About	People	Research	Publications	Software	Data	Blog	Join	Internal
	Introduction to biological data analysis in python Stilianos Louca (2022), self-published. This book introduces python programming as a tool for biological data analysis. The following is a non-exhaustive list of covered topics: Variables, in particular strings and floats String formatting If statements, for loops Custom functions Lists, sets, dictionaries, list comprehension Reading and writing files (including fasta and CSV/TSV files) Batch-processing multiple files Numpy arrays Plotting with pyplot (scatterplots, curves, bar plots, histograms, heatmaps, box plots, maps) Boolean arrays and boolean indexing Pandas dataframes Randomness, hypothesis testing Basic time series analysis Regular expressions The book targets undergraduate and graduate students in biology with a strong interest in computational methods, but could also be of interest to students in other sciences. Numerous examples and exercises are included throughout the book, many based on realistic datasets from the scientific literature (exercise solutions are not made public since the book may be used for university courses). Examples and exercises cover a broad range of topics, including neuroscience, cell biology, genetics, ecology, microbiology, physiology, epidemiology and conservation. References to the scientific literature are provided throughout for the interested reader. This book is suitable as reading material in related university courses as well as for self-teaching. Where to get the book: The book is available on the Google Play Bookstore (GGKEY:UTJQTJSHTD3). If you are an educator wishing to use this book in your course and need the solutions to the exercises, please email the author with your request. Supporting datasets (for examples and exercises): albatross_foraging_routes_Dodge2013.htsv amphibian_upper_temperature_limits_Pottier2022.htsv animal_movement_2D.tsv animal_species_names.txt.gz animal_species_names_1000.txt animal_species_names_200000.txt.gz animal_traits_Herberstein2022.htsv Australian_ocean_zooplankton_biomass_McEnnulty2020.htsv.gz AVONET_bird_traits.htsv AVONET_bird_traits_with_nans.htsv Bacillus_subtilis_genomes.zip BenBioDen_benthic_biomasses_Stratmann2020.htsv.gz BenBioDen_benthic_densities_Stratmann2020.htsv.gz bird_nesting_sites.htsv bromeliad_OTU_overlaps_Louca2016_nonames.tsv captured_lobsters_Atlantic_Koepper2022.htsv cetacean_abundances_Branch2001.htsv cetacean_species_names.txt coastline_coordinates_50m.tsv.gz codon_table.csv Copepod_population_density_GPDD.htsv deep_ocean_temperature_Scotese2021.tsv EEG_IRF_Kanda1996.htsv EEG_S03EC_resting_state_Azar2020.tsv.gz Enterobacterales_genome_sizes.htsv Escherichia_coli_eggNOG_table_Louca2022.htsv.gz Escherichia_coli_genes_KOfam_GCF_008124005.1.txt Escherichia_coli_genes_KOfam_GCF_015831325.1.txt Escherichia_coli_ZZb4_GCF_013403045.1.fasta Eugene_airport_hourly_temperatures_NOAA_2022.01.01.txt falcon_migration_route_Burnham2012.htsv falcon_migration_route_Burnham2012.tsv FAPROTAX_function_table.htsv fin_whale_route_Silva2013.htsv forest_patch_properties.tsv gene_expression_data_Fujita2007.tsv gene_expression_Hughes2009.htsv.gz global_chlA_Martinez2020_2010.06.15_scatter.htsv.gz global_chlA_Martinez2020_multiple_months.zip gull_egg_and_chick_properties_Yurlov2022.htsv gull_egg_lengths_Yurlov2022.txt Haemophilus_influenzae_GCF_020731605.1.fasta.gz HapMap_human_relatedness_matrix_Gross2017.tsv HIV1_genome_NC_001802.1.txt HOTS_monthly_pp.csv HOTS_monthly_pp.htsv HOTS_monthly_pp.tsv Hudson_Bay_fur_bearing_animals.tsv Krebs2011_hare.htsv Krebs2011_lynx.htsv MAG_subset_AAIs_ANIs_GCDs.htsv.gz MAG_subset_taxonomies.htsv mass_metabolic_rate_Hatton2019.htsv mass_metabolic_rate_Hatton2019_mammals.htsv mass_vs_growth_rate_Hatton2019.htsv mass_vs_growth_rate_Hatton2019_mammals.htsv mouse_microbiomes_OTU_table_Marino2014.htsv mouse_microbiomes_OTU_taxonomies_Marino2014.htsv multiple_albatross_routes_Dodge2013.zip museum_inventory.txt Mycobacterium_lepraemurium_Hawaii_genome_CP021238.1.txt.gz Mycoplasma_pneumoniae_GCF_001455795.1.fasta.gz primate_body_masses.tsv prokaryote_genome_sizes.htsv red_grouse_shot_annually_Potts1984.htsv RefSeq_prokaryotic_genome_properties.htsv sei_whale_route_Silva2013.htsv sequences.fasta SST_NOAA_2023.01.01_grid.htsv.gz SST_NOAA_2023.01.01_scatter.htsv.gz Staphylococcus_aureus_A69_GCF_000698045.1.fasta Strep_mutans_AND_vs_eggNOG_differences.htsv subterranean_spider_traits_Mammola2022.tsv WHO_COVID19_US_daily_counts.htsv WHO_COVID19_US_weekly_cumulative_counts.htsv WWTP_AOB_abundances_Ofiteru2010.htsv × × × × × × × × × × × × × × × × × × × × Louca lab. Department of Biology, University of Oregon, Eugene, USA © 2024 Stilianos Louca all rights reserved