Merge pull request #68 from iamamutt/public2021

Updates to external data access and training criteria

Author: guzman-raphael

README.md

@@ -108,4 +108,9 @@ make sure to move over to the `master` branch by `git checkout master`
 `docker-compose -f docker-compose-deploy.yml pull` to get the ibl-navigator container
 `docker-compose -f docker-compose-deploy.yml up -d`
 
--------------------------------------
+-------------------------------------
+
+## External links
+
+- ![Training Pipeline Diagram (draw.io)](https://drive.google.com/file/d/1PrSq6JbLMzBLAijxop-hgb4A__aSNPfZ/view?usp=sharing)
+- ![Internal Navigator Documentation (Google)](https://docs.google.com/document/d/18RVyk0pDQpLR_uX9I6s0YMpoF-bETzFSy2NZB-oNcAM/edit?usp=sharing)

ibl-frontend/frontend-content/src/app/overview/overview.component.html

@@ -42,39 +42,49 @@ <h2 class="top-title">International Brain Laboratory Behavioral Data Portal</h2>
 
   <div class="home-shaded-container">
     <div class="detail-container">
-      <h3>How can you access the data?</h3>
-      <ol class="detail-text">
-        <li>To access the <b>data associated with the electrophysiology recordings</b>, follow <a href="https://int-brain-lab.github.io/iblenv/public_docs/public_one.html" target="_blank">
-          these guidelines</a>.
-        </li>
-        <li>To access the <b>behavior data</b> used in this online portal, you have three options:
-          <ol style="list-style-type: lower-alpha">
-            <li><b>Access the DataJoint database via <a target="_blank" href="https://jupyterhub.internationalbrainlab.org">JupyterHub</a>:</b> this site hosts 
-              several notebooks that allow you to directly interact with the database with DataJoint. You do not need to download or install anything locally.
-              <ol style="list-style-type: lower-roman">
-                <li>Log in with your GitHub account.</li>
-                <li>Read the README</li>
-                <li>Click on <span class="code-style">public_notebooks/Explore IBL pipeline</span> to run several notebooks (one of which replicates 
-                  figure 2 of <a target="_blank" href="https://doi.org/10.1101/2020.01.17.909838">The International Brain Laboratory et al. 2020</a>).</li>
-              </ol>
-            </li>
+        <h3>How can you access the data?</h3>
+        <h5>To access the data outside of this online portal, you have several options:</h5>
+        <ol class="detail-text">
+            <li><b>Access the data using <a
+                    href=" https://int-brain-lab.github.io/iblenv/notebooks_external/one_quickstart.html"
+                    target="_blank">ONE</a></b> by following the <a
+                    href="https://int-brain-lab.github.io/iblenv/public_docs/public_one.html"
+                    target="_blank">guidelines</a>. The data includes both compressed raw ephys data and preprocessed
+                data, as well as behaviour and video data.</li>
             <br>
-            <li><b>Access the database locally with <a target="_blank" href="https://datajoint.org">DataJoint</a>.</b>
-              <ol style="list-style-type: lower-roman">
-                <li>See detailed instructions on <a href="https://int-brain-lab.github.io/iblenv/public_docs/public_datajoint.html" target="_blank">accessing the database locally</a></li>
-              </ol>
+            <li><b>Access the data using <a target="_blank"
+              href="https://datajoint.org">DataJoint</a> via <a target="_blank"
+                    href="https://jupyterhub.internationalbrainlab.org">JupyterHub</a></b>. There we host
+                several notebooks that allow you to directly interact with the database with DataJoint. You do not
+                need to download or install anything locally.
+                <ol style="list-style-type: lower-alpha">
+                    <li>Log in with your GitHub account.</li>
+                    <li>Read the README.</li>
+                    <li>Click on <span class="code-style">public_notebooks/Explore IBL pipeline</span> to run
+                        the notebooks (one of which replicates
+                        Figure 2 of <a target="_blank" href="https://doi.org/10.1101/2020.01.17.909838">The
+                            International Brain Laboratory et al. 2020</a>).</li>
+                </ol>
             </li>
             <br>
-            <li>You may also directly download the data through your web browser without running any code. Simply load an internet browser and use the provided link from the <a href="http://ibl.flatironinstitute.org/public/behavior_paper_data.zip" target="_blank"><b>Behavior paper data URL</b></a>
+            <li><b>Access the data locally using <a target="_blank" href="https://datajoint.org">DataJoint</a></b>. See
+                the detailed <a
+                    href="https://int-brain-lab.github.io/iblenv/public_docs/public_datajoint.html"
+                    target="_blank">instructions</a>.</li> <br>
+            <li><b>Access the data via a direct download from your browser</b> without running any code. Simply
+                load a Google Chrome browser window and use the provided link from the <a
+                    href="http://ibl.flatironinstitute.org/public/behavior_paper_data.zip" target="_blank">Behavior
+                    paper data URL</a>.
             </li>
             <br>
-          </ol>
-        </li>
-      </ol>
-      <p class="detail-text">Issues with accessing the data? Email <a href="mailto:[email protected]" target="_blank">[email protected]</a>.</p>
-      <p class="detail-text">General questions about the paper <a target="_blank" href="https://doi.org/10.1101/2020.01.17.909838">The International Brain Laboratory et al. 2020</a>? 
-        Email <a href="mailto:[email protected]" target="_blank">[email protected]</a>.
-      </p>
+        </ol>
+        <p class="detail-text">Issues with accessing the data? Email <a href="mailto:[email protected]"
+                target="_blank">[email protected]</a>.</p>
+        <p class="detail-text">General questions about the paper <a target="_blank"
+                href="https://doi.org/10.1101/2020.01.17.909838">The International Brain Laboratory et al. 2020</a>?
+            Email <a href="mailto:[email protected]"
+                target="_blank">[email protected]</a>.
+        </p>
     </div>
 
     <!-- temporary for NMA events -->
@@ -154,19 +164,19 @@ <h3>Training Criteria</h3>
         The related training status indicated on the website are marked in bold and quoted.
       </p>
       <p class="detail-text">
-        When the animal starts behavioral training, it first undergoes a period of habituation, then it is trained in the basic task 
-        until reaching full proficiency (‘<b>trained</b>’). If the mouse does not reach proficiency in the basic task without 40 days of 
-        training, it is marked as untrainable (‘<b>over 40 days</b>’). Once proficiency in the basic task is reached, the animal is trained 
+        When the animal starts behavioral training, it first undergoes a period of habituation, then it is trained on the basic task 
+        until reaching full proficiency (‘<b>trained</b>’). If the mouse does not reach proficiency in the basic task within 40 days of 
+        training, it is marked as untrainable. Once proficiency in the basic task is reached, the animal is trained 
         in the biased task until proficiency is achieved (‘<b>ready for ephys rig</b>’).
       </p>
       <p class="detail-text">
-        Once the animal is placed on the ephys rig, it undergoes a habituation to that rig, until it is deemed ready for electrophysiological 
-        recording to be conducted (‘<b>ready for recording</b>’). Once a recording has been completed, the behavior quality is validated for 
+        Once the animal is placed on the ephys rig, it undergoes a habituation to that rig until it is deemed ready for electrophysiological 
+        recordings to be conducted (‘<b>ready for neuropixels recording</b>’). Once a recording has been completed, the behavior quality is validated for 
         downstream analysis (‘<b>good enough for brainwide map</b>’). The associated methods and protocols to habituate a mouse to the ephys rig and 
         perform the Neuropixels recording have not been yet publicly released; please see the figure below for a preliminary introduction 
         to our full training pipeline.
         <br>
-        <img id="fig5" src="assets/images/pipeline_NP.png" alt="figure pipeline">
+        <img id="fig5" src="assets/images/training_pipeline.svg" alt="Training procedure">
       </p>
     </div>
   </div>