Remove remaining lab- and study-specific content

.claude/skills/perturbNMF-runner/scripts/convert_igvf_mudata_to_h5ad.py

@@ -14,7 +14,7 @@
 **binary assignment in layers['guide_assignment']**. This script uses the layer; using
 X would treat ambient guide reads as perturbations.
 
-Generalises the one-off ``Convert_file_adata.py`` written for IGVF_Gersbach_iHep.
+Generalises a one-off ``Convert_file_adata.py`` written for a single IGVF dataset.
 """
 
 import argparse

.claude/skills/perturbNMF-runner/scripts/run_add_umap.sh

@@ -8,40 +8,50 @@
 # Run directly and it measures the h5mu, derives --mem/--time/--cpus-per-task, and
 # re-submits itself with those overrides. Do NOT prefix it with sbatch -- if you do,
 # that job just re-submits a correctly sized one and exits, costing an extra hop.
-# To pin resources yourself, set ADD_UMAP_INJOB to skip the sizing path entirely:
+# To pin resources yourself, set ADD_UMAP_INJOB to skip the sizing path entirely
+# (Slurm does not create the log directory, so make it first):
+#   mkdir -p add_umap_logs
 #   ADD_UMAP_INJOB=1 sbatch --mem=64G --time=06:00:00 run_add_umap.sh <h5mu>
 # The static #SBATCH directives below only apply on that manual path; they are
-# sized for the largest jamboree input.
+# sized for the largest input measured (below) and log to ./add_umap_logs.
+# Edit <partition> (or export SBATCH_PARTITION) and <your_email>, and set
+# PIPELINE_ROOT first:
+#   export PIPELINE_ROOT=/path/to/PerturbNMF
+# On the self-sizing path, logs go to $ADD_UMAP_LOG_DIR (default: ./add_umap_logs
+# in the directory you run it from), which is created automatically.
 #
 # Sizing basis (measured 2026-09-15). Peak RSS is driven by the expression matrix
 # and, in the dense case, by the temporary numpy allocates for X.var(axis=0) inside
-# ensure_umap -- that temporary is the full size of X again, which is why the dense
-# Gersbach matrix dominates everything else:
+# ensure_umap -- that temporary is the full size of X again, which is why a dense
+# matrix dominates everything else:
 #
-#   dataset       rna/X resident                      est. peak
-#   Gersbach      46.95 GB dense f32 1.05M x 11138    ~95-115 GB
-#   Hon_CM         9.91 GB sparse    nnz 1.24e9        ~30-40 GB
-#   Huangfu DE     5.01 GB sparse    nnz 627M          ~15-20 GB
-#   Huangfu ESC    3.37 GB sparse    nnz 422M          ~10-14 GB
+#   rna/X resident                      est. peak
+#   46.95 GB dense f32 1.05M x 11138    ~95-115 GB
+#    9.91 GB sparse    nnz 1.24e9        ~30-40 GB
+#    5.01 GB sparse    nnz 627M          ~15-20 GB
+#    3.37 GB sparse    nnz 422M          ~10-14 GB
 #
 # --in_place additionally needs free disk for a second copy of the h5mu while it
-# writes (48 GB for Gersbach; Oak had ~11 TB free at time of writing).
+# writes (48 GB for the largest input above).
 
 #SBATCH --job-name=add_umap
-#SBATCH --output=/scratch/users/ymo/add_umap_logs/%j.out
-#SBATCH --error=/scratch/users/ymo/add_umap_logs/%j.err
-#SBATCH --partition=engreitz,owners
+#SBATCH --output=add_umap_logs/%j.out   # relative to the submit dir
+#SBATCH --error=add_umap_logs/%j.err
+#SBATCH --partition=<partition>
 #SBATCH --time=16:00:00
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=16
 #SBATCH --mem=192G
 #SBATCH --mail-type=BEGIN,END,FAIL
-#SBATCH --mail-user=ymo@stanford.edu
+#SBATCH --mail-user=<your_email>
 
 set -o pipefail
 
-SCRIPT_DIR="/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/.claude/skills/perturbNMF-runner/scripts"
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF first)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/.claude/skills/perturbNMF-runner/scripts"
+LOG_DIR="${ADD_UMAP_LOG_DIR:-$PWD/add_umap_logs}"
 
 MDATA_PATH="$1"
 if [ -z "$MDATA_PATH" ]; then
@@ -57,8 +67,8 @@ fi
 # Self-sizing submit path.
 #
 # The guard is the ADD_UMAP_INJOB sentinel this script sets on its own sbatch
-# call -- NOT $SLURM_JOB_ID. On Sherlock an OnDemand/code-server session is itself
-# a Slurm allocation that exports SLURM_JOB_ID (and SLURM_CPUS_PER_TASK=2), so a
+# call -- NOT $SLURM_JOB_ID. On clusters where an OnDemand/code-server session is
+# itself a Slurm allocation that exports SLURM_JOB_ID (and SLURM_CPUS_PER_TASK=2), a
 # SLURM_JOB_ID check reads as "already in a batch job" from any interactive shell
 # there and silently runs the whole UMAP in that 2-CPU session instead of queuing.
 # ---------------------------------------------------------------------------
@@ -83,14 +93,16 @@ if [ -z "$ADD_UMAP_INJOB" ]; then
     echo "h5mu:  $MDATA_PATH"
     echo "size:  ${SIZE_GB} GB"
     echo "sized: --mem=${MEM_GB}G --time=${TIME_H}:00:00 --cpus-per-task=${CPUS}"
-    mkdir -p /scratch/users/ymo/add_umap_logs
+    mkdir -p "$LOG_DIR"
     # Absolute self-reference so this works regardless of the caller's cwd.
     # ADD_UMAP_INJOB=1 is what makes the submitted copy run the workload instead of
     # re-submitting again; --export=ALL keeps the rest of the environment.
     exec sbatch --mem="${MEM_GB}G" \
                 --time="${TIME_H}:00:00" \
                 --cpus-per-task="${CPUS}" \
-                --export=ALL,ADD_UMAP_INJOB=1 \
+                --output="$LOG_DIR/%j.out" \
+                --error="$LOG_DIR/%j.err" \
+                --export=ALL,ADD_UMAP_INJOB=1,ADD_UMAP_LOG_DIR="$LOG_DIR" \
                 "$SCRIPT_DIR/run_add_umap.sh" "$@"
 fi
 
@@ -115,8 +127,6 @@ echo "h5mu: $MDATA_PATH"
 echo "Size: $(du -h "$MDATA_PATH" | cut -f1)"
 echo "Extra args: ${EXTRA_ARGS[*]}"
 
-mkdir -p /scratch/users/ymo/add_umap_logs
-
 echo "Activating conda environment: NMF_Benchmarking"
 eval "$(conda shell.bash hook)"
 conda activate NMF_Benchmarking

CHANGELOG.md

@@ -22,6 +22,9 @@ Entries marked ⚠️ change pipeline output — re-run affected analyses.
   repo from their own location instead of a hardcoded checkout path.
 - Annotation defaults are cell-type neutral; the PubMed keyword is optional, and
   Vertex AI project/bucket come from env vars (`VERTEX_PROJECT_ID`, `VERTEX_BUCKET`).
+- Annotation runners locate their scripts via `PIPELINE_ROOT` (fixing paths into a
+  nonexistent `AGeneTic/` folder); `gpe_export.py` reads the GeneProgramExplorer
+  location from `GPE_DIR`.
 
 ### Added
 - `tools/check_no_lab_specific_content.py` guard (CI + pre-commit) that blocks

src/Stage2_Evaluation/A_Metrics/src/association_categorical.py

@@ -365,7 +365,7 @@ def compute_categorical_association(
 
     # If test = 'pearsonr' with mode = 'one_vs_all' we are going to do something special until we can more properly integrate this
     if test=='pearsonr' and mode=='one_vs_all':
-        logging.info('Running jamboree specific version of posthoc with pearsonr, this is not yet integrated into the main pipeline')
+        logging.info('Running a one-vs-all pearsonr version of posthoc, this is not yet integrated into the main pipeline')
         res = []        
         # Run posthoc-tests and append results
         Parallel(n_jobs=n_jobs,

src/Stage3_Interpretation/C_Annotation/0.Prepare/Extract_program_information.py

@@ -284,7 +284,7 @@ def build_parser():
 
     # context info
     p.add_argument("--programs", type=int, nargs="+", help="Program ids, space separated (e.g. 1 2 3). Default: all.")
-    p.add_argument("--cell_type", default="", help="Cell type, e.g. 'teloHAEC aortic endothelial cell'.")
+    p.add_argument("--cell_type", default="", help="Cell type, e.g. 'aortic endothelial cell'.")
     p.add_argument("--organism", default="human")
 
     # select top items of the program

src/Stage3_Interpretation/C_Annotation/0.Prepare/run_extract_program_information.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=extract_prog_info
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=00:30:00
 #SBATCH --cpus-per-task=4
 #SBATCH --mem=16GB
@@ -17,11 +17,13 @@
 # literature steps investigate exactly these pairs.
 
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate NMF_Benchmarking
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/0.Prepare
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/0.Prepare"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 OUT=$RESULT/Interpretation/AGeneTic_test
 
 python $SCRIPT_DIR/Extract_program_information.py \
@@ -35,7 +37,7 @@ python $SCRIPT_DIR/Extract_program_information.py \
   --gene_name_key var_names \
   --categorical_key type \
   --log2fc_key log2FC \
-  --cell_type "teloHAEC aortic endothelial cell" \
+  --cell_type "aortic endothelial cell" \
   --organism human \
   --top_gene 15 \
   --top_unique_gene 8 \

src/Stage3_Interpretation/C_Annotation/1.Search/1.1.Search_literature/search_nature.py

@@ -13,11 +13,11 @@
 
 # Nature portfolio search (Crossref, DOI prefix 10.1038) + PDF download from nature.com.
 #
-# PDFs come from nature.com under Stanford's institutional subscription, which Nature grants
-# by IP address: it works from Sherlock / campus / Stanford VPN (Sherlock egresses from a
-# Stanford 171.67.x address) with no SUNet login. Off the Stanford network, only open-access
-# articles download. Stanford's license covers research use, not bulk harvesting, so results
-# are capped and PDF requests are spaced out.
+# PDFs come from nature.com under an institutional subscription, which Nature grants by IP
+# address: it works from a network covered by your institution's license (campus, VPN, or a
+# cluster that egresses from an institutional address) with no login. Elsewhere, only
+# open-access articles download. Institutional licenses cover research use, not bulk
+# harvesting, so results are capped and PDF requests are spaced out.
 CROSSREF_BASE_URL = "https://api.crossref.org"
 NATURE_BASE_URL = "https://www.nature.com"
 NATURE_DOI_PREFIX = "10.1038"
@@ -122,7 +122,7 @@ def search_Nature(
        bibliographic (title, authors, journal, year) via Crossref, restricted to DOI prefix 10.1038
     2. Adding a journal name or year to the query biases toward it (e.g. "... Nature Genetics 2023")
     3. Only journal articles are returned (no news, editorials split out by Crossref type)
-    4. PDF download uses Stanford's subscription by IP: run on Sherlock / campus / Stanford VPN
+    4. PDF download uses an institutional subscription by IP: run on a licensed network
 
     Env (optional): CROSSREF_MAILTO / PUBMED_EMAIL (Crossref polite pool). No API key needed.
 
@@ -168,7 +168,7 @@ def search_Nature(
             pdf_path, msg = download_paper(out_dir, f"nature_{rec['article_id']}",
                                            doi=rec["doi"], pdf_urls=[rec["pdf_url"]])
             if not pdf_path:
-                msg += "; is this running on the Stanford network (Sherlock / campus / VPN)?"
+                msg += "; is this running on a network with institutional access (campus / VPN)?"
             downloads.append((rec["title"], pdf_path, msg))
             pdf_line = '\n' + 'PDF: ' + (pdf_path or f'Not downloaded ({msg})')
 
@@ -177,7 +177,7 @@ def search_Nature(
     if out_dir:
         report_downloads("Nature", query, downloads, out_dir)
 
-    return "\n".join(data_list) + '\n' + "Data source: Nature (nature.com, Stanford subscription)"
+    return "\n".join(data_list) + '\n' + "Data source: Nature (nature.com, institutional subscription)"
 
 
 if __name__ == "__main__":

src/Stage3_Interpretation/C_Annotation/1.Search/run_MyGene.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=mygene_extend
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=00:15:00
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=4GB
@@ -15,11 +15,13 @@
 # --programs (required) takes space-separated ids (e.g. 1 2 3); only those P<k>.json are read.
 
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate NMF_Benchmarking
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/1.Search/1.0.Search_database/search_gene
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/1.Search/1.0.Search_database/search_gene"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 BUNDLE_DIR=$RESULT/Interpretation/AGeneTic_test/PerturbNMF_Info 
 OVERWRITE=""   # default off; set to --overwrite to re-query genes that already have MyGene info
 OUT_DIR=$RESULT/Interpretation/AGeneTic_test/Gene_info_extended_PerturbNMF_Info

src/Stage3_Interpretation/C_Annotation/1.Search/run_NCBI.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=ncbi_extend
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=00:15:00
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=4GB
@@ -16,11 +16,13 @@
 
 # Optional: export NCBI_API_KEY (10 req/s instead of 3) and NCBI_EMAIL.
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate NMF_Benchmarking
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/1.Search/1.0.Search_database/search_gene
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/1.Search/1.0.Search_database/search_gene"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 BUNDLE_DIR=$RESULT/Interpretation/AGeneTic_test/PerturbNMF_Info
 OVERWRITE=""   # default off; set to --overwrite to re-query genes that already have NCBI info
 OUT_DIR=$RESULT/Interpretation/AGeneTic_test/Gene_info_extended_PerturbNMF_Info

src/Stage3_Interpretation/C_Annotation/1.Search/run_OmniPath.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=omnipath_interact
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=00:30:00
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=4GB
@@ -18,11 +18,13 @@
 # --programs (required) takes space-separated ids (e.g. 1 2 3); only those P<k>.json are read.
 
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate NMF_Benchmarking
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/1.Search/1.0.Search_database/search_gene_interaction
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/1.Search/1.0.Search_database/search_gene_interaction"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 BUNDLE_DIR=$RESULT/Interpretation/AGeneTic_test/PerturbNMF_Info
 
 python $SCRIPT_DIR/search_OmniPath.py \

src/Stage3_Interpretation/C_Annotation/1.Search/run_UniProt.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=uniprot_extend
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=00:15:00
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=4GB
@@ -15,11 +15,13 @@
 # --programs (required) takes space-separated ids (e.g. 1 2 3); only those P<k>.json are read.
 
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate NMF_Benchmarking
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/1.Search/1.0.Search_database/search_gene
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/1.Search/1.0.Search_database/search_gene"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 BUNDLE_DIR=$RESULT/Interpretation/AGeneTic_test/PerturbNMF_Info
 OVERWRITE=""   # default off; set to --overwrite to re-query genes that already have UniProt info
 OUT_DIR=$RESULT/Interpretation/AGeneTic_test/Gene_info_extended_PerturbNMF_Info

src/Stage3_Interpretation/C_Annotation/1.Search/run_literature_search.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=lit_search
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=04:00:00
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=8GB
@@ -14,11 +14,13 @@
 # Tasks with a search_log.json are skipped; add --overwrite to re-search.
 # Uses the Claude Agent SDK (ANTHROPIC_API_KEY or a Claude Code login); spend is capped per task.
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate geneqa
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/1.Search
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/1.Search"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 INFO_DIR=$RESULT/Interpretation/AGeneTic_test/Gene_info_extended_PerturbNMF_Info
 LIT_DIR=$RESULT/Interpretation/AGeneTic_test/Literature_info_extended_PerturbNMF_Info
 OVERWRITE=""   # set to --overwrite to re-search

src/Stage3_Interpretation/C_Annotation/1.Search/run_llm_query_agent.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --job-name=lit_query_agent
-#SBATCH -p normal
+#SBATCH -p <partition>
 #SBATCH --time=00:30:00
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=4GB
@@ -14,11 +14,13 @@
 # agent sees which genes lack cell-type evidence (optional). Programs that already have the plan are
 # skipped; add --overwrite to re-plan. Needs ANTHROPIC_API_KEY in AGeneTic/.env.
 set -euo pipefail
-source /oak/stanford/groups/engreitz/Users/ymo/miniforge3/etc/profile.d/conda.sh
+eval "$(conda shell.bash hook)"
 conda activate geneqa
 
-SCRIPT_DIR=/oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/src/Stage3_Interpretation/C_Annotation/AGeneTic/1.Search
-RESULT=/oak/stanford/groups/engreitz/Users/ymo/Project/Helen_telohaec/Result/073126_2kG_torch_e8_64
+# Path to your PerturbNMF checkout (export PIPELINE_ROOT=/path/to/PerturbNMF before sbatch)
+: "${PIPELINE_ROOT:?set PIPELINE_ROOT to the PerturbNMF repo root}"
+SCRIPT_DIR="$PIPELINE_ROOT/src/Stage3_Interpretation/C_Annotation/1.Search"
+RESULT="/path/to/output_dir/<run_name>"   # edit: run directory with Interpretation/
 INFO_DIR=$RESULT/Interpretation/AGeneTic_test/Gene_info_extended_PerturbNMF_Info
 OUT_DIR=$RESULT/Interpretation/AGeneTic_test/Literature_info_extended_PerturbNMF_Info
 QUESTION=()                       # e.g. QUESTION=(--question "why does VIRMA knockdown reduce translation genes" --plan_name virma)