# Academy Documentation ## Academy Documentation - [Usage of Academy Documentation](https://academy.dnanexus.com/readme.md) - [Getting Started](https://academy.dnanexus.com/getting-started.md) - [Background Information](https://academy.dnanexus.com/getting-started/docs_programming.md) - [For Apollo Users](https://academy.dnanexus.com/getting-started/apollo_users.md) - [For Titan Users](https://academy.dnanexus.com/getting-started/titan_users.md) - [For Scientists](https://academy.dnanexus.com/getting-started/for_scientists.md) - [For HPC Users](https://academy.dnanexus.com/getting-started/for_hpc.md) - [For Experienced Users](https://academy.dnanexus.com/getting-started/for_experienced.md) - [Cloud Computing](https://academy.dnanexus.com/cloud-computing.md) - [General Information](https://academy.dnanexus.com/cloud-computing/general_information.md) - [Cloud Computing for Scientists](https://academy.dnanexus.com/cloud-computing/cloud_computing_scientists.md) - [Cloud Computing for HPC Users](https://academy.dnanexus.com/cloud-computing/cloud_computing_hpc.md) - [Overview of the Platform](https://academy.dnanexus.com/overview-of-the-platform.md) - [Overview of the Platform User Interface](https://academy.dnanexus.com/overview-of-the-platform/overview-of-the-gui.md) - [Setting Up a Project](https://academy.dnanexus.com/overview-of-the-platform/setting-up-a-project.md) - [Adding Users to a Project](https://academy.dnanexus.com/overview-of-the-platform/adding-users-to-a-project.md) - [Adding Data to a Project](https://academy.dnanexus.com/overview-of-the-platform/adding-data-to-a-project.md) - [Metadata](https://academy.dnanexus.com/overview-of-the-platform/metadata.md) - [Tool Library and App Introduction](https://academy.dnanexus.com/overview-of-the-platform/tool_library_and_workflow_intro.md) - [Omics Data Catalog](https://academy.dnanexus.com/omics-data-catalog.md) - [Billing Access and Orgs](https://academy.dnanexus.com/billing-access-and-orgs.md) - [Orgs and Account Management](https://academy.dnanexus.com/billing-access-and-orgs/account_management_and_orgs.md) - [Org Membership Settings](https://academy.dnanexus.com/billing-access-and-orgs/org-membership-settings.md) - [Billing and Pricing](https://academy.dnanexus.com/billing-access-and-orgs/billing_and_pricing.md) - [Cohort Browser](https://academy.dnanexus.com/cohortbrowser.md) - [Introduction to Datasets](https://academy.dnanexus.com/cohortbrowser/apollo_introduction.md) - [Overview of the Cohort Browser](https://academy.dnanexus.com/cohortbrowser/cohort_browser.md) - [Phenotypic Data Exploration](https://academy.dnanexus.com/cohortbrowser/cohort_browser/phenotypic-data-exploration.md) - [Germline Data Exploration](https://academy.dnanexus.com/cohortbrowser/cohort_browser/germline-data-exploration.md) - [Somatic Data Exploration](https://academy.dnanexus.com/cohortbrowser/cohort_browser/somatic-data-exploration.md) - [Gene Expression Data Exploration](https://academy.dnanexus.com/cohortbrowser/cohort_browser/gene-expression-data-exploration.md) - [How to Create Cohorts](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts.md) - [Phenotypic Filtering](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts/phenotypic-filtering.md) - [Germline Data Filtering](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts/germline-data-filtering.md) - [Somatic Data Filtering](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts/somatic-data-filtering.md) - [Gene Expression Filtering](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts/gene-expression-filtering.md) - [Combining Different Filtering Types](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts/combining-different-filtering-types.md) - [Cohort Combine](https://academy.dnanexus.com/cohortbrowser/how-to-create-cohorts/cohort-combine.md) - [Omics Data Assistant](https://academy.dnanexus.com/cohortbrowser/omics-data-assistant.md) - [JSON](https://academy.dnanexus.com/json.md) - [Introduction](https://academy.dnanexus.com/json/introduction.md) - [JSON on the Platform](https://academy.dnanexus.com/json/using_json_platform.md) - [Command Line Interface (CLI)](https://academy.dnanexus.com/command_line_interface_cli.md) - [Introduction to CLI](https://academy.dnanexus.com/command_line_interface_cli/introduction_to_cli.md) - [Advanced CLI](https://academy.dnanexus.com/command_line_interface_cli/cliadvanced.md) - [Building Applets](https://academy.dnanexus.com/buildingapplets.md) - [Introduction](https://academy.dnanexus.com/buildingapplets/intro.md) - [Bash](https://academy.dnanexus.com/buildingapplets/bash.md) - [Example 1: Word Count (wc)](https://academy.dnanexus.com/buildingapplets/bash/bash_wc.md) - [Example 2: fastq\_quality\_trimmer](https://academy.dnanexus.com/buildingapplets/bash/bash_fastq_trimmer.md) - [Example 3: samtools](https://academy.dnanexus.com/buildingapplets/bash/bash_samtools.md) - [Example 4: cnvkit](https://academy.dnanexus.com/buildingapplets/bash/bash_cnvkit.md) - [Example 5: samtools with a Docker Image](https://academy.dnanexus.com/buildingapplets/bash/example-5-samtools-with-a-docker-image.md) - [Python](https://academy.dnanexus.com/buildingapplets/python.md) - [Example 1: Word Count (wc)](https://academy.dnanexus.com/buildingapplets/python/python_wc.md) - [Example 2: fastq\_quality\_trimmer](https://academy.dnanexus.com/buildingapplets/python/python_fastq_trimmer.md) - [Example 3: cnvkit](https://academy.dnanexus.com/buildingapplets/python/python_cnvkit.md) - [Publishing Applets to Apps](https://academy.dnanexus.com/buildingapplets/publishing-applets-to-apps.md) - [Building Workflows](https://academy.dnanexus.com/buildingworkflows.md) - [Native Workflows](https://academy.dnanexus.com/buildingworkflows/native.md) - [WDL](https://academy.dnanexus.com/buildingworkflows/wdl.md) - [Example 1: hello](https://academy.dnanexus.com/buildingworkflows/wdl/wdl_hello.md) - [Example 2: Word Count (wc)](https://academy.dnanexus.com/buildingworkflows/wdl/wdl_wc.md) - [Example 3: fastq\_trimmer](https://academy.dnanexus.com/buildingworkflows/wdl/wdl_fastq_trimmer.md) - [Example 4: cnvkit](https://academy.dnanexus.com/buildingworkflows/wdl/wdl_cnvkit.md) - [Example 5: workflow](https://academy.dnanexus.com/buildingworkflows/wdl/wdl_view_and_count.md) - [Nextflow](https://academy.dnanexus.com/buildingworkflows/nf.md) - [Resources To Learn Nextflow](https://academy.dnanexus.com/buildingworkflows/nf/resourcestolearnnextflow.md) - [Overview of Nextflow](https://academy.dnanexus.com/buildingworkflows/nf/overviewnextflow.md) - [Nextflow Setup](https://academy.dnanexus.com/buildingworkflows/nf/nextflowsetup.md) - [Importing Nf-Core](https://academy.dnanexus.com/buildingworkflows/nf/importingandrunningnfcore.md) - [Building Nextflow Applets](https://academy.dnanexus.com/buildingworkflows/nf/buildingnextflowapplets.md) - [Error Strategies for Nextflow](https://academy.dnanexus.com/buildingworkflows/nf/errorstrategies.md) - [Job Failures](https://academy.dnanexus.com/buildingworkflows/nf/jobfailures.md) - [Useful Information](https://academy.dnanexus.com/buildingworkflows/nf/usefulinformation.md) - [Interactive Cloud Computing](https://academy.dnanexus.com/interactivecloudcomputing.md) - [Cloud Workstation](https://academy.dnanexus.com/interactivecloudcomputing/cloudworkstation.md) - [TTYD](https://academy.dnanexus.com/interactivecloudcomputing/ttyd.md) - [TTYD vs Cloud Workstation](https://academy.dnanexus.com/interactivecloudcomputing/ttyd-vs-cloud-workstation.md) - [JupyterLab](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab.md) - [Introduction to JupyterLab](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/introduction.md) - [Utilizing a Snapshot](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/utilizing-a-snapshot.md) - [Running a JupyterLab Notebook](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/running_notebook.md) - [Running a Spark JupyterLab Notebook](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/running-a-spark-jupyterlab-notebook.md) - [Tips and Tricks for JupyterLab](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/tips-and-tricks-for-jupyterlab.md) - [Docker](https://academy.dnanexus.com/docker.md) - [Using Docker](https://academy.dnanexus.com/docker/usingdocker.md) - [Creating Docker Snapshots](https://academy.dnanexus.com/docker/creating_docker_snapshots.md) - [Running Docker with Swiss Army Knife](https://academy.dnanexus.com/docker/swissarmyknife.md) - [Portals](https://academy.dnanexus.com/portals.md) - [Overview of JSON files for Portals](https://academy.dnanexus.com/portals/portaloverview.md) - [Branding JSON File](https://academy.dnanexus.com/portals/branding_json.md) - [Home JSON File](https://academy.dnanexus.com/portals/home_json.md) - [Navigation JSON File](https://academy.dnanexus.com/portals/navigation_json.md) - [Updating Your Portal](https://academy.dnanexus.com/portals/updatingportal.md) - [AI/ ML Accelerator](https://academy.dnanexus.com/mlaccelerator.md) - [Data Profiler](https://academy.dnanexus.com/mlaccelerator/dataprofiler.md) - [Introduction to Data Profiler](https://academy.dnanexus.com/mlaccelerator/dataprofiler/introductiondataprofiler.md) - [Utilizing Data Profiler Navigator](https://academy.dnanexus.com/mlaccelerator/dataprofiler/utilizingdataprofilernavigator.md) - [Dataset Level Screen](https://academy.dnanexus.com/mlaccelerator/dataprofiler/datasetlevelscreen.md) - [Table Level Screen](https://academy.dnanexus.com/mlaccelerator/dataprofiler/tablelevelscreen.md) - [Column Level Screen](https://academy.dnanexus.com/mlaccelerator/dataprofiler/columnlevelscreen.md) - [Explorer Mode](https://academy.dnanexus.com/mlaccelerator/dataprofiler/explorermode.md) - [Accessing Data Profiler in ML JupyterLab](https://academy.dnanexus.com/mlaccelerator/dataprofiler/accessingdataprofilerml.md) - [ML JupyterLab](https://academy.dnanexus.com/mlaccelerator/mljupterlab.md) - [Introduction to ML JupyterLab](https://academy.dnanexus.com/mlaccelerator/mljupterlab/introductionmljl.md) - [Launching a ML JupyterLab Job](https://academy.dnanexus.com/mlaccelerator/mljupterlab/gettingstartedmljl.md) - [In App Features](https://academy.dnanexus.com/mlaccelerator/mljupterlab/inappfeaturesmljl.md) - [Getting Started with ML JupyterLab](https://academy.dnanexus.com/mlaccelerator/mljupterlab/hyperparametertuningmljupyterlab.md) - [MLflow](https://academy.dnanexus.com/mlaccelerator/mlflow.md) - [Introduction to MLflow](https://academy.dnanexus.com/mlaccelerator/mlflow/introduction_mlflow.md) - [Getting Started with MLflow](https://academy.dnanexus.com/mlaccelerator/mlflow/gettingstartedmlflow.md) - [Using MLflow Tracking Server](https://academy.dnanexus.com/mlaccelerator/mlflow/usingmlflowtrackingserver.md) - [Model Registry](https://academy.dnanexus.com/mlaccelerator/mlflow/modelregistrymlflow.md) - [Using Existing Model](https://academy.dnanexus.com/mlaccelerator/mlflow/usingexistingmodels.md) - [Utilizing MLflow in JupyterLab](https://academy.dnanexus.com/mlaccelerator/mlflow/mlflowjlexample.md) - [AutoML Assistant](https://academy.dnanexus.com/mlaccelerator/automlassistant.md) - [Usage and Limitations](https://academy.dnanexus.com/mlaccelerator/automlassistant/usage-and-limitations.md) - [Introduction to AutoML Assistant](https://academy.dnanexus.com/mlaccelerator/automlassistant/introduction-to-automl-assistant.md) - [Data Privacy](https://academy.dnanexus.com/mlaccelerator/automlassistant/dataprivacy.md) - [Storage Architecture & File Specification](https://academy.dnanexus.com/mlaccelerator/automlassistant/storage-architecture-and-file-specification.md) - [Getting Started with AutoML Assistant](https://academy.dnanexus.com/mlaccelerator/automlassistant/getting-started-with-automl-assistant.md) - [In App Features](https://academy.dnanexus.com/mlaccelerator/automlassistant/in-app-features.md) - [Example Use Case of AutoML Assistant](https://academy.dnanexus.com/mlaccelerator/automlassistant/example-use-case-of-automl-assistant.md) - [Comprehensive Disclaimer Appendix for AutoML Assistant](https://academy.dnanexus.com/mlaccelerator/automlassistant/comprehensive-disclaimer-appendix-for-automl-assistant.md) - [Public Datasets on the DNAnexus Platform](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform.md) - [Single Cell](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/single-cell.md) - [Tahoe-100M](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/single-cell/tahoe-100m.md) - [scvi-tools and CZ CELLxGENE](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/single-cell/scvi-tools-and-cz-cellxgene.md) - [Molecular Modeling](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/molecular-modeling.md) - [nf-core: Proteinfold](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/molecular-modeling/nf-core-proteinfold.md) - [Protein Data Bank (PDB) Curation](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/molecular-modeling/protein-data-bank-pdb-curation.md) - [AlphaFold2](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/molecular-modeling/alphafold2.md) - [Target Validation](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/target-validation.md) - [Open Targets](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/target-validation/open-targets.md)