LABLOOP · THE DECK

455 CARDS · 41 WEEKS · EVERY SOURCE THE PLAN NAMES

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171 cards shown. Stashes: LABLOOP-W00 Notebook (15) LABLOOP-W01 Notebook (18) LABLOOP-W02 Notebook (15) LABLOOP-W03 Notebook (19) LABLOOP-W04 Notebook (17) LABLOOP-W05 Notebook (16) LABLOOP-W06 Notebook (12) LABLOOP-W07 Notebook (12) LABLOOP-W08 Notebook (15) LABLOOP-W09 Notebook (10) LABLOOP-W10 Notebook (11) LABLOOP-W11 Notebook (12) LABLOOP-W12 Notebook (12) LABLOOP-W13 Notebook (13) LABLOOP-W14 Notebook (12) LABLOOP-W15 Notebook (10) LABLOOP-W16 Notebook (14) LABLOOP-W17 Notebook (13) LABLOOP-W18 Notebook (10) LABLOOP-W19 Notebook (10) LABLOOP-W20 Notebook (10) LABLOOP-W21 Notebook (13) LABLOOP-W22 Notebook (10) LABLOOP-W23 Notebook (9) LABLOOP-W24 Notebook (9) LABLOOP-W25 Notebook (12) LABLOOP-W26 Notebook (11) LABLOOP-W27 Notebook (10) LABLOOP-W28 Notebook (6) LABLOOP-W29 Notebook (7) LABLOOP-W30 Notebook (10) LABLOOP-W31 Notebook (8) LABLOOP-W32 Notebook (5) LABLOOP-W33 Notebook (13) LABLOOP-W34 Notebook (12) LABLOOP-W35 Notebook (10) LABLOOP-W36 Notebook (8) LABLOOP-W37 Notebook (7) LABLOOP-W38 Notebook (6) LABLOOP-W39 Notebook (6) LABLOOP-W40 Notebook (6)

4/15 Run 30 min? W00 Saturday Sandbox optional

Good enough practices in scientific computing, Wilson et al., PLoS Computational Biology 2017. T…

Saturday sandbox

Good enough practices in scientific computing, Wilson et al., PLoS Computational Biology 2017. The repo habits you are setting up today, justified

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In: LABLOOP-W00 Notebook

7/15 Run 30 min? W00 Saturday Sandbox optional

carpentries-lab/good-enough-practices

Saturday sandbox · after Elliot Hershberg, Century of Biology newsletter

carpentries-lab/good-enough-practices — the lesson version of R3, if you would rather do it than read it

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In: LABLOOP-W00 Notebook

12/15 Run 30 min W00 Build

astral-sh/uv

uv init batchlens && uv add numpy scipy pandas matplotlib; your environment manager for all 40 weeks

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In: LABLOOP-W00 Notebook

13/15 Run 30 min W00 Build

ollama/ollama

ollama run qwen2.5:7b-instruct-q4_K_M "explain Monod growth in two sentences"; confirm it fits the 3050

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In: LABLOOP-W00 Notebook

14/15 Run 30 min W00 Build

drivendataorg/cookiecutter-data-science

Read the folder structure in the README; copy only the ideas (data/raw never committed, reports/figures) into your skeletons

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In: LABLOOP-W00 Notebook

15/15 Run 30 min W00 Build

the-turing-way/the-turing-way

Browse the "Guide for reproducible research" table of contents; save two checklists to PARKING.md

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In: LABLOOP-W00 Notebook

15/18 Run 30 min W01 Build

jakevdp/PythonDataScienceHandbook

Colab: notebook 02.00-Introduction-to-NumPy and 02.02-The-Basics-Of-NumPy-Arrays; re-do the 3Blue1Brown matrix-on-vector examples in NumPy

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In: LABLOOP-W01 Notebook

16/18 Run 30 min W01 Build

fastai/numerical-linear-algebra

Colab: lesson 1 notebook; skim, run the first cells. Linear algebra as computation, not proofs

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In: LABLOOP-W01 Notebook

17/18 Run 30 min W01 Build

scipy/scipy

Copy the solve_ivp Lotka-Volterra example; replace predator-prey with biomass-substrate. This is 70% of your Monday task

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In: LABLOOP-W01 Notebook

18/18 Run 30 min W01 Build

Pioreactor/pioreactor

Read README and the docs page on growth-rate estimation; no hardware needed. Shows how real online signals look

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In: LABLOOP-W01 Notebook

9/15 Run 30 min? W02 Saturday Sandbox optional

Deisenroth, Faisal & Ong, Mathematics for Machine Learning, ch. 10 "Dimensionality Reduction wit…

Saturday sandbox · after Steve Brunton

Deisenroth, Faisal & Ong, Mathematics for Machine Learning, ch. 10 "Dimensionality Reduction with PCA" — free PDF at mml-book.github.io

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In: LABLOOP-W02 Notebook

12/15 Run 30 min W02 Build

StephenGoldie/indpensim-notebook

Open IndPenSim_Summary_data_notebook_V3.ipynb in Colab; compare their variable list with your tidy table

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In: LABLOOP-W02 Notebook

13/15 Run 30 min W02 Build

jakevdp/PythonDataScienceHandbook

Colab: 03.08-Aggregation-and-Grouping and 05.09-Principal-Component-Analysis

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In: LABLOOP-W02 Notebook

14/15 Run 30 min W02 Build

scikit-learn/scikit-learn

Run the gallery example "PCA example with Iris Data-set", then swap Iris for 20 IndPenSim batches unfolded

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In: LABLOOP-W02 Notebook

15/15 Run 30 min W02 Build

pandas-dev/pandas / pola-rs/polars

melt your wide CSVs to long format, save as parquet; time both libraries on the 100 batches

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In: LABLOOP-W02 Notebook

14/20 Run 30 min? W03 Saturday Sandbox optional

Nomikos P. & MacGregor J.F., "Multivariate SPC Charts for Monitoring Batch Processes", Technomet…

Saturday sandbox · after Stanford Online · Statistical Learning with Python

Nomikos P. & MacGregor J.F., "Multivariate SPC Charts for Monitoring Batch Processes", Technometrics 37(1):41-59, 1995. DOI 10.1080/00401706.1995.10485888 · author PDF mirror: three-mode.leidenuniv.nl/pdf/n/nomikosmacgregor1995tmet.pdf. The founding paper of batch MSPC — abstract and figures are enough. Cite it in week 08's report

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In: LABLOOP-W03 Notebook

16/20 Run 30 min? W03 Saturday Sandbox optional

salvadorgarciamunoz/pyphi

Saturday sandbox · after Kourti T. & MacGregor J.F., "Process analysis, monitoring and diagnosis, using multivariate proj…

salvadorgarciamunoz/pyphi — a pharma practitioner's PCA/PLS with T² and SPE. Niche, but written by someone who does this for a living

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In: LABLOOP-W03 Notebook

18/20 Run 30 min W03 Build

intro-stat-learning/ISLP_labs

Colab: Ch02-statlearn-lab.ipynb, then Ch03-linreg-lab.ipynb; redo the regression on two IndPenSim variables

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In: LABLOOP-W03 Notebook

19/20 Run 30 min W03 Build

erdogant/pca

Its README shows Hotelling T² and SPE outlier detection on top of PCA; run the example, then compare its limits with yours (never ship its numbers without understanding them)

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In: LABLOOP-W03 Notebook

20/20 Run 30 min W03 Build

statsmodels/statsmodels

Fit an OLS on two variables and read the summary table line by line with ISLP ch. 3 open

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In: LABLOOP-W03 Notebook

11/17 Run 30 min? W04 Saturday Sandbox optional

carpentries-lab/good-enough-practices

Saturday sandbox · after The Turing Way — book.the-turing-way.org, chapters on "Version control"

carpentries-lab/good-enough-practices — the hands-on lesson behind week 00's R3

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In: LABLOOP-W04 Notebook

12/17 Run 30 min? W04 Saturday Sandbox optional

Zenodo help

Saturday sandbox · after carpentries-lab/good-enough-practices

Zenodo help — versioning and GitHub integration, if the DOI badge misbehaves

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In: LABLOOP-W04 Notebook

14/17 Run 30 min W04 Build

intro-stat-learning/ISLP_labs

Colab: Ch05-resample-lab.ipynb; then rewrite one cell using GroupKFold with batch as the group

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In: LABLOOP-W04 Notebook

15/17 Run 30 min W04 Build

scikit-learn/scikit-learn

User guide "Cross-validation: evaluating estimator performance", section on group-wise splitters; run the visualization example "Visualizing cross-validation behavior"

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In: LABLOOP-W04 Notebook

16/17 Run 30 min W04 Build

google-research/tuning_playbook

Read only the section on evaluation and "incremental tuning"; one page of habits you will reuse in weeks 8 and 17

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In: LABLOOP-W04 Notebook

17/17 Run 30 min W04 Build

drivendataorg/cookiecutter-data-science

Compare your Makefile with its conventions; add make report FAKE=1

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In: LABLOOP-W04 Notebook

12/16 Run 30 min W05 Build

J535D165/pyalex

Query OpenAlex for works on "fed-batch fermentation titer" per year; plot counts. Tells you the size of the ocean before you fish

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In: LABLOOP-W05 Notebook

13/16 Run 30 min W05 Build

danielnsilva/semanticscholar

Search Semantic Scholar for "literature-derived fermentation dataset"; save the top 20 to RELATED.md with citation counts

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In: LABLOOP-W05 Notebook

14/16 Run 30 min W05 Build

titipata/pubmed_parser

Parse one PMC OA XML into title, abstract, methods paragraphs; this becomes corpus/parse.py

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In: LABLOOP-W05 Notebook

15/16 Run 30 min W05 Build

google/langextract

Read the README and run the quickstart example: extraction with source grounding (every value mapped to its exact span). This is the provenance idea FermLit needs, already implemented

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In: LABLOOP-W05 Notebook

16/16 Run 30 min W05 Build

intro-stat-learning/ISLP_labs

Colab: Ch08-baggboost-lab.ipynb (trees and boosting)

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In: LABLOOP-W05 Notebook

8/12 Run 30 min? W06 Saturday Sandbox optional

STRENDA guidelines (Standards for Reporting Enzymology Data) — search "STRENDA guidelines"

Saturday sandbox · after 3Blue1Brown "Bayes theorem, the geometry of changing beliefs"

STRENDA guidelines (Standards for Reporting Enzymology Data) — search "STRENDA guidelines" (verify URL). A real "minimum information" standard; it shows what a reporting checklist looks like and will inspire your completeness analysis

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In: LABLOOP-W06 Notebook

9/12 Run 30 min W06 Build

HumanSignal/label-studio

pip install label-studio, create a text-span project with 5 FermLit fields; annotate 2 papers to feel the difference from JSON-by-hand. Use it only if it speeds you up

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In: LABLOOP-W06 Notebook

10/12 Run 15 min W06 Build

doccano/doccano

Lighter alternative for span annotation; compare in 15 minutes, pick one, never revisit

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In: LABLOOP-W06 Notebook

11/12 Run 30 min W06 Build

argilla-io/argilla

Read the "human feedback on LLM outputs" quickstart; you will use this pattern in week 7 to correct agent outputs

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In: LABLOOP-W06 Notebook

12/12 Run 30 min W06 Build

pymc-devs/pymc-resources

Colab: Statistical Rethinking chapter 2 notebook (grid approximation); do the globe-tossing update by hand, then in code

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In: LABLOOP-W06 Notebook

5/12 Run 30 min? W07 Saturday Sandbox optional

Anthropic Claude Cookbooks (github.com/anthropics/claude-cookbooks) — "extracting structured JSON"

Saturday sandbox

Anthropic Claude Cookbooks (github.com/anthropics/claude-cookbooks) — "extracting structured JSON" and "tool use" recipes

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In: LABLOOP-W07 Notebook

9/12 Run 30 min W07 Build

567-labs/instructor

Define your schema as a Pydantic model and let instructor enforce valid JSON from Claude and Ollama; kills 80% of parsing bugs

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In: LABLOOP-W07 Notebook

10/12 Run 30 min W07 Build

google/langextract

Run an example in examples/notebooks with a local Ollama model; compare its grounded spans with your provenance sentences

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In: LABLOOP-W07 Notebook

11/12 Run 30 min W07 Build

stanfordnlp/dspy

Tutorial on "information extraction" in the docs: define a signature, a metric (your F1), and let an optimizer improve the prompt. Only after your manual baseline exists

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In: LABLOOP-W07 Notebook

12/12 Run 30 min W07 Build

lmfit/lmfit-py

Fit Michaelis-Menten to a small public dataset with confidence intervals on Km and Vmax

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In: LABLOOP-W07 Notebook

1/15 Run 30 min? W08 Monday Craft

Luttmann et al. (2012), "Soft sensors in bioprocessing: a status report and recommendations"

Monday build block · Read it inside Monday's build block

Build-block reading · Luttmann et al. (2012), "Soft sensors in bioprocessing: a status report and recommendations", Biotechnology Journal 7(8):1040-1048. The reference framing for your soft-sensor section

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In: LABLOOP-W08 Notebook

7/15 Run 30 min? W08 Saturday Sandbox optional

Stanford CS231n notes "Backpropagation, intuitions"

Saturday sandbox · after 3Blue1Brown Neural Networks ch. 3-4 ("Backpropagation, intuitively"

Stanford CS231n notes "Backpropagation, intuitions" (cs231n.github.io/optimization-2) — a classic written explanation

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In: LABLOOP-W08 Notebook

10/15 Run 30 min W08 Build

karpathy/micrograd

Read engine.py (~100 lines); run demo.ipynb in Colab; then close it and rewrite from memory on Saturday

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In: LABLOOP-W08 Notebook

11/15 Run 30 min W08 Build

karpathy/nn-zero-to-hero

Lecture notebooks under lectures/micrograd; follow along with the video

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In: LABLOOP-W08 Notebook

12/15 Run 30 min W08 Build

lightgbm-org/LightGBM

Python quickstart regression; train on your unfolded features with batch-wise CV

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In: LABLOOP-W08 Notebook

13/15 Run 30 min W08 Build

rlabbe/Kalman-and-Bayesian-Filters-in-Python

Colab: chapter 1 "The g-h filter". The intuition behind estimating a hidden variable from noisy sensors, which is what a soft sensor does

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In: LABLOOP-W08 Notebook

14/15 Run 30 min W08 Build

JustusvLiebig/Soft_Sensor_Experiments

Browse the model zoo for industrial soft sensors; note which baselines they compare, to justify your LightGBM vs PLS choice

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In: LABLOOP-W08 Notebook

15/15 Run 30 min W08 Build

quarto-dev/quarto-cli

quarto create project manuscript; build a PDF with one figure regenerated from code

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In: LABLOOP-W08 Notebook

7/10 Run 30 min W09 Build

karpathy/makemore

Run makemore.py on a text file of 2,000 organism names extracted by FermLit; sample new "organisms" for fun

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In: LABLOOP-W09 Notebook

8/10 Run 30 min W09 Build

karpathy/nn-zero-to-hero

lectures/makemore part 1 notebook in Colab

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In: LABLOOP-W09 Notebook

9/10 Run 30 min W09 Build

UKGovernmentBEIS/inspect_ai

Read the "Tutorial" page; model your batch extraction as an eval task with logged cost and tokens (the Vara telemetry idea, done by a government AI institute)

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In: LABLOOP-W09 Notebook

10/10 Run 30 min W09 Build

ollama/ollama

Benchmark tokens/second of your local Qwen 7B on 20 papers; add the row to the cost table

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In: LABLOOP-W09 Notebook

8/11 Run 30 min W10 Build

scikit-learn/scikit-learn

sklearn.metrics.cohen_kappa_score per field; gallery example "Gaussian process regression: basic introductory example"

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In: LABLOOP-W10 Notebook

9/11 Run 30 min W10 Build

cornellius-gp/gpytorch

"Simple GP Regression" tutorial notebook in Colab; add predictive variance bands to one soft-sensor feature

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In: LABLOOP-W10 Notebook

10/11 Run 30 min W10 Build

pln-fing-udelar/fast-krippendorff

Compute alpha on the same annotations; compare with kappa and write one sentence on why they differ

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In: LABLOOP-W10 Notebook

11/11 Run 30 min W10 Build

plotly/plotly.py / mwaskom/seaborn

Build figure 1 (completeness by field) as a static, publication-ready image

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In: LABLOOP-W10 Notebook

9/12 Run 30 min W11 Build

meta-pytorch/botorch

Tutorial closed_loop_botorch_only in Colab; replace the test function with your simulator's final titer as a function of 2 feed parameters

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In: LABLOOP-W11 Notebook

10/12 Run 30 min W11 Build

facebook/Ax

"Getting started" BO loop in 10 lines; the higher-level alternative if BoTorch feels heavy

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In: LABLOOP-W11 Notebook

11/12 Run 30 min W11 Build

biopython/biopython

Bio.Entrez to map 20 organism names to taxonomy IDs; cache results

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In: LABLOOP-W11 Notebook

12/12 Run 30 min W11 Build

huggingface/datasets (docs)

Create a private dataset repo, push a 100-row sample with a card; check the viewer renders

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In: LABLOOP-W11 Notebook

9/12 Run 30 min W12 Build

dynamicslab/pysindy

Colab: examples/tutorial_1; then feed it X and S from your simulator and see whether it recovers a Monod-like term

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In: LABLOOP-W12 Notebook

10/12 Run 30 min W12 Build

dynamicslab/databook_python

The book's Python notebooks for chapter 7 (SINDy) in Colab

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In: LABLOOP-W12 Notebook

11/12 Run 30 min W12 Build

jrcramos/Hybrid-modeling-of-bioreactor-with-LSTM

Read the README and model structure; a published example of "mechanistic + neural" for cell culture to compare against your "Monod + GBM"

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In: LABLOOP-W12 Notebook

12/12 Run 30 min W12 Build

casadi/casadi

Optional: fit Monod parameters per batch with an optimizer; only if scipy.optimize struggles

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In: LABLOOP-W12 Notebook

10/13 Run 30 min W13 Build

rtqichen/torchdiffeq

examples/ode_demo.py: learn a spiral's dynamics; read how a neural network replaces the right-hand side of an ODE

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In: LABLOOP-W13 Notebook

11/13 Run 30 min W13 Build

patrick-kidger/diffrax

Optional JAX alternative with excellent docs on neural ODEs

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In: LABLOOP-W13 Notebook

12/13 Run 30 min W13 Build

quarto-dev/quarto-cli

Put the Paper 1 skeleton into a Quarto manuscript; make paper builds a PDF with placeholder figures

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In: LABLOOP-W13 Notebook

13/13 Run 30 min W13 Build

huggingface/notebooks

Browse the datasets examples for pushing a dataset with a card from code

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In: LABLOOP-W13 Notebook

9/12 Run 30 min W14 Build

statsmodels/statsmodels

statsmodels.stats.multitest.multipletests with fdr_bh on the journal comparison; report adjusted p-values

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In: LABLOOP-W14 Notebook

10/12 Run 30 min W14 Build

UKGovernmentBEIS/inspect_ai

Implement the fuzzy-field judge as a scorer; log judge vs human agreement on 50 pairs

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In: LABLOOP-W14 Notebook

11/12 Run 30 min W14 Build

EleutherAI/lm-evaluation-harness

Read how tasks define metrics and few-shot prompts; borrow the discipline, not the tool

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In: LABLOOP-W14 Notebook

12/12 Run 30 min W14 Build

Future-House/paper-qa

Point it at your RELATED.md PDFs and ask "which of these papers report inter-annotator agreement?" to double-check your related-work claims (verify every answer by opening the paper)

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In: LABLOOP-W14 Notebook

7/10 Run 30 min W15 Build

allenai/scispacy

Run a biomedical NER model on 3 FermLit papers; compare what it finds (organisms, chemicals) with your agent's extraction. A classic baseline reviewers may ask about

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In: LABLOOP-W15 Notebook

8/10 Run 30 min W15 Build

grobidOrg/grobid

Parse one PDF-only paper into TEI XML; note how references and sections are recovered. Useful for the non-XML tail of the corpus

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In: LABLOOP-W15 Notebook

9/10 Run 30 min W15 Build

docling-project/docling

Convert the same PDF with Docling; compare tables extraction with GROBID

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In: LABLOOP-W15 Notebook

10/10 Run 30 min W15 Build

quarto-dev/quarto-cli

Final make paper; check figures regenerate from a clean clone

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In: LABLOOP-W15 Notebook

10/14 Run 30 min W16 Build

huggingface/notebooks

Colab: examples/protein_language_modeling.ipynb — fine-tune/embed with ESM-2 through transformers; switch the model to facebook/esm2_t33_650M_UR50D in fp16 on your 3050

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In: LABLOOP-W16 Notebook

11/14 Run 30 min W16 Build

facebookresearch/esm

Read the README's "ESM-2" and embedding extraction sections; the original reference

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In: LABLOOP-W16 Notebook

12/14 Run 30 min W16 Build

evolutionaryscale/esm (now redirects to Biohub/esm)

Read only; the newer ESM C/ESM3 family. Parked for Half 2

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In: LABLOOP-W16 Notebook

13/14 Run 30 min W16 Build

aangelopoulos/conformal-prediction

Colab: notebooks/meps-cqr.ipynb (conformalized quantile regression on tabular data); map it onto your soft sensor

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In: LABLOOP-W16 Notebook

14/14 Run 30 min W16 Build

scikit-learn-contrib/MAPIE

Regression example with SplitConformalRegressor (or the current API); get coverage on held-out batches in 20 lines

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In: LABLOOP-W16 Notebook

7/13 Run 30 min? W17 Saturday Sandbox optional

Andrew White, Deep Learning for Molecules and Materials — dmol.pub, chapter on "Deep learning on…

Saturday sandbox · after Notin et al. (2023), "ProteinGym: large-scale benchmarks for protein fitness prediction and desi…

Andrew White, Deep Learning for Molecules and Materials — dmol.pub, chapter on "Deep learning on sequences" (with Colab buttons)

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In: LABLOOP-W17 Notebook

9/13 Run 30 min W17 Build

J-SNACKKB/FLIP

Download the meltome splits; read the README on "mixed", "human" and "human_cell" splits; load them with pandas

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In: LABLOOP-W17 Notebook

10/13 Run 30 min W17 Build

OATML-Markslab/ProteinGym

Browse the leaderboard page and the baselines list; note where ESM-2 sits

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In: LABLOOP-W17 Notebook

11/13 Run 30 min W17 Build

huggingface/notebooks

Reuse protein_language_modeling.ipynb to cache mean-pooled embeddings to disk

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In: LABLOOP-W17 Notebook

12/13 Run 30 min W17 Build

yangkky/Machine-learning-for-proteins

The curated reading list by Kevin Yang; pick 2 papers for PARKING.md, not more

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In: LABLOOP-W17 Notebook

13/13 Run 30 min W17 Build

scikit-learn/scikit-learn

RidgeCV on embeddings → melting temperature; report Spearman correlation with a bootstrap interval

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In: LABLOOP-W17 Notebook

7/10 Run 30 min W18 Build

quarto-dev/quarto-cli

Paper 2 manuscript project; cross-references for figures and equations

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In: LABLOOP-W18 Notebook

8/10 Run 30 min W18 Build

lukasmasuch/best-of-ml-python

Check the "interpretability" and "time series" sections for any widely used soft-sensor baseline you forgot to cite

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In: LABLOOP-W18 Notebook

9/10 Run 30 min W18 Build

google-research/tuning_playbook

Re-read "scientific vs nuisance hyperparameters" and write two sentences in Methods on how you tuned fairly across arms

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In: LABLOOP-W18 Notebook

10/10 Run 30 min W18 Build

paper-2-hybrid-softsensor (your repo)

Clean clone → make figs → compare hashes with your local figures

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In: LABLOOP-W18 Notebook

2/10 Run 40 min W19 Thursday AI & stats

Modern Statistics for Modern Biology sections on reporting and ISLP

Modern Statistics for Modern Biology sections on reporting and ISLP ch. 5.2 (bootstrap) re-read (40 min); apply bootstrap intervals across both papers

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In: LABLOOP-W19 Notebook

8/10 Run 30 min W19 Build

scverse/scanpy

PBMC 3k tutorial notebook (in the docs; scverse/scanpy-tutorials is archived, ★ 242) in Colab

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In: LABLOOP-W19 Notebook

9/10 Run 30 min W19 Build

theislab/single-cell-best-practices

Run the quality-control notebook on the same data; compare cell counts after filtering

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In: LABLOOP-W19 Notebook

10/10 Run 30 min W19 Build

scipy/scipy

scipy.stats.bootstrap on your key metrics; replace every naked number in both papers

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In: LABLOOP-W19 Notebook

8/10 Run 30 min W20 Build

marimo-team/marimo

Turn the Paper 2 learning curve into a reactive notebook with a slider for number of batches; share it as the "try it yourself" link in the arXiv abstract

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In: LABLOOP-W20 Notebook

9/10 Run 30 min W20 Build

quarto-dev/quarto-cli

Build the arXiv-ready LaTeX source from Quarto; check it compiles in arXiv's TeX Live

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In: LABLOOP-W20 Notebook

10/10 Run 30 min W20 Build

your repos

Tag paper-2-v1.0 and mint a Zenodo DOI for the exact code used

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In: LABLOOP-W20 Notebook

9/13 Run 30 min W21 Build

ievapudz/TemStaPro

Run it on 50 Meltome sequences; compare its predictions with your ridge head. This is your most relevant external baseline

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In: LABLOOP-W21 Notebook

10/13 Run 30 min W21 Build

J-SNACKKB/FLIP

Use their exact splits so your numbers are comparable with the paper

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In: LABLOOP-W21 Notebook

11/13 Run 30 min W21 Build

huggingface/transformers

EsmModel with torch_dtype=torch.float16; batch by sequence length to fit 6 GB

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In: LABLOOP-W21 Notebook

12/13 Run 30 min W21 Build

agemagician/ProtTrans

Read the README; note ProtT5 as an alternative embedding for the ablation you might run in week 22

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In: LABLOOP-W21 Notebook

13/13 Run 30 min W21 Build

biopython/biopython

Bio.SeqIO to read and length-filter FASTA; drop sequences > 1,022 residues or chunk them

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In: LABLOOP-W21 Notebook

7/10 Run 30 min W22 Build

py-why/dowhy

Run the "getting started" notebook; draw a DAG for "organism growth temperature → sequence composition → Tm" to see where confounding lives

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In: LABLOOP-W22 Notebook

8/10 Run 30 min W22 Build

scikit-learn/scikit-learn

GroupKFold / StratifiedGroupKFold with sequence-cluster IDs

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In: LABLOOP-W22 Notebook

9/10 Run 30 min W22 Build

scikit-learn-contrib/MAPIE

Conformal intervals on the grouped folds; report coverage per fold

Open ↗

In: LABLOOP-W22 Notebook

10/10 Run 30 min W22 Build

soedinglab/MMseqs2

mmseqs easy-cluster on Meltome FASTA at 30% identity; save cluster TSV

Open ↗

In: LABLOOP-W22 Notebook

6/9 Run 30 min W23 Build

biopython/biopython

Parse UniProt FASTA, compute length and composition features as a sanity baseline next to embeddings

Open ↗

In: LABLOOP-W23 Notebook

7/9 Run 30 min W23 Build

sokrypton/ColabFold

Colab: predict the structure of your top 2 candidates; look at them in 3D. Not used as a feature, only to build intuition and a figure

Open ↗

In: LABLOOP-W23 Notebook

8/9 Run 30 min W23 Build

google-deepmind/alphafold

Read the README on the AlphaFold Protein Structure Database; check if your candidates already have predicted structures there (no GPU needed)

Open ↗

In: LABLOOP-W23 Notebook

9/9 Run 30 min W23 Build

deepchem/deepchem

Browse "The Basic Tools of the Deep Life Sciences" tutorial list; one notebook on protein sequences, only if curious (Saturday)

Open ↗

In: LABLOOP-W23 Notebook

7/9 Run 30 min W24 Build

lmfit/lmfit-py

Build the analysis you pre-registered on simulated numbers: fit a thermal inactivation curve, get intervals; the code is frozen before real data arrives

Open ↗

In: LABLOOP-W24 Notebook

8/9 Run 30 min W24 Build

scipy/scipy

Power check by simulation: with n = 3 replicates per candidate, how big a difference can you detect? Write the answer into the plan

Open ↗

In: LABLOOP-W24 Notebook

9/9 Run 30 min W24 Build

the-turing-way/the-turing-way

Read the chapter on "Collaboration" and "Credit"; adapt its checklist for the authorship paragraph

Open ↗

In: LABLOOP-W24 Notebook

3/12 Run 30 min? W25 Saturday Sandbox optional

Michael Clark, Mixed Models with R

Saturday sandbox

Michael Clark, Mixed Models with R — m-clark.github.io/mixed-models-with-R (concepts transfer to Python)

Open ↗

In: LABLOOP-W25 Notebook

4/12 Run 30 min? W25 Saturday Sandbox optional

Bambi documentation

Saturday sandbox · after Michael Clark, Mixed Models with R

Bambi documentation (bambinos.github.io/bambi), Bayesian mixed models in one formula

Open ↗

In: LABLOOP-W25 Notebook

8/12 Run 30 min W25 Build

statsmodels/statsmodels

MixedLM example from the docs (random intercept per block); then fit one agridat trial

Open ↗

In: LABLOOP-W25 Notebook

9/12 Run 30 min W25 Build

bambinos/bambi

Same trial as a Bayesian mixed model; compare intervals with MixedLM

Open ↗

In: LABLOOP-W25 Notebook

10/12 Run 30 min W25 Build

vincentarelbundock/Rdatasets

Pull 10 agridat CSVs by URL; this is your public data source

Open ↗

In: LABLOOP-W25 Notebook

11/12 Run 30 min W25 Build

567-labs/instructor

Spreadsheet header → schema mapping with a Pydantic model, as in FermLit

Open ↗

In: LABLOOP-W25 Notebook

12/12 Run 30 min W25 Build

m-clark/mixed-models-with-R

Read the "random intercepts" chapter for intuition

Open ↗

In: LABLOOP-W25 Notebook

8/11 Run 30 min W26 Build

lmfit/lmfit-py

Fit logistic and Gompertz to a public growth curve with parameter intervals

Open ↗

In: LABLOOP-W26 Notebook

9/11 Run 30 min W26 Build

scipy/scipy

curve_fit for 4PL; compare with lmfit output

Open ↗

In: LABLOOP-W26 Notebook

10/11 Run 30 min W26 Build

DoseResponse/drc

Read the README and one vignette to check your Python 4PL reproduces drc on the same data

Open ↗

In: LABLOOP-W26 Notebook

11/11 Run 30 min W26 Build

Pioreactor/pioreactor

Look at how it estimates growth rate from optical density online; compare with your offline fit

Open ↗

In: LABLOOP-W26 Notebook

8/10 Run 30 min W27 Build

batchlens + trialkit (yours)

Record a 60-second demo of each running on public data (v4 Template C) and link both in the one-pager

Find it ↗ search

In: LABLOOP-W27 Notebook

9/10 Run 30 min W27 Build

marimo-team/marimo

A "loop calculator" notebook: inputs (cycle length, cycles/year, burn/month, days saved) → months of runway; screenshot it for the one-pager

Open ↗

In: LABLOOP-W27 Notebook

10/10 Run 30 min W27 Build

anthropics/claude-cookbooks

Borrow a summarisation recipe to turn discovery-call notes into a structured scoping sheet (never with confidential data in a cloud model without consent)

Open ↗

In: LABLOOP-W27 Notebook

5/6 Run 30 min W28 Build

Your proposal and invoice templates

Keep them in a private business/ repo; version every proposal

Find it ↗ search

In: LABLOOP-W28 Notebook

6/6 Run 30 min W28 Build

enzymelens/validation/

sha256sum every raw result file; commit the checksums, not confidential data if the partner prefers

Find it ↗ search

In: LABLOOP-W28 Notebook

5/7 Run 30 min W29 Build

pola-rs/polars

Compute cycle times from the client's timestamps (experiment start → decision) with group-bys

Open ↗

In: LABLOOP-W29 Notebook

6/7 Run 30 min W29 Build

docling-project/docling

If their records are PDFs, convert a sample locally (on-prem; no data leaves your machine)

Open ↗

In: LABLOOP-W29 Notebook

7/7 Run 30 min W29 Build

batchlens / trialkit (yours)

Run the relevant instrument on their sample in a private branch; never push client data

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In: LABLOOP-W29 Notebook

4/10 Run 30 min? W30 Saturday Sandbox optional

Vaux, Fidler & Cumming (2012), "Replicates and repeats—what is the difference and is it signific…

Saturday sandbox

Vaux, Fidler & Cumming (2012), "Replicates and repeats—what is the difference and is it significant?", EMBO Reports 13:291-296

Find it ↗ search

In: LABLOOP-W30 Notebook

7/10 Run 30 min W30 Build

ACCLAB/DABEST-python

Estimation plots (Gardner-Altman) for measured activity vs control; the library from Ho et al. 2019

Open ↗

In: LABLOOP-W30 Notebook

8/10 Run 30 min W30 Build

mwaskom/seaborn

Strip plots with every replicate over the predicted ranking

Open ↗

In: LABLOOP-W30 Notebook

9/10 Run 30 min W30 Build

arviz-devs/arviz

If you fit a small Bayesian model, plot posteriors per candidate

Open ↗

In: LABLOOP-W30 Notebook

10/10 Run 30 min W30 Build

lmfit/lmfit-py

Run the frozen week 24 analysis script on the real data, unchanged

Open ↗

In: LABLOOP-W30 Notebook

6/8 Run 30 min W31 Build

quarto-dev/quarto-cli

Paper 3 manuscript; export to .docx for a co-author who uses Word track changes

Open ↗

In: LABLOOP-W31 Notebook

7/8 Run 30 min W31 Build

enzymelens (yours)

make paper from a clean clone; tag paper-3-draft-1

Find it ↗ search

In: LABLOOP-W31 Notebook

8/8 Run 30 min W31 Build

Future-House/paper-qa

Check the Discussion's claims about prior work against the PDFs you cite (verify manually)

Open ↗

In: LABLOOP-W31 Notebook

4/5 Run 30 min W32 Build

Zenodo + GitHub (yours)

Release enzymelens v1.0 with DOI; link from the preprint

Find it ↗ search

In: LABLOOP-W32 Notebook

5/5 Run 30 min W32 Build

marimo-team/marimo

Interactive "candidate explorer" for the paper's supplementary material (public data only)

Open ↗

In: LABLOOP-W32 Notebook

9/13 Run 30 min W33 Build

elabftw/elabftw

Docker install per docs; create a team, a template, an experiment

Open ↗

In: LABLOOP-W33 Notebook

10/13 Run 30 min W33 Build

elabftw/elabapi-python

Create and update an experiment from Python; read the revision history eLabFTW keeps

Open ↗

In: LABLOOP-W33 Notebook

11/13 Run 30 min W33 Build

docling-project/docling

Convert 10 synthetic SOP PDFs; compare layout/table fidelity with the VLM

Open ↗

In: LABLOOP-W33 Notebook

12/13 Run 30 min W33 Build

datalab-to/marker

Same 10 PDFs; note speed on the 3050

Open ↗

In: LABLOOP-W33 Notebook

13/13 Run 30 min W33 Build

ollama/ollama

Run a vision model (e.g., qwen2.5vl:3b or gemma3:4b) on one scanned page; measure seconds per page

Open ↗

In: LABLOOP-W33 Notebook

8/12 Run 30 min W34 Build

vibrantlabsai/ragas

Compute context recall and faithfulness on 10 of your Q&A; compare with your human labels before trusting it

Open ↗

In: LABLOOP-W34 Notebook

9/12 Run 30 min W34 Build

run-llama/llama_index

Only as a reference implementation of chunking and citation; keep your own pipeline small

Open ↗

In: LABLOOP-W34 Notebook

10/12 Run 30 min W34 Build

illuin-tech/colpali

Try page-image retrieval on 20 scanned SOP pages; compare recall@5 with text chunks

Open ↗

In: LABLOOP-W34 Notebook

11/12 Run 30 min W34 Build

UKGovernmentBEIS/inspect_ai

Wrap the 60 Q&A as an eval with a model-graded scorer and your human labels

Open ↗

In: LABLOOP-W34 Notebook

12/12 Run 30 min W34 Build

ggml-org/llama.cpp

Serve the embedding model locally on the mini PC for the on-prem story

Open ↗

In: LABLOOP-W34 Notebook

5/10 Run 30 min? W35 Saturday Sandbox optional

Stanford HAI AI Index report, chapter on responsible AI

Saturday sandbox · after NIST Privacy Framework overview

Stanford HAI AI Index report, chapter on responsible AI (for context in M5)

Find it ↗ search

In: LABLOOP-W35 Notebook

7/10 Run 30 min W35 Build

ggml-org/llama.cpp

llama-bench on the mini PC and the 3050 for the same quantised model

Open ↗

In: LABLOOP-W35 Notebook

8/10 Run 30 min W35 Build

ollama/ollama

Same model via Ollama; record tokens/s and memory

Open ↗

In: LABLOOP-W35 Notebook

9/10 Run 30 min W35 Build

docling-project/docling / opendatalab/MinerU

Add one row per converter to the benchmark (accuracy on tables, seconds/page)

Find it ↗ search

In: LABLOOP-W35 Notebook

10/10 Run 30 min W35 Build

allenai/olmocr

Optional OCR row if a GPU run fits; mark hardware requirements honestly

Open ↗

In: LABLOOP-W35 Notebook

6/8 Run 30 min W36 Build

openjournals/joss

Read the docs folder on paper format; open two recently accepted JOSS review issues for bioprocess or scientific tools to see what reviewers ask

Open ↗

In: LABLOOP-W36 Notebook

7/8 Run 30 min W36 Build

batchlens (yours)

Check the JOSS checklist: license, tests run in CI, docs, contribution guide, example usage

Find it ↗ search

In: LABLOOP-W36 Notebook

8/8 Run 30 min W36 Build

quarto-dev/quarto-cli

Export to the journal's LaTeX template where available

Open ↗

In: LABLOOP-W36 Notebook

5/7 Run 30 min W37 Build

chiphuyen/ml-interviews-book

Practise 5 questions aloud, record, compare with the book's guidance

Open ↗

In: LABLOOP-W37 Notebook

6/7 Run 30 min W37 Build

chiphuyen/aie-book

Skim the resources list for evaluation and deployment topics likely in a scientific-data interview

Open ↗

In: LABLOOP-W37 Notebook

7/7 Run 30 min W37 Build

marimo-team/marimo

A one-page interactive pilot dashboard for the weekly readout (client data stays on their machine)

Open ↗

In: LABLOOP-W37 Notebook

5/6 Run 30 min W38 Build

marimo-team/marimo

One live demo cell (the learning-curve slider) as the talk's "wow" moment; have a screenshot fallback

Open ↗

In: LABLOOP-W38 Notebook

6/6 Run 30 min W38 Build

quarto-dev/quarto-cli

Optional reveal.js slides from Markdown so figures regenerate from code

Open ↗

In: LABLOOP-W38 Notebook

5/6 Run 30 min W39 Build

marimo-team/marimo

Sample consolidated-report page from synthetic data: 5 companies, cycle time, readiness, days saved

Open ↗

In: LABLOOP-W39 Notebook

6/6 Run 30 min W39 Build

pola-rs/polars / plotly/plotly.py

Generate the sample report figures reproducibly

Find it ↗ search

In: LABLOOP-W39 Notebook

5/6 Run 30 min W40 Build

Your cockpit repo

Script that counts blocks, lost weeks and gates from LOG.md and PROGRESS.md; the only dashboard you ever need

Find it ↗ search

In: LABLOOP-W40 Notebook

6/6 Run 30 min W40 Build

marimo-team/marimo

One-page interactive "40 weeks" timeline for the public retro

Open ↗

In: LABLOOP-W40 Notebook

⏱ Focus Focus25:00 0 min today