> ## Documentation Index
> Fetch the complete documentation index at: https://docs.cosmosid.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Quickstart

> Go from raw omics data to publication-ready figures in your browser, with no code required.

# Steps to get started

<Steps>
  <Step title="Sign in" titleSize="h2">
    Navigate to [https://dap.cosmosid.com/](https://dap.cosmosid.com/) in your browser. You can log in through your Cosmos-Hub email address and password, or through SSO with your corporate or academic email address.

    <img src="https://mintcdn.com/cmbio/IvW3mcdgB0VWEfpX/images/login_dap-1.jpg?fit=max&auto=format&n=IvW3mcdgB0VWEfpX&q=85&s=1bef34a65f111457a35f87fdbb2eebd5" alt="Login Dap 1" width="900" height="1310" data-path="images/login_dap-1.jpg" />

    * **Don't have an account?** [Contact us](https://cosmos-hub.com/contact-us) to create one or to request a free trial.
    * **Forgot your password?**[ Reset it here](https://app.cosmosid.com/recover-password).
  </Step>

  <Step title="Set up or join a workspace" titleSize="h2">
    A [Workspace](https://docs.cosmosid.com/DAP_docs/workspaces) is a shared environment where your team can organize, manage, and collaborate on microbiome research projects, with all relevant data and bioinformatics tools centralised in one place.

    <Frame>
      <img src="https://mintcdn.com/cmbio/IvW3mcdgB0VWEfpX/images/image-22.png?fit=max&auto=format&n=IvW3mcdgB0VWEfpX&q=85&s=7648ec33c2e548a0b09097c0828651e9" alt="Image" width="3102" height="916" data-path="images/image-22.png" />
    </Frame>

    * **Starting fresh?** Create a new workspace by clicking the **+ New Workspace** button in the top-right corner of the Workspaces Dashboard, give it a name and invite  team members to collaborate.
    * **Invited to collaborate on an existing workspace?** Select any workspace in the Workspaces dashboard that your organization has made available or that has been shared with you.
  </Step>

  <Step title="Create or join a Study to organize your research project" titleSize="h2">
    <Frame>
      <img src="https://mintcdn.com/cmbio/rXnT_KRi2R3YfV3p/images/studies_dashboard-1.jpg?fit=max&auto=format&n=rXnT_KRi2R3YfV3p&q=85&s=2b0c6e4408271fd646cc69db5d4afd22" alt="Studies Dashboard" width="3100" height="798" data-path="images/studies_dashboard-1.jpg" />
    </Frame>

    * **Create a new study** with the **+ New Study** button at the top of the current workspace interface.
    * **Join an existing study** by selecting any of the studies available in the current workspace.
  </Step>

  <Step title="Import 'omics data into a Study" titleSize="h2">
    Omics data tables are the starting point of any microbiome analysis. Once a study is created, it's time to import data into it. You can import data from Cosmos-Hub Pipelines or use data already available in the workspace to build a cohort.

    <Frame>
      <img src="https://mintcdn.com/cmbio/IvW3mcdgB0VWEfpX/images/importdata_dap.jpg?fit=max&auto=format&n=IvW3mcdgB0VWEfpX&q=85&s=8d64f7939c78aee5a911b5e164a1898f" alt="Importdata Dap" width="1724" height="726" data-path="images/importdata_dap.jpg" />
    </Frame>

    <Note>
      **Joined a study that already has data?** Skip to step 5 and start building your Cohort and Analysis Project.
    </Note>

    There are two routes to import sample profiles into a study or workspace:

    * **Import from Hub:** import any profiles previously generated by the [Cosmos-Hub Bioinformatic Pipelines](https://docs.cosmosid.com/docs/about#cosmos-hub-bioinformatic-pipelines).
      * Select **Import from Hub** → **Hub Folder Path** → select the folder containing the profiles you want to import into your Cosmos-Hub 2.0 study.

    <Info>
      If you already have some experience with Cosmos-Hub 1.0 (now Cosmos-Hub Pipelines), you can export data directly from Cosmos-Hub Pipelines into a Cosmos-Hub 2.0 workspace. See [Exporting Data from Cosmos-Hub Pipelines](https://docs.cosmosid.com/DAP_docs/export-from-cosmos-hub-pipelines).
    </Info>

    <Info />

    <img src="https://mintcdn.com/cmbio/IvW3mcdgB0VWEfpX/images/import_from_hub.jpg?fit=max&auto=format&n=IvW3mcdgB0VWEfpX&q=85&s=678575271e62652e2d7436f2aec0bd79" alt="Import From Hub" width="1712" height="502" data-path="images/import_from_hub.jpg" />

    * **Use existing workspace data:** if you joined a workspace that already contains data, you are ready to create your first analysis.

    To learn more about data import, see [Importing Data from Cosmos-Hub Pipelines](https://docs.cosmosid.com/DAP_docs/export-from-cosmos-hub-pipelines) and [Importing data into a study](DAP_docs/importing-data-in-studies).
  </Step>

  <Step title="Create your first Analysis Project and build a Cohort with the Query Builder" titleSize="h2">
    Assembling that cohort manually across multiple datasets can be one of the most time-consuming parts of a microbiome project. The [**Query Builder**](untitled-page-5) is designed to simplify this step by helping you identify and select the samples that match your analysis criteria.

    1. Click any study, either one shared with you or the one you created in step 4, to open its dashboard (shown below).

    <Frame caption="Inside Studies: the Study Dashboard">
      <img src="https://mintcdn.com/cmbio/IvW3mcdgB0VWEfpX/images/inside_a_study.jpg?fit=max&auto=format&n=IvW3mcdgB0VWEfpX&q=85&s=66a41f0b80321c7a5fafb1cbab5f746f" alt="Inside A Study" width="2956" height="1056" data-path="images/inside_a_study.jpg" />
    </Frame>

    <Note />

    Meet the [**Query Builder (QB)**](untitled-page-5): an AI-powered assistant that helps you querying your team's workspace data lake to build a cohort  through an interactive experience, so you can build the right query for the cohort you need.

    <img src="https://mintcdn.com/cmbio/rXnT_KRi2R3YfV3p/images/query-builder-dataset-selection-1.png?fit=max&auto=format&n=rXnT_KRi2R3YfV3p&q=85&s=b3fa563a3350d5233338610b81a6ba2c" alt="Query Builder Dataset Selection 1" width="2968" height="920" data-path="images/query-builder-dataset-selection-1.png" />

    Building the Cohort with the Query Builder is a hybrid experience: you can either click on the metadata filters it suggests, or type a request in natural language through the chat bar.

    <Columns cols={2}>
      <Column>
        * **Choose your data.** Click one of the suggested datasets available in the workspace (for example, Champ Taxa 1.0).
        * **Explore the metadata.** Ask which attributes are available and what values they contain — for example, "which body sites are represented in my cohort?"
        * **Filter the samples.** Ask the QB to restrict the cohort by body site, collection country, sequencing depth, or any other attribute — for example, "keep only samples from patients over 30."
        * **Select metadata columns.** Choose the columns you will need for the analysis by clicking the suggestions or by typing a request such as "include Subject ID, Bodysite, Treatment group, and collection country as metadata columns."

          As your conversation with the QB moves on, keep track of which filters have been applied to your dataset so far in the **Active Filters** panel.
      </Column>

      <Column>
        <img src="https://mintcdn.com/cmbio/9IPlECfVJPWdo6z4/images/active_filters_squared.jpg?fit=max&auto=format&n=9IPlECfVJPWdo6z4&q=85&s=806af140f98930203405a83b9299de32" alt="Active Filters Squared" width="738" height="688" data-path="images/active_filters_squared.jpg" />
      </Column>
    </Columns>

    3. When your query is ready:

       * Click **Looks good — create the analysis**.
       * Select the analysis modules you would like to run on the cohort.
       * Click **Confirm and Create Analysis**.

           <img src="https://mintcdn.com/cmbio/rXnT_KRi2R3YfV3p/images/ready_to_create.jpg?fit=max&auto=format&n=rXnT_KRi2R3YfV3p&q=85&s=e3a5b47cd6e7510d6d45db0bbe15da91" alt="Ready To Create" width="2724" height="536" data-path="images/ready_to_create.jpg" />

    <Note>
      Filters and requests can be made at any point in the conversation with the QB. You can undo filters, apply new ones, or change the metadata columns you selected.
    </Note>

    Your analysis then appears in the [Study Dashboard](DAP_docs/studies), ready to be explored through the Analysis Modules of Cosmos-Hub 2.0.
  </Step>

  <Step title="Analyze your cohort in the Analysis Studio" titleSize="h2">
    1. Navigate to the analysis you created to open its Analysis Dashboard.
    2. Click **Open Current Analysis** to open the Analysis Studio for the Analysis Project you just created.

    <Frame>
      <img src="https://mintcdn.com/cmbio/IvW3mcdgB0VWEfpX/images/inside_analysis-2.jpg?fit=max&auto=format&n=IvW3mcdgB0VWEfpX&q=85&s=0a00473837e0ce961a1f2dee2effd831" alt="Inside Analysis 2" width="2466" height="976" data-path="images/inside_analysis-2.jpg" />
    </Frame>

    ### The Analysis Studio

    The Analysis Studio is the no-code analysis toolbox in Cosmos-Hub 2.0. It is designed to help you explore and analyze the cohort defined in an Analysis Project and create publication-ready figures and results.

    <Frame>
      <img src="https://mintcdn.com/cmbio/9IPlECfVJPWdo6z4/images/analysis_studio.jpg?fit=max&auto=format&n=9IPlECfVJPWdo6z4&q=85&s=cb42913257e48463b84b39296f69bacd" alt="Analysis Studio" width="3610" height="1840" data-path="images/analysis_studio.jpg" />
    </Frame>

    1. Choose one of the [nine Analysis Modules](/untitled-page-6#running-analysis-modules) currently supported in Cosmos-Hub 2.0.
    2. Customize the analysis by adjusting its parameters in the panel on the right.
    3. Click **Run and Apply** to run the analysis and generate publication-ready figures and results.

    <Tip>
      Don't worry about getting it wrong: you can run the analysis as many times as you want.

      See [Analysis Modules](/untitled-page-6#running-analysis-modules) for detailed guidance on how to tune the parameters of each module.
    </Tip>
  </Step>

  <Step title="Export and share your analysis" titleSize="h2">
    #### Export your analysis

    Every analysis in Cosmos-Hub 2.0 produces figures and statistical results that you can either visualize on the platform or export in the format you prefer, for example to add to a slide deck.

    * Click **Export** to download all the figures, the parameters used for the analysis, all the input data used to perform it, and any statistical output table generated by the module.

    #### Save and share [Snapshots](untitled-page-8) of your Analysis Project

    * **Analysis Modules** can be configured in many different ways, often using several parameters. When multiple people are working on the same analysis, saving the parameter configuration makes it easier to keep track of how a specific figure or result was generated.
    * To save a Snapshot of your current Analysis Project configuration, click the floppy-disk icon and select **Save**. The snapshot stores the current parameters and output, and is available to other collaborators in the Workspace. They can open it, review the saved configuration, and continue the analysis from that point.
  </Step>
</Steps>