diff --git a/overview/tool_catalog/index.html b/overview/tool_catalog/index.html
index 8babedfb..35caf765 100644
--- a/overview/tool_catalog/index.html
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diff --git a/resources/js/config.js b/resources/js/config.js
index bb616022..25adca70 100644
--- a/resources/js/config.js
+++ b/resources/js/config.js
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diff --git a/resources/js/prism.js b/resources/js/prism.js
new file mode 100644
index 00000000..88476e3c
--- /dev/null
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s=["comment","function-name","for-or-select","assign-left","parameter","string","environment","function","keyword","builtin","boolean","file-descriptor","operator","punctuation","number"],o=n.variable[1].inside,i=0;i Personal Access Tokens.","Create a new token with “View and Download” permissions and copy the token.","Configure Synapse client with the Token:","In the JupyterLab Terminal, type:","When prompted, enter your Synapse username (optional) and paste the token."]},{"l":"3. Select Files from the HTAN Data Portal","p":["Visit the HTAN Data Portal and find the data files you need (e.g., single-cell RNA-seq data in H5AD format).","Click the purple “Download selected files” button for the chosen files.","Copy the download commands (e.g., synapse get syn1234)."]},{"l":"4. Download Files into the Data Studio Instance","p":["Paste the copied download commands into the JupyterLab Terminal.","Verify that the files are in the workspace directory. You can now use these files within notebooks in the Data Studio instance."]},{"l":"5. Move Files to Output Folder","p":["Move files to the output-files directory to ensure they sync with your CGC project:"]},{"l":"6. Stop Data Studio Instance","p":["Stop the Data Studio instance to trigger synchronization.","Check your project files on CGC; the downloaded files should now be available for further use."]},{"l":"Useful Links","p":["SevenBridges CGC","Synapse","HTAN Data Portal","Synapse Python/CLI Client Documentation"]}],[{"l":"Access-Controlled Data","p":["Access-controlled HTAN data requires dbGaP access approval for study phs002371, and is currently only available via the National Cancer Institute's Cancer Data Services (CDS)."]}],[{"l":"Requesting dbGaP Access","p":["For access-controlled HTAN data, you must first complete a dbGaP request.","To get started on your dbGaP request, first navigate to the HTAN dbGap page at: phs002371, and click the Request Access button. You will be prompted to login to dbGaP. Once logged in, click the Create New Research Project button, and follow the on-screen application process.","As per dbGaP instructions, you will be prompted for relevant information, including:","A research statement and a nontechnical summary statement describing your planned use of the data.","The name of the institutional signing official who will certify the terms of use assurances on behalf of your institution.","A list of all internal investigators at your institution who will share access to the data for the proposed research.","A list of external collaborating investigators.","The name of the information technology (IT) Director.","dbGaP will notify you when your application has been approved."]}],[{"i":"accessing-sequence-data-via-ncis-cancer-data-service-cds","l":"Accessing Sequence Data via NCI's Cancer Data Service (CDS)","p":["NOTE: dbGaP approval for HTAN study phs002371 is required in order to access HTAN lower-level genomics data, such as RNAseq FASTQ and BAM files.","The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides an interface to filter and select data from a variety of NCI programs, including controlled-access, primary sequence data from the Human Tumor Atlas Network (HTAN). This page provides directions for importing sequencing data from CDS to the Cancer Genomics Commons (CGC).","The directions for accessing sequencing data on CDS are similar to those for Level 2 Imaging Data Access, including Direct Export from CDS to CGC and importing data using a Data Repository Service (DRS) Manifest. Please follow the Level 2 Imaging Data Access directions to access sequencing data, noting the following changes:","For Direct Export or Generating a DRS Manifest from CDS, choose Human Tumor Atlas (HTAN) primary sequence data on the STUDY section of the left hand sidebar instead of Human Tumor Atlas (HTAN) imaging data.","To generate a DRS Manifest from the HTAN Data Portal, click CDS/SB-CGC (dbGaP) under the Data Access filter instead of CDS/SB-CGC (Open Access).","HTAN Portal: Accessing Genomic Data in CDS"]}],[{"l":"Introduction","p":["Only HTAN Centers and Associate Members can submit data to the HTAN Network's repositories. The Data Submission Section of this Manual is intended as a guide for HTAN Centers and Associate Members. Please note that the manual currently reflects the data submission process used in HTAN Phase 1. Changes may be implemented for HTAN Phase 2.","❗ Prior to submitting data, all data must be de-identified. Please see Data De-identification for more information.","Data Submission involves two key steps:","Uploading assay data files to Synapse; and","Completing and validating manifests using the Data Curator App (DCA).","Data Submission Overview","Specific details regarding data submission and the DCA are included in later sections of this manual. Please contact your Data Liaison if you have any questions or issues. Please also keep your data liaison informed of any data submissions.","The current status of data uploads (refreshed every 4 hours) is available on the HTAN Dashboard."]}],[{"l":"Information for New HTAN Centers","p":["Welcome to the Human Tumor Atlas Network!","The Goverance and Policy page of this manual provides documentation and applicable policies detailing the requirements for publications, data sharing, and data use.","All HTAN centers must have an executed Human Tumor Atlas Network DMSA (Internal Data and Materials Sharing Agreement) (HTAN DMSA) with Sage Bionetworks prior to contributing data to the HTAN Data Coordinating Center (DCC). See also HTAN Checklist for Acceptance of Data. Sean Hanlon from the NCI will be reaching out to new Centers to coordinate collection of DMSA signatures.","HTAN centers are assigned a data liaison from the (DCC). Trans-Network Projects (TNPs) are also assigned liaisons. Your liaison will help guide you through setting up a new atlas or project, creating HTAN identifiers, and submitting metadata and data files. Please keep your liaison informed of publications timelines and new data submissions.","Please see the appropriate page of this manual for additional details about HTAN center responsibilities for data de-identification, including submitting a data de-identification plan, and specific instructions regarding how to submit data. Clinical, biospecimen, and assay data submitted to the DCC are distributed to repositories based on access levels. Information regarding how data are accessed by external users is described more in other parts of this manual.","In order to support the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for scientific data production, the DCC has developed a data model based on established standards in the scientific research community. The HTAN Data Model is expected to evolve with advances in science. This evolution is a community-driven, peer-reviewed process, where members of a working group will first assess established community data standards and create a request for comment (RFC) document soliciting community feedback. We look forward to working with you and learning from your expertise as we improve upon our current model."]}],[{"l":"HTAN Checklist for Acceptance of Data","p":["Agreement / Policy Reference","Checklist of Requirements","HTAN Data Standards","HTAN DMSA 2.c: “[...] Data quality corrections will be submitted as soon as possible.”","HTAN DMSA Section 2.a: “Contributor will transfer to the HTAN-DCC De-identified Datasets generated as part of the HTAN that either pass the QC standards that are in effect for HTAN at the time, or pass the Contributor’s QC standards in cases where HTAN standards do not exist.”","HTAN DMSA Section 2.b: “Supporting information including the Data annotation manifest necessary to interpret the submitted Data must be included with the submission and will be reviewed by the HTAN-DCC for completeness.”","HTAN DMSA Section 2.c: “The HTAN-DCC and the Data Contributor will review Data after submission, before it is released, to verify that no PHI has been submitted accidentally. If there is presence of PHI, i. HTAN-DCC will notify the Contributor of the presence of PHI and delete files that contain PHI from the HTAN-DCC Portal, ii. Contributor will resubmit Data without PHI. Data quality corrections will be submitted as soon as possible. [...]”","HTAN DMSA Section 3.a: ”Any Data that Contributor generates as part of the HTAN Project will be hosted and shared using the HTAN-DCC Portal or other HTAN-designated repositories and will be subject to and governed by all the terms and conditions of this Agreement, the NIH Data Sharing Policy and NIH Genomic Data Sharing Policy.”","HTAN DMSA Section 6.a: “The Parties agree that all Data disclosed to and from the Parties shall be De-identified so that Data Subjects cannot be ascertained directly or through secondary data use in accordance with HIPAA.”","HTAN DMSA Section 6.b: “Contributor represents that all Data and Material derived from HTAN that Contributor provides to Recipient were collected pursuant to and in accordance with protocols approved by an IRB or its equivalent;[...]”","HTAN DMSA Section 6.c: “Contributor represents that the Data and Material submission to the HTAN-DCC and/or Recipient are consistent with applicable U.S. laws, regulations, and its institutional policies;{...]”","HTAN DMSA Section 6.d: “The Contributor represents that an IRB/Privacy Board or equivalent body, as applicable, has assured that submission and subsequent sharing of Data and Materials are consistent with the Informed Consent of the Data Subject(s) from whom the Data and Materials were obtained.”","I affirm that an IRB or its equivalent assures that the data and sharing of the data is consistent with the Informed Consent of the Data Subject(s) from whom the Data and Materials were obtained.","I understand that if data quality corrections for the data are required, then I am responsible for removing the data from the HTAN-DCC Portal, making corrections, and re-submitting the data as soon as possible.","I understand that if the data are found to include PHI, then the data will be removed from the HTAN-DCC Portal and that it is my responsibility to remove the PHI and re-submit the data to the HTAN-DCC as soon as possible.","I understand the data I contribute will be hosted and shared via the HTAN-DCC Portal or other HTAN-designated repositories and will be subject to and governed by all the terms and conditions of this Agreement, the NIH Data Sharing Policy and NIH Genomic Data Sharing Policy.","If the Data Contributor has concerns about the acceptability of their data contribution, the Data Contributor may contact the HTAN DCC to request Data Contribution Support via the HTAN Help Desk: https://sagebionetworks.jira.com/servicedesk/customer/portal/1","If the Data Contributor is able to affirm their understanding of this checklist and that the data meet the criteria in this checklist, then the Data Contributor may engage their HTAN Data Liaison to begin the data contribution process.","The contribution of the data is consistent with applicable U.S. laws, regulations, and its institutional policies.","The data are de-identified according to the current standards for HTAN. See Data De-identification.","The data contribution includes acceptable HTAN data types: clinical data, biospecimen data, genomic sequencing data and/or multiplex imaging, contextual assay metadata and/or assay data files.","The data contribution includes all extra information needed to interpret and understand the data.","The data meets my data quality control standards and those established by the HTAN DCC.","The data were collected according to protocols approved by an IRB or its equivalent.","When an HTAN Data Contributor is considering contribution of data to the HTAN DCC, this checklist should be used by the Data Contributor to determine if the data meets basic HTAN contribution requirements.","When necessary, a final determination regarding acceptability of data to HTAN DCC will be at the discretion of NCI and the HTAN DCC PIs. If the decision is that the data should not be shared with the HTAN DCC, Sage can work with the Data Contributor to share the data elsewhere in Synapse."]}],[{"l":"Data Liaisons","p":["Upon joining HTAN, Centers are assigned a data liaison from the DCC. Trans-Network Projects (TNPs) are also assigned liaisons. The DCC liaisons assist each of the research centers in successfully uploading data and metadata files."]},{"l":"Phase 2 Liaisons","p":["Adam Taylor","adam.taylor@sagebase.org","Atlas","Atlas ID","Awardee Organization","CalTech","Dar'ya Pozhidayeva","debruiji@mskcc.org","DFCI","dpozhida@systemsbiology.org","Email","HTA200","HTA201","HTA202","HTA203","HTA204","HTA205","HTA206","HTA207","HTA208","HTA209","HTAN2_Colorectal_HTA","HTAN2_Gastric_PCA","HTAN2_Glioma_PCA","HTAN2_Lymphoma_HTA","HTAN2_Myeloma_PCA","HTAN2_Ovary_HTA","HTAN2_Pancreas_PCA","HTAN2_Pediatric_HTA","HTAN2_Prostate_HTA","HTAN2_Skin_PCA","Ino de Bruijn","Jennifer Altreuter","jennifer@ds.dfci.harvard.edu","Liaison","MD Anderson","OHSU","UCSF","USC/CHLA","Vanderbilt","WUSTL","Yale"]},{"l":"Phase 1 Liaisons","p":["Adam Taylor","adam.taylor@sagebase.org","Atlas","Atlas ID","Dar'ya Pozhidayeva","Dave Gibbs","debruiji@mskcc.org","dgibbs@systemsbiology.org","dpozhida@systemsbiology.org","Email","HTA1","HTA10","HTA11","HTA12","HTA13","HTA14","HTA15","HTA16","HTA2","HTA3","HTA4","HTA5","HTA6","HTA7","HTA8","HTA9","HTAN BU","HTAN CHOP","HTAN DFCI","HTAN Duke","HTAN HMS","HTAN MSK","HTAN OHSU","HTAN Stanford","HTAN Vanderbilt","HTAN WUSTL","Ino de Bruijn","Jennifer Altreuter","jennifer@ds.dfci.harvard.edu","Liaison","PILOT - HTAPP","PILOT - PCAPP","thorsson@isbscience.org","TNP CASI","TNP SARDANA","TNP SRRS","TNP TMA","Vesteinn Thorsson"]}],[{"l":"Creating HTAN Identifiers","p":["The following are step by step instructions for HTAN Centers and Trans Network Projects (TNPs) to create and manage HTAN identifiers. HTAN identifiers should be created for all entities (participants, biospecimens and data-files) within individual research projects."]},{"i":"step-1-determine-you-htan-center-id","l":"Step 1: Determine you HTAN Center ID","p":["Please see HTAN Centers to determine your HTAN Center ID. If the data are part of a Trans Network Project (TNP), use the HTAN Center ID assigned to the TNP."]},{"i":"step-2-assign-htan-identifiers-for-all-research-participants","l":"Step 2: Assign HTAN Identifiers for all Research Participants.","p":["Create a unique HTAN Identifier for each research participant in the following format:","participant_id::= htan_center_id_integer","e.g. HTA3_1","Each HTAN Center/TNP controls their own namespaces, and therefore owns all identifiers that begins with their prefix. The integer value following htan_center_id is determined by the HTAN Center/TNP.","HTAN Centers/TNPs may choose to use integer blocks to assign groups. For example, CHOP may have four clinical sites, and may wish to reserve HTA4_1 to HTA4_1000 for all patients from site 1, and HTA4_1001 to HTA4_2000 for all patients from site 2. These blocks are entirely up to the research project and not managed by the DCC. The assigned integers in a set of identifiers need not be consecutive.","Leading zeros(e.g. HTA3_01) should not be used in the ID."]},{"i":"step-2b-optional-if-needed-assign-htan-identifiers-for-external-controls","l":"Step 2b [optional]: If needed, assign HTAN identifiers for external controls","p":["Each external control participant, if present, in your atlas must also have a unique HTAN Identifier. These identifiers are meant only for participants without precancerous or cancerous lesions, and therefore explicitly indicate lack of HTAN-relevant clinical data within the identifier itself. These participant identifiers look like:","participant_id::= htan_center_id_EXTinteger","For example, if you are part of the Duke research center, and you have three external control research participants, you will need to create three HTAN Identifiers. For example:","HTA6_EXT1 HTA6_EXT2 HTA6_EXT3","As with regular research participants, the HTAN Center/TNP controls their own namespace, and therefore owns all identifiers that begin with the prefix e.g. HTA6_EXT. The integer value following HTA6_EXT is determined entirely by the HTAN Center/TNP."]},{"i":"step-3-assign-htan-identifiers-for-all-htan-biospecimen-and-data-files","l":"Step 3: Assign HTAN Identifiers for all HTAN Biospecimen and Data Files","p":["Derivative entities include anything derived from a research participant, including biospecimens such as samples, tissue blocks, slides, aliquots, analytes, and data files that result from assaying those biospecimens. Each derivative entity in your atlas must also have a unique HTAN Identifier. These identifiers look like:","derivative_entity_id::= participant_id_integer","Analogous to research participant IDs, the unique integer value following participant_id is determined entirely by the source HTAN Center/TNP. The ID must not have leading zeros.","If a single data file is derived from multiple participants, the file identifier can contain a wildcard string, e.g. ‘0000’, after the HTAN center identifier. For example:","HTA4_0000_1 HTA4_0000_2 HTA4_0000_3","If a data file is derived from an external control participant, the biospecimen and file identifiers will contain the string ‘EXT’ before the external control participant integer (see Step 2b, above). For example:","HTA6_EXT1_1 HTA4_EXT2_2 HTA4_EXT3_3"]},{"i":"step-4-keep-track-of-all-metadata-associated-with-entities","l":"Step 4: Keep Track of all Metadata Associated with Entities","p":["Complex relationships among entities can emerge in any research study. For example, one or more samples may be collected from a research participant at multiple times, and each of those samples processed through a variety of analytic workflows. It is recommended that each HTAN Center/TNP maintain their own mechanism for storing annotation of entities and relationships among those --- for example, many atlases already have in place LIMs systems or spreadsheet-based systems."]}],[{"l":"Data De-identification","p":["As outlined in the HTAN DMSA, data submitted to the Data Coordinating Center (DCC) must be fully de-identified.","By signing the HTAN DMSA, HTAN members’ institutional signing officials and PIs accept responsibility for the de-identification of data prior to transfer to the DCC and confirm that:","all data disclosed to the DCC (Synapse) are fully de-identified in accordance with HIPAA;","all data were collected in accordance with protocols approved by an IRB or its equivalent;","all data are consistent with applicable U.S. laws, regulations, and its institutional policies; and","an IRB/Privacy Board or equivalent body has assured that submission and subsequent sharing of data are consistent with the Informed Consent of the Data Subject(s) from whom the data were obtained. In addition, the data are protected by an NIH Certificate of Confidentiality.","New HTAN Centers should develop and submit a De-identification Plan using the HTAN Atlas De-Identification Plan Template.","Prior to transferring data to the HTAN DCC, members are responsible for fully de-identifying the data being transferred. Full de-identification of data includes confirmation that data file names do not contain any information that could be used to re-identify that data subject."]}],[{"i":"what-is-metadata","l":"What is Metadata?","p":["Metadata means data about data. Metadata enables both data searchability and interpretability. For HTAN, this includes sample and case identifiers, patient information (e.g. demographics), biospecimen information (e.g. tumor type), and assay-specific information (e.g. experiment protocol, assay reagents or assay technology).","Example HTAN Metadata vs Assay Data","HTAN's Data Model is a framework for collecting and storing metadata. The Data Model in turn supports effective searching for data on HTAN's Data Portal.","Metadata is submitted to HTAN via the Synapse Data Curator App (DCA), developed and maintained by Sage Bionetworks. The DCA performs several automated validation checks to make sure the metadata complies with the HTAN Data Model. Please see Submitting Assay Data and Metadata for more information about the DCA.","The term \"manifests\" refers to the spreadsheets used to submit metadata. \"Metadata templates\" are available via the DCA. These are manifests which can be filled out, validated and submitted using the DCA's web interface."]}],[{"i":"what-is-the-index-date","l":"What is the index date?","p":["HTAN cannot accept dates because they are considered Protect Health Information (PHI). In order to obfuscate dates, they should be converted to days from an index date. For most data, the index date is the participant's date of birth. For example, a participant's therapy start date would be recorded as 365 days if the therapy took place 365 days after a participant's date of birth.","⚠️ If your center has data indexed to enrollment date, the data needs to be converted to days from birth."]},{"i":"index-exceptions","l":"\"Index\" exceptions","p":["For sequencing data, there are four attributes with 'index' in their names for which 'index' is not the date of birth. These include:","Single Cell Dissociation Days from Index;","Library Preparation Days from Index;","Sequencing Library Construction Days from Index; and","Nucleic Acid Capture Days from Index.","Please note the descriptions for these fields in the data model."]},{"l":"Time intervals","p":["The 'Diagnosis' manifest includes two attributes which are not indexed:","Days to Last Follow up; and","Days to Last Known Disease Status.","Please provide these time intervals as described in the data model."]}],[{"l":"Submitting Assay Data and Metadata","p":["As stated in Data Submission Introduction, data submission involves two key steps:","Uploading assay data files to Synapse; and","Completing and validating metadata using the Data Curator App (DCA).","This page provides details regarding those steps. Please note that the manual currently reflects the data submission process used in HTAN Phase 1. Changes may be implemented for HTAN Phase 2.","HTAN Data Submission Process","To submit data, you will also need to understand the HTAN data model and specific requirements for your particular data type. For a general overview of the HTAN data model, please see HTAN Data Model. To understand specific requirements for your data type, please see Data Standards.","HTAN uses the Synapse Portal and DCA, developed and maintained by Sage Bionetworks, to manage clinical, biospecimen and assay data submissions (dataset ingress). In order to submit data, your center should:","Have at least one user with Certified User status on Synapse.","Contact your Data Liaison to set up your project and cloud bucket.","Ensure the assay dataset conforms to the HTAN Data Model, uses HTAN Identifiers and does not contain Protected Health Information (PHI).","Organize and upload your dataset to the Synapse Project","Validate and submit metadata using the DCA.","Please read the rest of this page for more information about each of these steps."]},{"i":"have-at-least-one-user-with-certified-user-status-on-synapse","l":"Have at least one user with Certified User status on Synapse.","p":["To upload files to the Synapse Platform, you need to be a Synapse Certified User. Because Synapse stores data from human subjects research, Sage Bionetworks requires that you demonstrate understanding of and compliance with privacy and security issues. You can complete your certification by taking a short certification quiz. Please see the Synapse Certified User Documentation for more information."]},{"i":"contact-your-data-liaison-to-set-up-your-project-and-cloud-bucket","l":"Contact your Data Liaison to set up your project and cloud bucket.","p":["When you are ready to upload data, please contact your data liaison. Your data liaison will need to know:","Your centers","Who on your team will be doing the data upload.","The synapse usernames for team members identified in #2.","Please have users obtain certified user status prior to contacting your data liaison.","With the above information, the DCC will initialize your Synapse project for metadata submission and a cloud storage location for dataset uploads. If the data submission is for a new atlas, the DCC will also create an HTAN atlas ID. Once your Synapse project has been initialized, your data liaison will reach out to you with the location of your Synapse project and you can begin uploading your data."]},{"i":"ensure-the-dataset-conforms-to-the-htan-data-model-uses-htan-identifiers-and-does-not-contain-phi","l":"Ensure the dataset conforms to the HTAN Data Model, uses HTAN Identifiers and does not contain PHI.","p":["The HTAN Data Model is built upon data standards described on the Data Standards page. All HTAN Centers are required to encode their clinical, biospecimen and assay data and metadata using the HTAN Data Model. If you have a new data type which is not currently represented in the HTAN Data Model, please contact your data liaison.","A concrete way to understand the expectations for data submissions is to view the metadata templates (manifests) for clinical, biospecimen and assay data available in the ( DCA). For any given dataset, you may be submitting:","clinical manifest(s), e.g. Demographics, Diagnosis","biospecimen manifest(s)","assay manifest(s), e.g. Bulk RNA-seq level 1","assay data files","The first three items will be validated and submitted using the DCA. The last item, assay data files, only needs to be uploaded to the synapse project itself.","All data should be identified using HTAN identifiers. Please see the HTAN Identifier section of this manual for more information regarding HTAN identifiers."]},{"l":"Organize and upload your dataset to the Synapse Project","p":["Please organize your data using the flattened data layout described in Synapse's Data Ingress Docs","Data files can be transferred using the Synapse User Interface (Synapse UI) or programmatically. Please see Synapse's Data Ingress Docs for more information on how to upload files."]},{"i":"validate-and-submit-metadata-using-synapses-data-curator-app-dca","l":"Validate and submit metadata using Synapse's Data Curator App (DCA).","p":["The DCA contains HTAN-specific manifests (metadata templates) which can be","completed on the app, or","downloaded, completed and uploaded back to the DCA.","Manifests for assay data will be pre-populated with assay file entityIDs once they are associated with a particular Synapse dataset folder. Once the manifests are completed by your center, they should then be validated and submitted via the DCA. DCA validation checks for a subset of common errors. If any of these errors are found, you can edit the metadata and then revalidate and submit.","Please see Synapse's Data Ingress Docs for more details regarding the web app."]}],[{"i":"specific-assaydata-element-details","l":"Specific Assay/Data Element Details","p":["Please see Data Standards for an overview of HTAN Data Levels and Metadata Attributes for each data type. The following links provide specific submission details for each data type.","Accessory Files","Biospecimen","Clinical Data","Imaging","Mass Spectrometry","RPPA","Sequencing Data","Spatial Transcriptomics"]}],[{"l":"HTAN Dashboard","p":["The HTAN Data Coordinating Center (DCC) hosts the HTAN Dashboard to help centers track submitted data, data completeness and data submission errors.","The main page of the dashboard provides an overview of submitted assay and metadata as well as total number of submission errors. The Atlas links on the main page provide additional details for each Atlas. The Synapse project links will take you directly to the Atlas' project in Synapse is you have Synapse access to the project.","HTAN Dashboard Main Page","On the Atlas-specific pages, there are several tables and visuals to help you assess the type of data available and any metadata validation errors. Examples include an expandable metadata validaton errors table, metadata submission matrices and a summary of available longitudinal data. Please see the figures below for examples.","Metadata Validation Errors Table","Clinical Data Matrix, Tier 1 and 2 Clinical Data","Longitudinal Data"]}],[{"l":"Submitting Tools","p":["Computational tools developed or used to support HTAN research projects can be added to the HTAN tool catalog by filling out the tool curation form available on HTAN's Synapse Wiki page.","The HTAN Synapse Wiki page is restricted to HTAN members. Please contact htandcc@ds.dfci.harvard.edu if you are a member of HTAN and need access to the wiki."]}],[{"l":"Submitting Publications","p":["To facilitate data sharing and adherence to FAIR (Findability, Accessibility, Interoperability, and Reusability) principles, the HTAN portal provides links to specimen files used in publications. Currently, the HTAN Data Coordinating Center (DCC) faciliates this linking once provided the appropriate information by HTAN Centers. To submit publication information, HTAN Center's should contact Alex Lash at alexl@ds.dfci.harvard.edu.","use HTAN identifiers in their publication; or","provide a lookup table in the publication to map publication identifiers to HTAN identifiers."]}],[{"l":"Data Release","p":["The Data Coordinating Center (DCC) prepares major data releases every 4-6 months. HTAN Centers are notified of the data submission deadline for an upcoming data release. After that deadline, the pre-release process involves a number of data processing and metadata verification steps. Data is released via the HTAN Data Portal, and then disseminated to various Cancer Data Research Commons (CRDC) nodes including Cancer Data Service (CDS) and the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) to enable download of controlled-access data and long-term cloud access","The HTAN Data Release Process","Please see HTAN Data Release Process for more information regarding the data release process."]}],[{"l":"Governance and Policy","p":["Responsible data sharing requires transparent governance approaches to ensure data contributors, data curators, and data consumers are empowered to share and use data effectively. To this end, members of the DCC work closely with members of the HTAN consortium to develop and implement data sharing agreements and operational policies following the principles of the NCI Cancer Moonshot Public Access and Data Sharing Policy. A Data and Materials Sharing Agreement (DMSA) establishes the responsibilities and boundaries associated with data sharing with the DCC and within the HTAN consortium, while an External Data Sharing Policy ensures a commitment to share all generated data publicly. An Associate Membership Policy provides a mechanism for experts from outside of HTAN to contribute their expertise and knowledge. In addition, specific policies related to publications and the sharing of research protocols and computational tools were developed. A key infrastructure component for the implementation of these data-sharing policies is the Synapse platform, which provides fine-grained access controls at individual and team levels to ensure that data contributors and DCC staff have appropriate access to their data. Synapse teams were used to enable project-level access and tracked against a table of HTAN membership.","Ensuring the privacy of HTAN research participants is critical and a joint responsibility of the HTAN Centers generating data and the DCC. HTAN Centers are required to fully de-identify data before submission to the DCC via the Synapse platform, and must describe their data and metadata de-identification process in a de-identification plan. Following data submission, the DCC is responsible for implementing additional checks, to ensure patient privacy. Verifying that HTAN imaging data is de-identified is a particular focus of the DCC. For example, the extensive metadata collected alongside HTAN data was noted to theoretically enable the reconstruction of HIPAA-protected dates (such as participant date of birth) from the date of imaging data acquisition through longitudinal metadata attributes. The HTAN DCC therefore developed policies and procedures to confirm that all date attributes, including those in TIFF tags, OME-XML, and other locations, were detected and reported back to data contributors for removal before data release."]},{"l":"Policy Documents","p":["Publication Policy","Protocol and Computational Tool Sharing Policy","External Data Sharing Policy","DUA/MTA","Cancer Moonshot Public Access Policy","Associate Membership Policy"]}],[{"l":"HTAN Data Usage Analytics","p":["The HTAN portal is used by thousands of people each month all over the world:","Google Analytics of HTAN Portal"]},{"l":"Data Submission Trajectory","p":["The HTAN Data Coordination Center (DCC) has been working with the HTAN Centers to collect and process data. The following figure shows the number of data submissions to the DCC over time:"]}],[{"l":"Working Groups and Internal Communications","p":["Information regarding Network Working Groups and Internal Communications can be found on HTAN's Synapse Wiki page. Access to the HTAN Wiki is restricted to HTAN Members.","The HTAN Synapse Wiki page is restricted to HTAN members. Please contact htandcc@ds.dfci.harvard.edu if you are a member of HTAN and need access to the wiki."]}],[{"l":"The RFC Process and Data Model Changes"},{"l":"RFC Overview","p":["The HTAN Data Model is expected to evolve with advances in science. This evolution is a community-driven, peer-reviewed process, where members of a working group will first assess established community data standards and create a request for comment (RFC) document soliciting community feedback.","The status of current RFCs is provided in the RFC Overview document. The RFC Overview can be used to:","Get a sense of what is available in DCA.","Get a sense of new assays being considered.","Look at old RFCs & get a sense of past discussions/considerations.","The links to specific RFC documents within the RFC Overview do not represent the final data model. Once an RFC is closed and an assay is available on the Data Curator App (DCA), the metadata template on the DCA represents the final data model. Details regarding the data model are also available on HTAN's Data Standards page and HTAN's data-models repository on github."]},{"l":"Data Model Changes","p":["The following are requests which require changes to the Data Model and may result in the initiation of a RFC:","New assay types which are expected to be used frequently by multiple centers.","New metadata templates or additional required metadata fields which should be validated.","HTAN members should contact their data liaison for help determining whether a Data Model change is needed and how to make a Data Model change request."]},{"l":"RFC Process","p":["Once a new assay type or a set of needed Data Model changes are identified, the following steps are taken:","A working group is organized by the Data Coordinating Center (DCC). As a part of this process, the following people are also designated:","A DCC Owner, who is responsible for finalizing the RFC and overall accepting/rejecting/integrating community feedback. The DCC Owner is also the primary point of contact for the specified RFC.","A single DCC PI, to monitor progress towards completion.","One or more Co-Authors from one or more HTAN centers, to help draft the RFC. Representatives from each HTAN center help identify individuals at their center who can contribute to a particular RFC.","A first draft of an RFC Google Document is created based upon feedback from the working group.","The RFC is open for public comment. All HTAN members can provide suggestions by adding comments directly to the document.","After a designated period of time, the RFC is closed. Feedback from HTAN community is no longer accepted. The content of the RFC will be reflected in the respective version of the HTAN Data Model used for validating metadata files uploaded to the DCC.","The metadata template is available on the Data Curator App (DCA)."]}],[{"i":"trans-network-projects-tnps","l":"Trans-Network Projects (TNPs)","p":["Code","Current Trans-Network Projects","Description","HTA13","HTA14","HTA15","HTA16","Name","The goal of the C ell A nnotations and S ignatures I nitiative TNP is to provide robust and accurate tools for cell type annotation from single-cell data.","The HTAN Synapse Wiki page is restricted to HTAN members. Please contact htandcc@ds.dfci.harvard.edu if you are a member of HTAN and need access to the wiki.","The S h a red R epositories, D ata, An alysis and A ccess TNP focuses on optimizing the repeatability, interpretability and accessibility of HTAN characterization methods and the data they generate.","The S tandardized R epository of R eference S pecimens TNP's mission is to assemble an extensive catalogue of cases from premalignant lesions, pre- and post-treatment tumor tissue and metastatic tumor tissue for protocol optimization and validation.","The T issue M icro A rray TNP extends the TNP SARDANA characterization and analytics methodologies for evaluation and validation to a large array of breast tumor TMA samples that provide a broad spectrum of disease states and subtypes.","TNP CASI","TNP SARDANA","TNP SRRS","TNP TMA","Trans-Network Projects are multi-center projects created to facilitate collaborative research. Examples include cross-testing experimental and analytical protocols, exchange of personnel to disseminate SOPs or pursuit of additional HTAN critical methods or technologies. Specific information about each TNP is available on HTAN's Synapse Wiki page for HTAN members."]}],[{"i":"frequently-asked-questions-faq","l":"Frequently Asked Questions (FAQ)","p":["Can I upload my own data to the HTAN Portal?","Can I use HTAN data for my own research?","Do I need an account to access the HTAN data?","How can I access the data on the HTAN Portal?","How can I contact the HTAN team for additional questions?","How is privacy and data security handled on the HTAN Portal?","How is the data on the HTAN Portal generated?","Is there 3D data?","Is there any support or documentation available for using the HTAN Portal?","Is there healthy data?","Is there temporal data?","What is the HTAN Portal?","What is the Human Tumor Atlas Network (HTAN)?","What types of data are available on the HTAN Portal?","Where can I find updates on new data or features added to the HTAN Portal?","Who can use the HTAN Portal?"]},{"i":"what-is-the-human-tumor-atlas-network-htan","l":"What is the Human Tumor Atlas Network (HTAN)?","p":["The Human Tumor Atlas Network (HTAN) is a collaborative research initiative funded by the National Cancer Institute (NCI). It aims to create comprehensive, dynamic 3D atlases of tumors across multiple cancer types and stages. These atlases provide insights into how tumors evolve, from early formation to metastasis and treatment resistance."]},{"i":"what-is-the-htan-portal","l":"What is the HTAN Portal?","p":["The HTAN Portal is an interactive platform where researchers, clinicians, and the public can access, explore, and analyze data generated by HTAN. The portal contains data such as genomic, transcriptomic, proteomic, and imaging data related to tumor development."]},{"i":"who-can-use-the-htan-portal","l":"Who can use the HTAN Portal?","p":["The HTAN Portal is open to anyone interested in cancer research, including scientists, clinicians, and students. It is especially useful for cancer researchers seeking to explore tumor evolution and heterogeneity through a rich collection of multi-omics and imaging datasets."]},{"i":"what-types-of-data-are-available-on-the-htan-portal","l":"What types of data are available on the HTAN Portal?","p":["The portal provides access to various types of data, including:","Genomic data","Transcriptomic data","Proteomic data","Single-cell sequencing data","Imaging and other spatial data","These datasets are gathered from different stages of cancer progression, including healthy, precancerous, primary tumors, metastases, and treatment-resistant cancers."]},{"i":"how-can-i-access-the-data-on-the-htan-portal","l":"How can I access the data on the HTAN Portal?","p":["Users can access the data through the Explore Page on the HTAN Portal"]},{"i":"do-i-need-an-account-to-access-the-htan-data","l":"Do I need an account to access the HTAN data?","p":["No, an account is not required to explore the public data available on the HTAN Portal. However for accessing the lower level data, dbGap access needs to be obtained. See the Acccess-Controlled Data section for more information."]},{"i":"how-is-the-data-on-the-htan-portal-generated","l":"How is the data on the HTAN Portal generated?","p":["The data is collected from participating HTAN centers across the United States. These centers generate multi-omics data, imaging datasets, and other relevant tumor information using advanced technologies, such as single-cell sequencing, proteomics, and spatial imaging techniques."]},{"i":"can-i-upload-my-own-data-to-the-htan-portal","l":"Can I upload my own data to the HTAN Portal?","p":["At this time, the HTAN Portal does not support user-uploaded data"]},{"i":"is-there-any-support-or-documentation-available-for-using-the-htan-portal","l":"Is there any support or documentation available for using the HTAN Portal?","p":["Yes, the HTAN Portal offers extensive documentation to help users navigate and utilize the platform effectively. Additionally, the portal provides a Help Desk for support."]},{"i":"how-is-privacy-and-data-security-handled-on-the-htan-portal","l":"How is privacy and data security handled on the HTAN Portal?","p":["The HTAN Portal adheres to strict data security and privacy protocols to ensure that sensitive information, including patient-related data, is protected. Any identifiable information is removed or de-identified before being made available to the public, in compliance with ethical standards and legal regulations. More information can be found in the Governance and Policy section."]},{"i":"can-i-use-htan-data-for-my-own-research","l":"Can I use HTAN data for my own research?","p":["Yes, researchers are encouraged to use HTAN data for their own studies. The data is publicly available, but users must acknowledge HTAN and the publication of the source data in any resulting publications"]},{"i":"where-can-i-find-updates-on-new-data-or-features-added-to-the-htan-portal","l":"Where can I find updates on new data or features added to the HTAN Portal?","p":["The portal is regularly updated with new data and features. You can find updates in the News section of the HTAN Portal."]},{"i":"is-there-healthy-data","l":"Is there healthy data?","p":["There is \"healthy\" and precancerous data on the HTAN Portal. No specific “healthy” filter exists at the moment, but one can find all samples without an unknown or reported disease with this HTAN portal filter. Note however that some of these may be tumors of unknown primary, or the information is missing for another reason. There is an open ticket to improve the selection of healthy/normal and precancerous tissue."]},{"i":"is-there-3d-data","l":"Is there 3D data?","p":["A number of three-dimensional datasets have been released on the HTAN data portal, including 3D microscopy data and serial sections for H&E and multiplexed tissue imaging. Examples include multiple serial section of CRC analyzed by CyCIF for the SARDANA trans-network partnership, and electron microscopy data from OHSU. The DCC expects to receive and share 3D datasets including confocal and light-sheet microscopy in the future."]},{"i":"is-there-temporal-data","l":"Is there temporal data?","p":["There are a few different types of temporal data, e.g., precancerous vs cancerous tumors, primary vs metastatic tumor samples, as well as a patient's longitudinal treatment and diagnosis information. The former can be found by search for specific biospecimens. The latter can now be explored per atlas in the longitudinal data section of the HTAN Data Submission Dashboard, as well as on cBioPortal for the OHSU breast cancer dataset. We are working on improving the search and filter capabilities for temporal data on the HTAN Portal."]},{"i":"how-can-i-contact-the-htan-team-for-additional-questions","l":"How can I contact the HTAN team for additional questions?","p":["You can contact the HTAN team through the Help Desk"]}]]
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