> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/cci/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/cci/the-onboarding/glossary.md). # Glossary Terms you might encounter #### [SMILE](https://github.com/mskcc/cmo-metadb) -> information associated with a sample. This is a current work-in-progress written in Java/Neo4J that is supposed to be the one source of truth for metadata associated with samples. Currently, these responsibilities are managed by Beagle. #### LIMS -> Laboratory information management system -- when sequencing is complete, metadata and file information on the sequences is first input into this system. #### [Beagle](https://github.com/mskcc/beagle) -> triggers and monitors workflows. There's also a part of it that tracks files and metadata associated with those files which may be splintered out in the future. A request typically comes from LIMS which begins the workflow process. #### [Hermes ](https://github.com/mskcc/hermes)-> a nicer interface for Beagle (sample workflow tracking) and soon the MDB (make updates to metadata) #### [Ridgeback](https://github.com/mskcc/ridgeback) -> An HTTP API for Toil which Beagle is reliant on for interacting with workflows. #### [Toil](https://toil.readthedocs.io/en/latest/running/cwl.html) -> A workflow engine that interfaces well with LSF. #### Voyager -> The suite of applications built by the Voyager team, including Ridgeback, Beagle, and Hermes. #### [HPC](http://actg.mskcc.org/hpc/getting-started/)-> Distributed high-performance computing that's managed in-house. Most data processing and files are housed here. #### [LSF](https://www.ibm.com/products/hpc-workload-management) -> IBM's Platform Computing (Load Sharing Facility) tool for scheduling workflows on HPC. It has a [suite of commands ](https://hpc.llnl.gov/banks-jobs/running-jobs/lsf-commands)specific to managing workloads. #### [Common workflow language](https://www.commonwl.org/) -> a YAML-like language for defining workflows. #### [Nextflow](https://www.nextflow.io/docs/latest/index.html) -> Reactive workflow framework and a programming [DSL](http://en.wikipedia.org/wiki/Domain-specific_language) that eases the writing of data-intensive computational pipelines. #### [DNA-SEQ](https://en.wikipedia.org/wiki/DNA_sequencing) -> Sequencing of the **Deoxyribonucleic acid (**[**DNA**](https://en.wikipedia.org/wiki/DNA)**)** #### [RNA-SEQ](https://en.wikipedia.org/wiki/RNA-Seq) -> Sequencing of the R**ibonucleic acid (**[**RNA**](https://en.wikipedia.org/wiki/RNA)**)** #### [MSK-ACCESS](https://www.mskcc.org/departments/division-solid-tumor-oncology/early-drug-development-service-phase-clinical-trials/precision-medicine-approach/msk-access) -> Cell-Free DNA assay for patients with solid tumors #### **CMO-CH -> Assay for profiling clonal hematopoiesis mutations from blood** #### [**MSK-IMPACT**](https://www.mskcc.org/departments/division-solid-tumor-oncology/early-drug-development-service-phase-clinical-trials/precision-medicine-approach/msk-impact) **-> Assay for profiling patients tissue DNA for solid tumors** #### [**MSK-IMPACT Heme**](https://aacrjournals.org/cancerres/article/79/13_Supplement/3409/542857/Abstract-3409-MSK-IMPACT-Heme-Validation-and) **-> Assay for profiling patients blood DNA for Heme malignancies** #### [**Facets**](https://pubmed.ncbi.nlm.nih.gov/27270079/) **-> A**llele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing #### [**WES**](https://en.wikipedia.org/wiki/Exome_sequencing) **-> Whole Exome Sequencing** #### [**WGS**](https://www.cdc.gov/pulsenet/pathogens/wgs.html) **-> Whole Genome Sequencing** #### [**WTS**](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233721/) **-> Whole Transcriptome Sequencing** #### [**Illumina**](https://en.wikipedia.org/wiki/Illumina,_Inc.) **-> one of the companies that provides sequencing machine** #### [**Novaseq**](https://www.illumina.com/systems/sequencing-platforms/novaseq.html) **-> Type of sequencer from Illumina** #### [**Nextseq**](https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html) **-> Type of sequencer from Illumina** #### [**Miseq**](https://www.illumina.com/systems/sequencing-platforms/miseq.html) **-> Type of sequencer from Illumina** #### [**Hiseq**](https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html) **-> Type of sequencer from Illumina** #### [**PacBio**](https://en.wikipedia.org/wiki/Pacific_Biosciences) **-> a company that sells instruments for long-read sequencing based on** [**zero-mode waveguide**](https://en.wikipedia.org/wiki/Zero-mode_waveguide) #### [**Oxford Nanopore**](https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies) **-> a company that sells instruments for long-read sequencing based on** [**Nanopore**](https://en.wikipedia.org/wiki/Nanopore_sequencing) **technology** --- # Agent Instructions This documentation is published with GitBook. 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