germline and cancer genomic analysis. The methylKit R package can calculate differential methylation and annotate differentially methylated sites6. We’re running lots of 10X Genomics, as well as some Fluidigm C1, Drop-Seq and other home-brew methods. An excisional lymph node biopsy was performed. Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample. Serve as instructor or lead instructor for R, python, OpenRefine, shell, SQL, & git course materials, teaching reproducible research and automation techniques to scientists across all disciplines and career stages in Australia. The women of 10x Genomics are turning exciting ideas into real-life solutions. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20. Genomics and evolution of bacterial pathogens. We develop machine-learning methods applied to genomics data for immune profiling in personalized cancer medicine. The main topic of this blog post is to detail a plugin that I have developed for the Torrent Browser. Breast, Thoracic, Gastrointestinal tract (GIT) and Genito-urinary tract (GUT) were included in this evaluation. Apply to Scientist, Research Scientist, Data Scientist and more!. If you plan to explore and make changes to the source code, or you have requested some bug-fix that is temporarily available only on the github dev branch, then you need to install velocyto directly from source. In addition to the MEX format, we also provide matrices in the Hierarchical Data Format (HDF5 or H5). If your input data is lower coverage you may need to reduce this value but the defaults are sensible. uses American Stock Transfer & Trust Company (“AST”) as our transfer agent. Using Git and Github for revision control 10X single-cell RNA-seq analysis in R genomics, RNA-seq, and proteomics. Separate processing prior to the batch correction step is more convenient, scalable and (on occasion) more reliable. The MG-RAST team has decided to follow the minimal checklist approach used by the Genomics Standards Consortium (GSC)(Field et al. - Attended lecture and hands-on training for: a. Must also have an index (. Data was subsequently analyzed to determine how cryopreservation impacted the cellular composition of the tumor microenvironment. Cell Ranger4. You can find out all the cell barcodes (16 bp) here: 737K-august-2016. The big advantage of XML, ASN. Details to follow. The genomic and transcriptomic platform was set up in 2017 to coordinate NGS CPTP analyses coming from RNAseq, ChIPseq and ATACseq experiments. While the GSC provides a GCDML (R. Recruited and trained over 40 new consultants which increased the size of the sales team by 10X within one year! Established and maintained more than 100 business accounts. An example of a large-scale scRNA-seq experiment is the recent ‘Mega-Cell Demonstration’ by 10× Genomics (10× Genomics Datasets, 2017) which features 1. Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. , present ARCS, the Assembly Round-up by Chromium Scaffolding algorithm. 4 includes a new feature to view aligned reads linked by the 10X barcode sequence (BX) or molecular identifier (MI) (right-click popup menu in alignment tracks). 10x Genomics Chromium Single Cell Gene Expression. So, I can then make a bigwig for each cluster to visualize in IGV. The cellranger pipeline requires FASTQ files as input, which typically come from running cellranger mkfastq, a 10x-aware convenience wrapper for bcl2fastq. Qiang Li Senior Software Engineer at 10x Genomics. There are currently two plugins which does variant calling: (1) Germ-lineVariantCaller is a general variant caller plugin and (2) AmpliSeqCancerVariantCaller is specific to the AmpliSeq Cancer Kit. (Nasdaq: TXG) today reported financial results for the second. 10x-pert Workshops Single Cell CNV Single Cell Gene Expression Single Cell Immune Profiling Single Cell ATAC Genome Sequencing English Japanese Chinese Korean French. 3 Medium - Free ebook download as Text File (. General Information: Business: We are a life science technology company building products to interrogate, understand and master biology. Details to follow. Cell Ranger4. 2011; Holt et al. So, there's a lot of interest in it. Opportunities. 10x Genomics to Participate in the UBS Genomics 2. of 16 liver cancer patients from multiple immune-relevant tissue. Watch our scientific video articles. View Article PubMed/NCBI Google Scholar 86. com, Electronic Arts, TripAdvisor and Yelp, migrated to Amazon Redshift and achieved agility and faster time to insight, while dramatically reducing costs. 仪器信息网是科学仪器最专业b2b门户,提供化学分析、实验室设备、生命科学、环境监测、物性测试等仪器的导购及产业研究,在线培训、招聘、仪器论坛等一站式服务。. Using graph-based clustering (Traag et al. (such as those produced by 10x Genomics' sequencing platform). Today, Nebula Genomics offers Whole Genome Sequencing for only $299. sajan has 1 job listed on their profile. Framework OWASP Testing Guide Framework with tools for OWASP Testing Guide v3 Brought to you by: wushubr. 5b”, a Transformer 1 neural network 10x larger than before trained (like a char-RNN with a predictive loss) by unsupervised learning on 40GB of high-quality text curated by Redditors. Epidemiology is the basic science of public health genomics, concerned with understanding how human and pathogen genomic variation affects the distribution of disease in populations. 5 1% ß-mercaptoethanol. Bioconductor version: 3. In its first day of trading, 10x Genomics’ initial share price of $39 jumped as high as 48% to $57. Datatype Approximate Coverage Download Size; 10x: 50. , before cell calling from the CellRanger pipeline. 10x Genomics Chromium Single Cell Gene Expression. After installing VirtualBox and. Apply to Scientist, Research Scientist, Data Scientist and more!. Project Management: Git, Jenkins, NSIS OS: Windows, Linux, MAC-OS, VMWare Senior Software Engineer in Test at 10X Genomics. How To Become a 10x Data Scientist, part 1 - Sep 18, 2017. Researchers are adapting CRISPR, synthetic biology, and other creative approaches to detect SARS-CoV-2 nucleic acids outside of the lab or doctors’ offices, in the hopes of making diagnostics more affordable and accessible. 10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling Python 4 20 3 1 Updated Jul 31, 2020. Place on magnet for 2 min. 1 This agreement ("Agreement") relates to the license, installation and/or use by you (the "Licensee") of the software product(s) of 10x Genomics, Inc. Illumina innovative sequencing and array technologies are fueling groundbreaking advancements in life science research, translational and consumer genomics, and molecular diagnostics. 00: API and toolkit for reading, writing, and manipulating BAM (genome alignment) files. 1 Gene Expression Cell Ranger 2. All of our pipelines have full HPC (LSF) and OpenStack Cloud integrations. General Information: Business: We are a life science technology company building products to interrogate, understand and master biology. How time flies! It is a good time to reflect what I have achieved during the past year and what to look forward in 2020. 9) 17, followed by application of Sealer to close gaps, yielded the version 3 assembly. The methylKit R package can calculate differential methylation and annotate differentially methylated sites6. 2011; Holt et al. 10xgenomics. Our multi-disciplinary team in microfluidics, biochemistry, mechanical engineering, computational biology, and software has a proven track record of delivering successful commercial products built on deep technological innovation. It is of note that the technology behind containers was in part developed by Google. Its integrated solutions include single cell. The full experimental setup is available here. Release Notes for Cell Ranger 2. Bioconductor version: Release (3. He served as President of Penumbra (NYSE: PEN), a global healthcare company focused on innovative therapies, until May 2020 when he stepped down to focus his efforts on Testing for America, a nonprofit established by leading academics, engineers, and entrepreneurs to address the COVID-19 testing crisis. I am not the only one who has impostor syndrome :) It is important to celebrate your small successes/achievements by writing them down. (Nasdaq: TXG) today reported financial results for the second. User Guide. In a new Bioinformatics publication, Yeo, et al. 1 This agreement ("Agreement") relates to the license, installation and/or use by you (the "Licensee") of the software product(s) of 10x Genomics, Inc. Honours and postgraduate* projects are available to work on the assembly and annotation. is a life science technology company, which engages in building products to interrogate, understand and master biology. 05 mg/ml streptomycin 0. People have done that because I saw figures from the scATAC papers. in November 2014. Datatype Approximate Coverage Download Size; 10x: 50. The cellranger pipeline requires FASTQ files as input, which typically come from running cellranger mkfastq, a 10x-aware convenience wrapper for bcl2fastq. H5 is a binary format that can compress and access data much more efficiently than text formats such as MEX. During the latest edition of Microsoft Build, Microsoft’s. This is complimented by existing PacBio data. JoVE publishes peer-reviewed scientific video protocols to accelerate biological, medical, chemical and physical research. Katie Pfeiffer, PhD, Staff Scientist, 10x Genomics May 20, 2020 High Throughput, Rapid Antibody Discovery and Validation Using 10x Genomics’ Single Cell Immune Profiling Solution. Data submission to ArrayExpress. For tutoring please call 856. Sri Kosaraju has been a Board member of 10x Genomics since March 2019. Katie Pfeiffer, PhD, Staff Scientist, 10x Genomics May 20, 2020 High Throughput, Rapid Antibody Discovery and Validation Using 10x Genomics' Single Cell Immune Profiling Solution. Physical exam revealed nontender left inguinal adenopathy, and computed tomography scans detected multiple lymph nodes in the mesenteric, aortocaval, and right common iliac regions. The Center for Algorithmic Biotechnology is a part of the Institute of Translational Biomedicine SPbU. 05 mg/ml streptomycin 0. NET Core is the future of. Getting Started Installing Martian. Download Ubuntu (I would recommend Ubuntu 12. 1, HDF5, YAML is the nightmare of parsing bad formats is eliminated; there are real standards here. It can outperform row-by-row insertion with 10x to 20x faster performance. 10X Genomics (2) 2001 (2) 2006 (2) 2D graphical representation of DNA (2) 2D plot (2) Algorithms for Molecular Biology (2) Applications in Plant Sciences (2) Applied and Environmental Microbiology (2) artificial indels (2). 25 million proposed initial public offering (IPO) that would be possibly triple, but no less than double, the size of the offering revealed last month. Demonstrated proficiency in working with large codebases and communicating results should be documented in the form of a publicly-available repository and written reports on the work. Apache Spark is one the hottest Big Data technologies in 2015. Note: This is expected to be the last version of Cell Ranger to support CentOS/RedHat 5 and Ubuntu 10. 10x Genomics Reports Second Quarter 2020 Financial Results. If your input data is lower coverage you may need to reduce this value but the defaults are sensible. 9) 17, followed by application of Sealer to close gaps, yielded the version 3 assembly. 0 (latest), printed on 09/03/2020. 1 Gene Expression Cell Ranger 2. 10X Genomics is lumped in with BioNano Genomics, Dovetail Genomics cHiCago (HiC) method, genetic maps and mate-pair mapping. 267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer. " XDI Protocol "The XDI protocol enables personal clouds, identity containers, agents, and similar concepts. It is based on a powerful identity graph that connects individuals, businesses, and relationships. 10x Genomics Chromium Single Cell Gene Expression. Getting Started; Selecting the Correct Single Cell Gene Expression User Guide; Technical Note. High quality sequencing metrics. Their annotations define 183 cell types. pdf) or read book online for free. See the complete profile on LinkedIn and discover sajan’s connections and jobs at similar companies. At 10x Genomics, we want ambitious, talented software engineers to join us in building revolutionary DNA sequencing technology. Support for IUPAC ordering of elements in Composition formulae (@utf) Various bug fixes including returning integer miller indices, catching negative values in Composition and fixes to graph analysis (@utf), fix to Composition serialization (@jmmshen), defect analysis (@HanmeiTang), removing sites in surfaces (@yiming-xu), and fix to support the new PROCAR format in VASP (@dkorotin). See full list on support. 1 Gene Expression. Bcl files were demultiplexed using their barcode-aware wrapper for bcl2fastq (version2. The first human genome was sequenced by the Human Genome Project (HGP) at a cost of over $3 billion. View Article PubMed/NCBI. For Research Use Only. 各項目に例題は多数存在するが、不完全なままのものも含むことなど。 2日目は主にトランスクリプトーム解析の話。様々な解析目的と参照項目。トランスクリプトームの発現量推定はTIGAR2 (Nariai et al. Use the HS DNA5000 or HS DNA1000 tape and appropriate reagent buffer. , (Harris et al. An excisional lymph node biopsy was performed. Analyzed client requirements, created a business plan and drove strategy development. The methylKit R package can calculate differential methylation and annotate differentially methylated sites6. 10xgenomics. 10X Genomics (2) 2001 (2) 2006 (2) 2D graphical representation of DNA (2) 2D plot (2) Algorithms for Molecular Biology (2) Applications in Plant Sciences (2) Applied and Environmental Microbiology (2) artificial indels (2). ("10x"), identified herein and/or that accompanies these license terms, including any and all associated modules, documentation, and updates or revisions thereto. 10x Genomics First Quarter 2020 Earnings Conference Call. 0, which can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. 267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer. The FASTQ files emitted by the tool should contain the same set of sequences that were input to the original pipeline run, although the order will not be preserved. A 10x developer is someone who is 10 times more productive than average. See full list on support. Preprocessing 10x data entails several steps,. However, it is possible to use FASTQ files from other sources, such as Illumina's bcl2fastq, a. This gets applied at the end of each SPAdes assembly, and filters out some of the noise. Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. Growth Medium: L-15 (Sigma) 0. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. How to use git and github Learn Python the hard way Python Numpy Tutorial Complete Genomics Public data. GATK4 best practice pipelines, published by Broad Institute,2 are widely adopted by the genomics community. 25 mM Na2H. Summary Variant Call Format (VCF), the prevailing representation for germline genotypes in population sequencing, suffers rapid size growth as larger cohorts are sequenced and more rare variants are discovered. Long read assembly workshop. Browse The Most Popular 96 Genomics Open Source Projects. Linked reads and synthetic long reads lack the continuous sequence information needed to reliably detect insertions, are prone to spurious false positive deletions, and are hampered by the well-documented context bias of Figure 3. Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. I have been a nurse since 1997. Framework OWASP Testing Guide Framework with tools for OWASP Testing Guide v3 Brought to you by: wushubr. 25 million proposed initial public offering (IPO) that would be possibly triple, but no less than double, the size of the offering revealed last month. (such as those produced by 10x Genomics' sequencing platform). Introduction. 6% of STRs characterized with ≥10x non-redundant sparsehash. g4b19ea8-1: 0: 0. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20. Presenters names in bold (for updates and changes email [email protected] At 10x Genomics, we want ambitious, talented software engineers to join us in building revolutionary DNA sequencing technology. Spearheaded "A Financial Fortress in Every Home", resulting in a 400% increase in revenue. " XDI Protocol "The XDI protocol enables personal clouds, identity containers, agents, and similar concepts. The latest versions of GATK, GATK4, contains Spark and traditional implementations, that is the Walker mode. Long read assembly workshop. 5 1% ß-mercaptoethanol. Epidemiology is the basic science of public health genomics, concerned with understanding how human and pathogen genomic variation affects the distribution of disease in populations. A typical experiment ranges from 30-60%. She discusses Airbnb’s architectural tenets around service building and dives deep into lessons learned and. 10x Genomics to Participate in the Morgan Stanley 2020 Healthcare Conference. 3 million brain cells from E18 mice, generated by 10X Genomics. See full list on github. Areas that sound interesting to me are graphics, computer vision, computational geometry, compiler development and genetics/genomics to name a few. 0 (latest), printed on 09/03/2020. pdf) or read book online for free. Senior Optical Engineer at 10x Genomics, 🔬+ 🧬 As a small startup I wore many other hats such as: developing our data analysis pipeline, introducing the use of Git and GitHub, helping set. OpenAI announced in February 2019 in “Better Language Models and Their Implications” their creation of “ GPT-2-1. I find for my customers, it can be a 10X, a 50X, or even 100X savings, if you have huge scale applications. The main topic of this blog post is to detail a plugin that I have developed for the Torrent Browser. Incubate at room temp for 5 min. From our website. The paper includes a great table highlighting the characteristics of the different 3rd-gen platforms (reproduced below). May 19, 2020 10x Genomics Becomes First One Medical Customer to Deploy Cohort-Based COVID-19 Employee Testing. A successful library preparation will have a broad peak with an average size between 400-1000 bp. NicheMarkers10x: Markers for populations defined by 10x genomics; To install from within R, you can use the install_git function from the devtools package. Analyzed client requirements, created a business plan and drove strategy development. , BMC Genomics, 2014)いいかも、とか。 乳酸菌RNA-seqデータの. Cell Ranger4. Insertions made up a smaller proportion of the total called errors ( Figure 3B), and required a lower coverage for complete correction ( Figure 3C). 10x Genomics, Inc. Getting Started; Selecting the Correct Single Cell Gene Expression User Guide; Technical Note. This includes standard Smart-seq2 and protocols requiring capped mRNA like the TeloPrime protocol (Lexogen) for bulk sample analysis. and changed its name to 10X Genomics, Inc. A 65-year-old gentleman presented with left groin swelling over the course of two months. I find for my customers, it can be a 10X, a 50X, or even 100X savings, if you have huge scale applications. In Zusammenarbeit mit interdisziplinären Teams stehst du für den… Sehen Sie sich dieses und weitere Jobangebote auf LinkedIn an. This gets applied at the end of each SPAdes assembly, and filters out some of the noise. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. Seurat aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single. August 11, 2020 10x Genomics Reports Second Quarter 2020 Financial Results. I am looking for opinions (hands-on based experience) towards your favourit feature selection method for 10x scRNA-seq data. Cell Ranger, printed on 08/28/2020. 2010; Croucher et al. Use the HS DNA5000 or HS DNA1000 tape and appropriate reagent buffer. Each dataset was obtained from the TENxPBMCData package and separately subjected to basic processing steps. 10x Genomics Biotechnology Pleasanton, California 53,753 followers Building tools for scientific discovery that reveal and address the true complexities of biology and disease. 10x Genomics Single Cell Gene Expression. You also might want to have a look at the Matlab or Python wrapper code: it has code that writes the data-file and reads the results-file that can be ported fairly easily to other languages. 10x Genomics to Participate in the Morgan Stanley 2020 Healthcare Conference. The kmer coverage value produced by SPAdes is half the read coverage, so a contig with 10X kmer coverage from SPAdes actually has 20X read coverage. 10X Genomics, Inc. The first human genome was sequenced by the Human Genome Project (HGP) at a cost of over $3 billion. 10x-pert Workshops Single Cell CNV Single Cell Gene Expression Single Cell Immune Profiling Single Cell ATAC Genome Sequencing English Japanese Chinese Korean French. g4b19ea8-1: 0: 0. - Self-motivated, meticulous, and organized. Please see 10X Genomics website for details. Conclusions The workflow described in this application note provides an. " XDI Protocol "The XDI protocol enables personal clouds, identity containers, agents, and similar concepts. The Office of Public Health Genomics tracks epidemiologic study results in our weekly horizon scan and Advanced Molecular Detection Clips and deposits relevant. 137 M NaCl 5. People have done that because I saw figures from the scATAC papers. Please get in touch if you are interested in the project. Visit our official Buy Bitcoin page. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0. 10x Genomics Chromium Single Cell Gene Expression. 1 Introduction. Qiang Li Senior Software Engineer at 10x Genomics. See Supplementary Methods for additional description of the. 10X Genomics Company Profile President & CEO: Serge Saxonov. A typical experiment ranges from 30-60%. What’s version control? Version control is a system that records changes to a file or a set of files over time so that you can recall specific versions later. If you would like to combine this solution with Feature Barcoding technology, select Feature Barcode type(s). 10X Genomics is lumped in with BioNano Genomics, Dovetail Genomics cHiCago (HiC) method, genetic maps and mate-pair mapping. All protocols were performed following the manufacturer’s instructions. Install from source¶. Jul 14 10x Genomics: Culture of Collaboration And A New Product Engine. buy into bitcoin mining - Buying Bitcoin. Single-cell RNA-seq data for 1. bam ch1这几天遇到了10x genomics. read_h5ad (filename[, backed, chunk_size]). 3 Medium - Free ebook download as Text File (. Bioconductor version: Release (3. 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells; 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells. I find for my customers, it can be a 10X, a 50X, or even 100X savings, if you have huge scale applications. All content is posted anonymously by employees working at 10x Genomics. 1 Gene Expression Cell Ranger 2. I am looking for opinions (hands-on based experience) towards your favourit feature selection method for 10x scRNA-seq data. 10X Genomics (2) 2001 (2) 2006 (2) 2D graphical representation of DNA (2) 2D plot (2) Algorithms for Molecular Biology (2) Applications in Plant Sciences (2) Applied and Environmental Microbiology (2) artificial indels (2). EMA is faster and more accurate than current aligners, and produces not only the final alignments but interpretable per-alignment probabilities. Roadmap project. September 2016 – June 2019, General Electric, Staff Software Engineer/Architect Led a team of over 12 engineers in the design, implementation, and release of [Flight Phase Analyzer](https://www. Introduction. Background Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. was founded in 2012 and is headquartered in Pleasanton. For example, PacBio, Illumina mate-pair reads, and 10X Genomics phased blocks can be used simultaneously for phasing. Cell Ranger4. Henrique tem 3 empregos no perfil. This command processes an AIRR-formatted dataset of BCR sequences that have been clonally clustered with germlines reconstructed. Serve as instructor or lead instructor for R, python, OpenRefine, shell, SQL, & git course materials, teaching reproducible research and automation techniques to scientists across all disciplines and career stages in Australia. Visit our official Buy Bitcoin page. A few years later, I wiped my Windows installation from. 5b”, a Transformer 1 neural network 10x larger than before trained (like a char-RNN with a predictive loss) by unsupervised learning on 40GB of high-quality text curated by Redditors. August 11, 2020 10x Genomics Reports Second Quarter 2020 Financial Results. An example of a large-scale scRNA-seq experiment is the recent ‘Mega-Cell Demonstration’ by 10× Genomics (10× Genomics Datasets, 2017) which features 1. I am looking for opinions (hands-on based experience) towards your favourit feature selection method for 10x scRNA-seq data. is a life science technology company, which engages in building products to interrogate, understand and master biology. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. Conclusions The workflow described in this application note provides an. Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences PRJCA002939 Cell size Microbiota Metagenome Zhejiang University PRJCA000481 test Beijing Institute of Genomics PRJCA002863. In contrast to bulk RNA-seq, scRNA-seq provides quantitative measurements of the expression of every gene in a single cell. scriptome data by the combination of 10x Genomics and. Read other formats using functions borrowed from anndata. The Investor Relations website contains information about 10x Genomics's business for stockholders, potential investors, and financial analysts. Libraries were prepared with 1 ng and 100 ng of microbial genomic DNA, amplified for 12 and 6 cycles respectively, and subsequently sequenced on Illumina MiSeq. 10x Genomics has filed an amended up-to-$362. Git is a distributed version control and source code management (SCM) system with an emphasis on speed. We develop a computational framework, Multi-Input-Multi-Output-Single-Cell-Analysis (MIMOSCA), to decipher the effect of individual perturbations and the marginal contributions of genetic interactions on the level of each transcript, program, and cell state. InfoQ spoke with Mehta an. SS2 and 10X are two frequently used scRNA-seq platforms with their unique strengths and weaknesses. Each directory should contain a matrix file, a gene/feature annotation file, and a barcode annotation file. 10x Genomics Chromium Single Cell Gene Expression. CEO photo:. scriptome data by the combination of 10x Genomics and. I have been a nurse since 1997. 00: The Crux mass spectrometry. View Sajan Sebastian’s profile on LinkedIn, the world's largest professional community. For patient DSN09, both 10x Genomics and SMART-seq2 methods were applied in parallel, giving us the opportunity to evaluate the power of integrated analysis on two types of datasets. In a new Bioinformatics publication, Yeo, et al. UBOS - "a new Linux distro that aims to make it 10x easier to run server-side apps for yourself, or for your family, on hardware you own. For patient DSN09, both 10x Genomics and SMART-seq2 methods were applied in parallel, giving us the opportunity to evaluate the power of integrated analysis on two types of datasets. As is often the case, some of the attendees shared some information, insight and ideas via Twitter. sparQ DNA Frag & Library Prep Kit generates high quality DNA libraries with minimal duplication artifacts. 6% of STRs characterized with ≥10x non-redundant sparsehash. So, there's a lot of interest in it. Its headquarters are located in Pleasanton, California. I have experience (10 years) building CRUD APIs for the web in all manner of interpreted languages and frameworks. Watch our scientific video articles. August 11, 2020 10x Genomics Reports Second Quarter 2020 Financial Results. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen. 2011; Mutreja et al. 5 –l 2 –a 0. Data sharing with external collaborators. Our flagship software product predicts patient’s response to cancer immunotherapy. The Chromium Single Cell 3’ Solution V2 chemistry is shown here. 仪器信息网是科学仪器最专业b2b门户,提供化学分析、实验室设备、生命科学、环境监测、物性测试等仪器的导购及产业研究,在线培训、招聘、仪器论坛等一站式服务。. sajan has 1 job listed on their profile. More information is available in our paper. --cell-barcodes (-c): A cell barcodes file as produced by Cell Ranger that defines which barcodes were called as cells. sparQ DNA Frag & Library Prep Kit generates high quality DNA libraries with minimal duplication artifacts. Git is a distributed version control and source code management (SCM) system with an emphasis on speed. Candidates are required have a strong proficiency of both C++ and Python in additional to tools such as git, Linux operating systems, makefiles, and Docker. 10x Genomics Chromium Single Cell Gene Expression. Our integrated solutions include instruments, consumables and software for analyzing biological systems at a resolution and scale that matches the complexity of biology. I wrote a post for 2018 here. Available for use only with the Chromium Controller (Part Numbers 120223 and 120246) or the Chromium Single Cell Controller (Part Numbers 120263 and 120212). Details to follow. All protocols were performed following the manufacturer’s instructions. 1 (−s 80 −c 5 −l 0 −d 0 −r 0. 10X Genomics (32) University of North Genomics: 1 year. Our flagship software product predicts patient’s response to cancer immunotherapy. 4438655b-1: 0: 0. A typical experiment ranges from 30-60%. The company was formerly known as 10X Technologies, Inc. Microsoft and TSMC announce Joint Innovation Lab to accelerate silicon design on Azure. Their product is called Container Engine. 1 M Tris-HCl pH 7. The Chromium Single Cell 3’ Solution V2 chemistry is shown here. uses American Stock Transfer & Trust Company (“AST”) as our transfer agent. This is the 10x Genomics company profile. SS2 is a plate-based full-length approach with high transcriptome coverage per cell and greater sensitivity10, whereas the microfluidic droplet-based method, 10X, generally has lower coverage per cell and a higher. More information is available in our paper. The 10x Genomics’ analysis pipeline, cellranger (version 2. , in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. Background Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. 原创 10X genomics scRNA_Seq 原理概念解说 单细胞分离--测序原理10X Genomics采用Drop-Seq技术, 横向孔道逐个导入凝胶微珠Gel beads,第一个纵向道输入细胞。当凝胶微珠和细胞碰撞会被吸附在微珠上,然后通过微流控技术运送到第二个纵向通道(“油管”)。. Recent News Jul 14 10x Genomics, Collaborators Develop Targeted Single-Cell Gene Expression Methods. Many of our customers, including Scholastic, King. 0 (latest), printed on 09/03/2020. The Office of Public Health Genomics tracks epidemiologic study results in our weekly horizon scan and Advanced Molecular Detection Clips and deposits relevant. Oligo sequence information is taken from The 10x Genomics Technical Note. 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells; 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells. Visualize o perfil de Henrique Dias no LinkedIn, a maior comunidade profissional do mundo. Institute, is an open source genomics analysis package that contains all variant tools for germline and cancer genomic analysis. EMA is an alignment tool for barcoded short-read sequencing data, such as those produced by 10x Genomics' Chromium platform. Right now, every industry and every customer is going through a massive transformation, and cloud computing is often a central enabler of this. NicheMarkers10x: Markers for populations defined by 10x genomics; To install from within R, you can use the install_git function from the devtools package. For single-cell analysis and in contrast to 1D reads, R2C2 reads will also likely be able to demultiplex reads in highly multiplexed cDNA pools generated by 10x Genomics and Drop-seq protocols. We focus on funding companies solving very hard problems and doing things that many people would say are impossible - whether that’s slashing the cost of working in space or using AI to dramatically lower the world’s energy usage. 11) Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. During the latest edition of Microsoft Build, Microsoft’s. Researchers are adapting CRISPR, synthetic biology, and other creative approaches to detect SARS-CoV-2 nucleic acids outside of the lab or doctors’ offices, in the hopes of making diagnostics more affordable and accessible. Preprocessing 10x data entails several steps,. Presenters names in bold (for updates and changes email [email protected] show that hPSC-derived venous endothelial cells are better able to upregulate markers of LSECs in vitro and in vivo compared to arterial cells. SMART-seq2, covering more than 75,000 individual CD45 + cells. Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample. , (Harris et al. The motivation for this is that I recently stumbled over the GLM-PCA approach from Rafael Irizarry's lab (links see on the bottom of the post) which made me dive into the literature. Senior Optical Engineer at 10x Genomics, 🔬+ 🧬 As a small startup I wore many other hats such as: developing our data analysis pipeline, introducing the use of Git and GitHub, helping set. A few years later, I wiped my Windows installation from. Hank's (Final): 9. This is complimented by existing PacBio data. 2,334 Genomics Scientist jobs available on Indeed. He served as President of Penumbra (NYSE: PEN), a global healthcare company focused on innovative therapies, until May 2020 when he stepped down to focus his efforts on Testing for America, a nonprofit established by leading academics, engineers, and entrepreneurs to address the COVID-19 testing crisis. SS2 is a plate-based full-length approach with high transcriptome coverage per cell and greater sensitivity10, whereas the microfluidic droplet-based method, 10X, generally has lower coverage per cell and a higher. View sajan sebastian’s profile on LinkedIn, the world's largest professional community. benwbooth: bcm2079x-i2c: 1-1: 0: 0. is an American company incorporated in 2012 that develops and manufactures integrated systems for whole genome sequencing, exome sequencing and single cell transcriptomics. subset-bam is a simple tool implemented in Rust that takes a 10x Genomics BAM file, a CSV file defining the subset of cells you want to isolate, and produces a new BAM file with only alignments associated with those cells. This is complimented by existing PacBio data. This allowed us to test and compare the 2 technologies. If your input data is lower coverage you may need to reduce this value but the defaults are sensible. I am not the only one who has impostor syndrome :) It is important to celebrate your small successes/achievements by writing them down. 9) 17, followed by application of Sealer to close gaps, yielded the version 3 assembly. bam ch1这几天遇到了10x genomics的bam结果,发现单细胞的reads全包含在一个bam文件里,用barcode进行区分,因此. May 20, 2020 Focusing on the Genes that Matter Most: 10x Genomics Launches Targeted Gene Expression Solution. See full list on github. This BAM must have the CB tag to define the barcodes of cell barcodes (or the tag defined by --bam-tag). Watch our scientific video articles. The Office of Public Health Genomics tracks epidemiologic study results in our weekly horizon scan and Advanced Molecular Detection Clips and deposits relevant. Amazon Redshift, is a fast, fully managed, petabyte-scale data warehousing service that makes it simple and cost-effective to analyze all of your data. This review of third-generation NGS systems describes 10X Genomics Chromium genome technology as a mapping, rather than a sequencing application. It is based on a powerful identity graph that connects individuals, businesses, and relationships. This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2. 1, HDF5, YAML is the nightmare of parsing bad formats is eliminated; there are real standards here.