{"id":35762874,"url":"https://github.com/bionetslab/python-intro","last_synced_at":"2026-01-07T00:00:35.107Z","repository":{"id":129970878,"uuid":"333798359","full_name":"bionetslab/python-intro","owner":"bionetslab","description":"Introduction to Python","archived":false,"fork":false,"pushed_at":"2024-04-10T17:26:00.000Z","size":28926,"stargazers_count":6,"open_issues_count":1,"forks_count":4,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-04-10T21:23:05.250Z","etag":null,"topics":["teaching-materials"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bionetslab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2021-01-28T15:21:20.000Z","updated_at":"2024-04-15T11:26:10.850Z","dependencies_parsed_at":null,"dependency_job_id":"6f09b578-7eec-4437-98ef-f00ae09864e3","html_url":"https://github.com/bionetslab/python-intro","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bionetslab/python-intro","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Fpython-intro","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Fpython-intro/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Fpython-intro/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Fpython-intro/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bionetslab","download_url":"https://codeload.github.com/bionetslab/python-intro/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Fpython-intro/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28230229,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2026-01-06T02:00:07.049Z","response_time":56,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["teaching-materials"],"created_at":"2026-01-07T00:00:11.745Z","updated_at":"2026-01-07T00:00:35.101Z","avatar_url":"https://github.com/bionetslab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"*David B. Blumenthal*\n\n# Introduction to Python for Bioinformatics\n\nIn this course, targeted at PhD students in the biomedical sciences, participants will receive an introduction to the programming language [Python 3](https://www.python.org/). We will start with the basics (I/O, basic data structures, loops and conditions, functions, classes) and then introduce widely used packages for data manipulation, scientific computing, and visualization ([NumPy](https://numpy.org/), [SciPy](https://www.scipy.org/), [pandas](https://pandas.pydata.org/), [seaborn](https://seaborn.pydata.org/)). Finally, the course will provide a first glimpse at two widely used packages for the analysis of biological data ([Biopython](https://biopython.org/), [GSEAPY](https://gseapy.readthedocs.io/en/latest/index.html)).\n\n# Getting Started\n\nAll course materials are provided as [Jupyter Notebooks](https://jupyter.org/index.html). To run Jupyter Notebooks on your machine, install an [Anaconda distribution](https://docs.anaconda.com/anaconda/install/) before the start of the course.\n\nNow download the course material into a directory called `python-intro`. For this, either click on **Code → Download ZIP**, or download the course material via [git](https://git-scm.com/): \n\n```bash\ngit clone https://github.com/dbblumenthal/python-intro\n```\n\nAfter downloading the course material, navigate to the `python-intro` directory and create a [conda](https://docs.conda.io/en/latest/) environment called **python-intro** with all dependencies:\n\n```bash\ncd python-intro\nconda env create -f environment.yml\n```\n\nYou can now activate the environment and connect it to your Jupyter Notebook:\n\n```bash\nconda activate python-intro\n(python-intro) python -m ipykernel install --user --name=python-intro\n```\n\nNow you can open your first notebook as follows:\n\n```bash\n(python-intro) jupyter notebook 1_first_steps.ipynb\n```\n\nIf the Notebook opens without any errors, you are ready for the course.\n\n# Writing Python Scripts\n\nThe entire course is based on Jupyter Notebooks, but sometimes it is useful to write Python scripts that can be executed from a terminal. As an example, you can have a look at the script `log_transform.py` (just open it in any text editor). You can execute the script as follows:\n\n```bash\n(python-intro) python log_transform.py input/P53.txt output/P53_log_transformed.tsv --drop DESCRIPTION\n```\n\n This will save a log-transformed version of the data saved in `input/P53.txt` in the file `output/P53_log_transformed.tsv` , where the column `DESCRIPTION` contained in the input file is discarded. \n\n# Acknowledgements\n\nThis course uses material from the following Python courses:\n\n- Mark Bakker's [Python for Exploratory Computing](http://mbakker7.github.io/exploratory_computing_with_python/) course.\n- Chris Rands' [biopython-coronavirus](https://github.com/chris-rands/biopython-coronavirus) course.\n\n# License\n\nThis course is licensed under the\n[Creative Commons Attribution 4.0 International License][cc-by].\n\n[![CC BY 4.0][cc-by-image]][cc-by]\n\n[cc-by]: http://creativecommons.org/licenses/by/4.0/\n[cc-by-image]: https://i.creativecommons.org/l/by/4.0/88x31.png\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionetslab%2Fpython-intro","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbionetslab%2Fpython-intro","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionetslab%2Fpython-intro/lists"}