DaneshjouLab
diff --git a/‎daneshjou-lab-manual.html‎
Lines changed: 38 additions & 25 deletions b/‎daneshjou-lab-manual.html‎
Lines changed: 38 additions & 25 deletions
@@ -443,7 +443,10 @@ <h2 id="s2-5">2.5 Meetings</h2>
   <p>Come to every meeting prepared with an agenda. Share updates, questions, and blockers. Document action items and follow through.</p>
 
   <h2 id="s2-6">2.6 Communication</h2>
-  <p><strong>Slack</strong> is our primary communication tool. Use it for quick questions, updates, sharing papers, and coordinating meetings. For longer discussions or sensitive topics, schedule a meeting or use email. Keep Slack channels organized and on-topic.</p>
+  <p><strong>Slack</strong> is our primary internal communication tool. Use it for quick questions, updates, sharing papers, and coordinating meetings. For longer discussions or sensitive topics, schedule a meeting or use email. Keep Slack channels organized and on-topic.</p>
+  <div class="callout principle">
+    <strong>Don't let things fall through the cracks.</strong> If you message Dr. Daneshjou or a teammate and don't hear back within a reasonable time, follow up. People get busy and messages get buried &mdash; a polite bump is always welcome and expected. It's far better to nudge again than to sit idle waiting for a response that may have been missed.
+  </div>
 
   <h2 id="s2-7">2.7 Recommendation Letters</h2>
   <p>Dr. Daneshjou is happy to write recommendation letters for lab members. Please provide at least <strong>4 weeks notice</strong> and include:</p>
@@ -474,6 +477,7 @@ <h2 id="s3-1">3.1 For Graduate Students</h2>
     <li><strong>Data Science Scholars:</strong> For students pursuing data science research.</li>
     <li><strong>Bio-X:</strong> Interdisciplinary biosciences research fellowships.</li>
     <li><strong>RAISE (Responsibility, AI, Society, and Ethics):</strong> For students working at the intersection of AI and society.</li>
+    <li><strong><a href="https://samvidscholars.org/">Samvid Scholars</a>:</strong> Merit-based scholarship funding tuition and fees up to $50,000/year for two years of graduate study (MD, MBA, JD, MPP/MPA, MPH, MS/MA in STEM or social sciences). Includes leadership development programming through the Aspen Institute. Must be a first-year graduate student and U.S. citizen or DACA recipient with &ge;3.50 undergraduate GPA.</li>
   </ul>
   <p>Talk to Dr. Daneshjou early about fellowship applications &mdash; many have fall deadlines.</p>
 
@@ -650,16 +654,12 @@ <h2 id="s5-6">5.6 Software</h2>
 <!-- ==================== CHAPTER 6 ==================== -->
 <section class="chapter" id="ch6">
   <h1>6. Conferences</h1>
-  <div class="missing-info-banner">
-    <strong>&#9888; Needs Daneshjou Lab Info</strong> &mdash; This section is adapted from the
-    <a href="https://stanfordhpds.github.io/lab_manual/">HPDS Lab Manual</a>.
-    Replace with Daneshjou Lab-specific content.
-  </div>
 
   <h2 id="s6-1">6.1 Stanford Travel Policies</h2>
   <p>All conference travel must comply with <a href="https://travel.stanford.edu/">Stanford's travel policies</a>. Key points:</p>
   <ul>
     <li>Get approval from Dr. Daneshjou before registering for or booking any conference travel.</li>
+    <li><strong>Request travel as soon as you are accepted.</strong> Contact Dr. Daneshjou immediately when you receive an acceptance notification so travel and registration can be arranged promptly. Last-minute requests make logistics harder and more expensive.</li>
     <li>Book travel through Stanford's approved channels when possible.</li>
     <li>Keep all receipts and submit expense reports promptly after returning.</li>
     <li>International travel requires additional approvals &mdash; start the process early.</li>
@@ -682,26 +682,19 @@ <h2 id="s6-3">6.3 Posters</h2>
     <li>Print through Stanford's poster printing services.</li>
   </ul>
 
-  <h2 id="s6-4">6.4 Conferences by Field</h2>
-  <p>Relevant conferences for Daneshjou Lab research areas include (but are not limited to):</p>
+  <h2 id="s6-4">6.4 Key Conferences</h2>
+  <p>Our lab primarily targets the following conferences:</p>
   <ul>
-    <li><strong>Clinical AI/ML:</strong> MLHC (Machine Learning for Healthcare), CHIL, AMIA</li>
-    <li><strong>Dermatology:</strong> AAD, SID, ESDR, WCD</li>
-    <li><strong>Machine Learning:</strong> NeurIPS, ICML, ICLR, AAAI</li>
-    <li><strong>Medical Informatics:</strong> AMIA Annual Symposium, AMIA Informatics Summit</li>
-    <li><strong>Health Equity:</strong> AcademyHealth, SGIM</li>
-    <li><strong>NLP/LLMs:</strong> ACL, EMNLP, NAACL</li>
+    <li><strong>Machine Learning:</strong> ICLR, ICML, NeurIPS</li>
+    <li><strong>Clinical AI/ML:</strong> CHIL (Conference on Health, Inference, and Learning), ML4H (Machine Learning for Health)</li>
+    <li><strong>Bioinformatics/Computational Biology:</strong> PSB (Pacific Symposium on Biocomputing)</li>
+    <li><strong>Dermatology:</strong> AAD (American Academy of Dermatology)</li>
   </ul>
 </section>
 
 <!-- ==================== CHAPTER 7 ==================== -->
 <section class="chapter" id="ch7">
   <h1>7. Publications</h1>
-  <div class="missing-info-banner">
-    <strong>&#9888; Needs Daneshjou Lab Info</strong> &mdash; This section is adapted from the
-    <a href="https://stanfordhpds.github.io/lab_manual/">HPDS Lab Manual</a>.
-    Replace with Daneshjou Lab-specific content.
-  </div>
 
   <h2 id="s7-1">7.1 Authorship</h2>
   <p>We follow <a href="https://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html">ICMJE guidelines</a> for authorship. To be an author, you must meet <strong>all four</strong> criteria:</p>
@@ -717,6 +710,17 @@ <h2 id="s7-1">7.1 Authorship</h2>
     <li><strong>No new authors without PI agreement.</strong> Adding authors mid-project requires discussion with Dr. Daneshjou.</li>
     <li>Authorship disputes should be raised early and resolved through open discussion.</li>
   </ul>
+  <div class="callout principle">
+    <strong>Corresponding author.</strong> Dr. Daneshjou is the corresponding author on all lab publications. If you're new to publishing, this may feel confusing since students often handle the submission paperwork (creating accounts, uploading files, filling out forms). That's normal &mdash; you're doing the logistical work of submission, but the corresponding author is the person journals contact for decisions about the paper. If you have questions about this, talk to Dr. Daneshjou.
+  </div>
+  <div class="callout callout-warning">
+    <div class="callout-title">Always Keep Dr. Daneshjou in the Loop</div>
+    <ul>
+      <li><strong>Before submitting anywhere</strong> &mdash; discuss target journal/venue with Dr. Daneshjou and get her approval before you submit.</li>
+      <li><strong>During revisions</strong> &mdash; share reviewer comments and your planned responses with her. Don't resubmit without her review.</li>
+      <li><strong>At every stage</strong> &mdash; from first draft to camera-ready, Dr. Daneshjou should know where things stand. No surprises.</li>
+    </ul>
+  </div>
 
   <h2 id="s7-2">7.2 Acknowledgments</h2>
   <p>Always acknowledge:</p>
@@ -728,13 +732,13 @@ <h2 id="s7-2">7.2 Acknowledgments</h2>
   </ul>
 
   <h2 id="s7-3">7.3 Preprints</h2>
-  <p>We strongly support preprinting. Post preprints to <strong>arXiv</strong>, <strong>medRxiv</strong>, or <strong>bioRxiv</strong> (as appropriate) before or concurrent with journal submission. Preprints:</p>
+  <p>Our lab policy is <strong>always post to arXiv first</strong> before or concurrent with journal/conference submission. Preprints:</p>
   <ul>
     <li>Establish priority for your findings</li>
     <li>Enable faster dissemination</li>
     <li>Allow community feedback before peer review</li>
   </ul>
-  <p>Discuss timing with Dr. Daneshjou before posting.</p>
+  <p><strong>Always get Dr. Daneshjou's approval before posting a preprint.</strong> She will review the manuscript and confirm it's ready for public release.</p>
 
   <h2 id="s7-4">7.4 Least Publishable Units</h2>
   <p><strong>Avoid &ldquo;salami slicing&rdquo;</strong> &mdash; the practice of splitting a coherent body of work into the smallest possible publishable pieces. This:</p>
@@ -1781,13 +1785,13 @@ <h3>What Your Audience Sees vs. What You See</h3>
   <h1>14. FAQs</h1>
 
   <h3>How do I get added to the Daneshjou Lab GitHub organization?</h3>
-  <p>Reach out to <a href="mailto:bikia@stanford.edu">bikia@stanford.edu</a>.</p>
+  <p>Reach out to <a href="mailto:bikia@stanford.edu">bikia@stanford.edu</a>. See the <a href="#s2-2">Onboarding Checklist</a> for the full setup process including GitHub requirements.</p>
 
   <h3>How am I added to lab meeting calendar invites?</h3>
-  <p>Contact <a href="mailto:daneshjoulab@stanford.edu">daneshjoulab@stanford.edu</a>.</p>
+  <p>Contact <a href="mailto:daneshjoulab@stanford.edu">daneshjoulab@stanford.edu</a>. This is part of the <a href="#s2-2">Onboarding Checklist</a> (step 10) and is typically done once all prior onboarding tasks are complete.</p>
 
   <h3>How am I added to the Daneshjou Lab Google shared drive?</h3>
-  <p>Contact <a href="mailto:daneshjoulab@stanford.edu">daneshjoulab@stanford.edu</a>.</p>
+  <p>Contact <a href="mailto:daneshjoulab@stanford.edu">daneshjoulab@stanford.edu</a>. This is part of the <a href="#s2-2">Onboarding Checklist</a> (step 11).</p>
 
   <h3>How do I request API keys (e.g., OpenAI, Claude, etc.)?</h3>
   <p>Email <a href="mailto:daneshjoulab@stanford.edu">daneshjoulab@stanford.edu</a> with subject line <strong>"SECURE: [DaneshjouLab] API Key Request"</strong>. Include a brief description of your task and the model you intend to use. Keys are sent securely via Stanford Secure Mail.</p>
@@ -1796,13 +1800,22 @@ <h3>How do I get access to Google Cloud Platform (GCP) for a specific project?</
   <p>After being granted permission to access the project on GCP and added to the respective IRB, reach out to <a href="mailto:daneshjoulab@stanford.edu">daneshjoulab@stanford.edu</a>.</p>
 
   <h3>How do I get IRB approval to access PHI data?</h3>
-  <p>Contact <strong>Sana Kidwai</strong> at <a href="mailto:kidwai@stanford.edu">kidwai@stanford.edu</a>. You will need to complete:</p>
+  <p>See <a href="#ch4">Chapter 4 (Data)</a> for full details on IRB and data access. In short: contact <strong>Sana Kidwai</strong> at <a href="mailto:kidwai@stanford.edu">kidwai@stanford.edu</a>. You will need to complete:</p>
   <ol>
     <li><strong>CITI Group 7 Training</strong> (<a href="https://www.citiprogram.org/">citiprogram.org</a>)</li>
     <li><strong>HIPAA Protecting Patient Privacy 2025</strong> (PRIV-2025-WEB) &mdash; via <a href="https://axess.stanford.edu/">Axess</a></li>
     <li><strong>HIPAA Privacy for Researchers 2025</strong> (CLIN-2025-WEB) &mdash; via <a href="https://axess.stanford.edu/">Axess</a></li>
   </ol>
   <p>If the HIPAA course links don't open directly, find them in Axess under <strong>STARS</strong>.</p>
+
+  <h3>Who is the corresponding author on lab publications?</h3>
+  <p>Dr. Daneshjou is the corresponding author on all lab publications. See <a href="#s7-1">Section 7.1 (Authorship)</a> for details on authorship policies and the submission process.</p>
+
+  <h3>Where should I post preprints?</h3>
+  <p>Always post to arXiv first, but get Dr. Daneshjou's approval before posting. See <a href="#s7-3">Section 7.3 (Preprints)</a>.</p>
+
+  <h3>How do I access Sherlock or OAK?</h3>
+  <p>See <a href="#s5-1">Section 5.1 (Sherlock)</a> and <a href="#s5-2">Section 5.2 (OAK)</a> for access instructions, documentation links, and best practices.</p>
 </section>
 
 <!-- ==================== CONTRIBUTORS ==================== -->