Datasets

The datasets used in the course exercises are organized by week. Click on the filenames to download the data files.

1 Week 45

Dataset	Exercise	Description
averag-prope-amino-acids.xlsx	Average properties of amino acids and proteins.	Amino acid frequency data
uv-spec-apo-holo-myo.csv	UV spectrum of apo- and holo-myoglobin	UV spectra for apo and holo myoglobin
trypt-absor-fluor-emission.xlsx	Tryptophan absorption and fluorescence	Tryptophan fluorescence emission data
trypt-absor-fluor-extinction.xlsx	Tryptophan absorption and fluorescence	Tryptophan fluorescence extinction data
trypt-absor-fluor-ph2.xlsx	Tryptophan absorption and fluorescence	Tryptophan fluorescence at pH 2
trypt-absor-fluor-ph7.xlsx	Tryptophan absorption and fluorescence	Tryptophan fluorescence at pH 7
extin-coeff-human-myogl.txt	Extinction coefficient of human myoglobin	Titin protein sequence data
the-fluor-protei-mcherr.csv	The fluorescent protein “mCherry”.	mCherry fluorescent protein spectra
protei-blood-plasma.xlsx	Proteins in blood plasma.	Protein concentration in blood plasma data

2 Week 46

Dataset	Exercise	Description
dialys-exper.xlsx	Dialysis experiment	Dialysis experiment data
adp-bindin-pyruva-kinase.csv	ADP binding to pyruvate kinase.	ADP binding to pyruvate kinase data
inter-bindin-data.xlsx	Interpretation of binding data.	Binding data for interpretation
deter-type-streng-coope.xlsx	Determination of type and strength of cooperativity	Cooperativity determination data
deter_delta_h_data.xlsx	Determination of ΔH° for a reaction from the van’t Hoff plot.	Determination of ΔH° for a reaction dataset (Excel format)
diff_q_keq_data.xlsx	Difference between \(Q\) and \(K_{eq}\)	Dataset of time and product concentrations.
exp_decay_data.xlsx	—	Exponential decay data for regression exercises.

3 Week 47

Dataset	Exercise	Description
reaction-orders.xlsx	Determination of reaction orders.	Reaction order determination data
deter-reacti-order-activ.csv	Determination of reaction order and activation energy	Reaction order and activation energy data
design-enzyme-kineti-exper.xlsx	Design of an enzyme kinetics experiment	Enzyme kinetics experimental design data
binding_data_sq.xlsx	A tricky protein binding.	Binding data for a tricky protein.
kinetics_data.xlsx	Lab Exercise Analysis: Michaelis Menten	Use your own data if you have it, use this dataset if you don’t or your data is of poor quality.

4 Week 48

Dataset	Exercise	Description
analys-data-set-obeyin.xlsx	Analysis of a data set obeying Michaelis-Menten kinetics	Data set analysis for enzyme kinetics
enzyme-inhib-i.xlsx	Enzyme inhibitors (I)	Enzyme inhibition data (part I)
enzyme-inhib-ii.xlsx	Enzyme inhibitors (II)	Enzyme inhibition data (part II)
enzyme-behav-atcase.csv	Enzymatic behaviour of the enzyme ATCase	Aspartate transcarbamoylase enzyme behavior data

5 Additional Datasets

These datasets are available but not yet assigned to specific weeks.

Dataset	Exercise	Description
chlorophyll_adsorption.xlsx	—	Chlorophyll absorption data (Excel format)
reverse_reaction.xlsx	—	Reversible reaction kinetics data (Excel format)

--- title: Datasets resources: - ../src/fysisk_biokemi/datasets/files/** - ../src/fysisk_biokemi/datasets/metadata.yml --- The datasets used in the course exercises are organized by week. Click on the filenames to download the data files. ```{python} #| echo: false import yaml import re import os from importlib.resources import files from pathlib import Path # Load metadata dataset_directory = files('fysisk_biokemi.datasets.files') dataset_files_path = str(dataset_directory) metadata_file_path = Path(dataset_directory).parent / 'metadata.yml' with open(metadata_file_path, 'r') as f: metadata = yaml.safe_load(f) ``` ```{python} #| echo: false def get_exercise_title(exercise_filename): """Extract exercise title from the exercise file.""" if not exercise_filename: return "—" exercise_path = f"lessons/exercises/{exercise_filename}" if not os.path.exists(exercise_path): return "—" try: with open(exercise_path, 'r', encoding='utf-8') as f: content = f.read() # Look for the first ## header (exercise title) match = re.search(r'^##\s+(.+)', content, re.MULTILINE) if match: return match.group(1).strip() else: # Fallback to filename conversion return exercise_filename.replace('.qmd', '').replace('-', ' ').title() except: # Fallback to filename conversion return exercise_filename.replace('.qmd', '').replace('-', ' ').title() def print_dataset_row(dataset): """Print a table row for a dataset.""" github_raw_url = f"https://raw.githubusercontent.com/au-mbg/fysisk-biokemi/main/src/fysisk_biokemi/datasets/files/{dataset['filename']}" download_link = f"[{dataset['filename']}]({github_raw_url})" exercise_title = get_exercise_title(dataset['exercise']) description = dataset['description'] print(f"| {download_link} | {exercise_title} | {description} |") ``` ```{python} #| echo: false # Group datasets by week datasets_by_week = {} for filename, info in metadata['datasets'].items(): week = info['week'] if week is not None: # Only include datasets assigned to weeks if week not in datasets_by_week: datasets_by_week[week] = [] datasets_by_week[week].append({ 'filename': filename, 'exercise': info['exercise'], 'description': info['description'], 'original_name': info.get('original_name', filename) }) # Collect unassigned datasets unassigned = [] for filename, info in metadata['datasets'].items(): if info['week'] is None: unassigned.append({ 'filename': filename, 'exercise': info['exercise'], 'description': info['description'] }) ``` ```{python} #| echo: false #| output: asis # Generate markdown for each week sorted_weeks = sorted(datasets_by_week.keys()) for week in sorted_weeks: print(f"## Week {week}\n") datasets = datasets_by_week[week] # Create table header print("| Dataset | Exercise | Description |") print("|---------|----------|-------------|") # Add each dataset as a table row for dataset in datasets: print_dataset_row(dataset) print("") # Empty line after each week section ``` ```{python} #| echo: false #| output: asis # Show unassigned datasets if unassigned: print("## Additional Datasets\n") print("*These datasets are available but not yet assigned to specific weeks.*\n") print("| Dataset | Exercise | Description |") print("|---------|----------|-------------|") for dataset in unassigned: print_dataset_row(dataset) ```