Update Use Case description and API change to accept GCP auth token (#4384)

* pass auth_token in create_http_client

* lint on the notebook

* feat:Removed the last update date

* Update notebooks/community/alphagenome/README.md

Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>

* Update notebooks/community/alphagenome/cloudai_alphagenome_vai_quickstart.ipynb

Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>

---------

Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>

notebooks/community/alphagenome/README.md

@@ -40,29 +40,13 @@ human and mouse cell types and tissues.
 ![Diagram showing an overview of the AlphaGenome model architecture and its inputs/outputs](https://www.alphagenomedocs.com/_images/model_overview.png)
 
 ## Use Cases
-*   **Predict outputs for a DNA sequence:** AlphaGenome is a model that makes
-    predictions from DNA sequences. AlphaGenome predicts multiple 'tracks' per
-    output type, covering a wide variety of tissues and cell-types.
+*   **Sequence-to-function predictions:** Predict multiple functional tracks (such as gene expression, splicing) from DNA sequences across a wide variety of tissues and cell types.
 
-*   **Open-vocabulary object retrieval:** AlphaGenome can make predictions for
-    a human reference genome sequence specified by a genomic interval.
-    For example, let's predict RNA-seq for tissue 'Right liver lobe' in a 1MB
-    region of Chromosome 19 around the gene CYP2B6, which encodes an enzyme
-    involved in drug metabolism, and is primarily expressed in the liver.
+*   **Variant effect scoring:** Assess the impact of genetic variants by comparing predictions for the reference and alternative alleles and summarising the differences between them.
 
-*   **Predict variant effects:** AlphaGenome can predict the effect of a
-    variant on a specific output type and tissue by making predictions for the
-    reference (REF) and alternative (ALT) allele sequences.
+*   **Identify functional regions:** Use in silico mutagenesis (ISM) to identify functionally important regions in the DNA sequence.
 
-*   **Scoring the effect of a genetic variant:** AlphaGenome can score the
-    effect of a genetic variant by making predictions for the REF and ALT
-    sequences and aggregating the track signal. To highlight which regions in a
-    DNA sequence are functionally important for a final variant prediction,
-    AlphaGenome can help you to perform an in silico mutagenesis (ISM) analysis
-    by scoring all possible single nucleotide variants in a specific interval.
-
-*   **Human and mouse predictions:** AlphaGenome can generate predictions for
-    both humans and mouse.
+*   **Human and mouse capability:** Generate predictions for both human and mouse genomes.
 
 ## Documentation
 This API provides access to AlphaGenome, Google DeepMind's unifying model for

notebooks/community/alphagenome/cloudai_alphagenome_vai_quickstart.ipynb

@@ -131,8 +131,12 @@
       "source": [
         "vertex_ai_url = \"\"  # @param {type:\"string\"}\n",
         "service_account = \"\"  # @param {type:\"string\"}\n",
-        "code_whl = \"alphagenome-0.4.2-py3-none-any.whl\"\n",
-        "file_path = f\"gs://alphagenome-whl/{code_whl}\""
+        "token = \"\"  # @param {type:\"string\"}\n",
+        "code_whl = \"alphagenome-0.4.2.2-py3-none-any.whl\"\n",
+        "file_path = f\"gs://alphagenome-whl/{code_whl}\"\n",
+        "\n",
+        "service_account = service_account or None\n",
+        "token = token or None\n"
       ]
     },
     {
@@ -268,9 +272,11 @@
       "source": [
         "print(\"Creating HttpDnaClient...\")\n",
         "dna_model = dna_client_http.create_http_client(\n",
-        "    vertex_ai_url=vertex_ai_url, model_version=\"FOLD_0\", service_account=service_account\n",
+        "    vertex_ai_url=vertex_ai_url,\n",
+        "    model_version=\"FOLD_0\",\n",
+        "    service_account=service_account,\n",
+        "    token=token,\n",
         ")\n",
-        "# dna_model = dna_client_http.create_http_client(vertex_ai_url=vertex_ai_url, model_version=\"FOLD_0\")\n",
         "print(\"HttpDnaClient created.\")"
       ]
     },
@@ -4616,7 +4622,9 @@
         }
       ],
       "source": [
-        "interval = Interval(chromosome=\"chr19\", start=2**20, end=2**20 + 2**20, strand=\".\")\n",
+        "interval = Interval(\n",
+        "    chromosome=\"chr19\", start=2**20, end=2**20 + 2**20, strand=\".\"\n",
+        ")\n",
         "\n",
         "scores = dna_model.score_interval(\n",
         "    interval,\n",