From 46e76b148ac09e1f3e6da7ee6e6e3db045f68840 Mon Sep 17 00:00:00 2001
From: Knut Finstermeier <finstermeier@mpusp.mpg.de>
Date: Tue, 12 May 2026 09:10:26 +0200
Subject: [PATCH] feat: removed NCBI access from lesson 8

---
 lessons/lesson_08.ipynb | 96 -----------------------------------------
 1 file changed, 96 deletions(-)

diff --git a/lessons/lesson_08.ipynb b/lessons/lesson_08.ipynb
index 5301d5e..bebf1ab 100644
--- a/lessons/lesson_08.ipynb
+++ b/lessons/lesson_08.ipynb
@@ -301,102 +301,6 @@
     "        break"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "0fc324f7",
-   "metadata": {},
-   "source": [
-    "# Accessing NCBI\n",
-    "- WARNING: NCBI can and will block your institute, if you misuse this, even unintentionally, but they will try to reach you first.\n",
-    "- NCBI guidelines: https://www.ncbi.nlm.nih.gov/books/NBK25497/\n",
-    "- In brief:\n",
-    "  - For more than 100 consecutive requests in a row, do that at a weekend or outside of US peak times\n",
-    "  - No more than 3 queries per second\n",
-    "  - **IMPORTANT**: always provide a valid email address for contacting you! \n",
-    "  - Entrez allows you to search and download large amounts of data. Save those files rather than downloading them over and over again!\n",
-    "  - Use alternatives to download large datasets, i.e. ftp server for all bacterial genomes etc.\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "a65f491c",
-   "metadata": {},
-   "source": [
-    "- Allows programmatic database search similar to website\n",
-    "- Multiple databases are supported, i.e. nucleotide, pubmed\n",
-    "- Will return identifiers for downloading / accessing data"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6d52bf4d",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from Bio import SeqIO\n",
-    "from Bio import Entrez\n",
-    "\n",
-    "Entrez.email = \"finstermeier@mpusp.mpg.de\"\n",
-    "handle = Entrez.esearch(db=\"pubmed\", term=\"biopython\")\n",
-    "record = Entrez.read(handle)\n",
-    "print(record[\"IdList\"][:5])"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "e428202c",
-   "metadata": {},
-   "source": [
-    "- Available databases: https://www.ncbi.nlm.nih.gov/books/NBK25497/table/chapter2.T._entrez_unique_identifiers_ui/?report=objectonly\n",
-    "- Keywords for search term can be found here: https://www.ncbi.nlm.nih.gov/books/NBK49540/\n",
-    "- Overview of available databases and parameters:\n",
-    "  - https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "d94519b6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "handle = Entrez.esearch(\n",
-    "    db=\"nucleotide\", term=\"Cypripedioideae[Orgn] AND matK[Gene]\", idtype=\"acc\"\n",
-    ")\n",
-    "record = Entrez.read(handle)\n",
-    "print(record[\"IdList\"][:5])"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "4fd85ecd",
-   "metadata": {},
-   "source": [
-    "# Downloading from NCBI"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6d794ccd",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "with Entrez.efetch(\n",
-    "    db=\"nucleotide\", rettype=\"gb\", retmode=\"text\", id=\"6273291\"\n",
-    ") as handle:\n",
-    "    seq_record = SeqIO.read(handle, \"gb\")  # using \"gb\" as an alias for \"genbank\"\n",
-    "    print(f\"{seq_record.id} with {len(seq_record.features)} features\")\n",
-    "\n",
-    "\n",
-    "with Entrez.efetch(\n",
-    "    db=\"nucleotide\", rettype=\"gb\", retmode=\"text\", id=\"6273291, 6273290, 6273289\"\n",
-    ") as handle:\n",
-    "    for seq_record in SeqIO.parse(handle, \"gb\"):\n",
-    "        print(f\"{seq_record.id}: {seq_record.description[:50]}...\")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "0642bc14",