{"id":13492118,"url":"https://github.com/ossu/bioinformatics","last_synced_at":"2025-09-28T23:30:58.298Z","repository":{"id":41063251,"uuid":"61673420","full_name":"ossu/bioinformatics","owner":"ossu","description":":microscope: Path to a free self-taught education in Bioinformatics!","archived":true,"fork":false,"pushed_at":"2024-04-08T00:22:09.000Z","size":63,"stargazers_count":5393,"open_issues_count":2,"forks_count":900,"subscribers_count":364,"default_branch":"master","last_synced_at":"2024-09-27T03:42:27.958Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ossu.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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,"publiccode":null,"codemeta":null}},"created_at":"2016-06-21T23:11:54.000Z","updated_at":"2024-09-26T20:00:13.000Z","dependencies_parsed_at":"2022-07-14T07:10:29.745Z","dependency_job_id":"96d66332-37ab-4267-b035-d8c877bf6567","html_url":"https://github.com/ossu/bioinformatics","commit_stats":{"total_commits":54,"total_committers":13,"mean_commits":4.153846153846154,"dds":0.6296296296296297,"last_synced_commit":"fa364d765f48a4da958e48d913b3232dcdefd96d"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ossu%2Fbioinformatics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ossu%2Fbioinformatics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ossu%2Fbioinformatics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ossu%2Fbioinformatics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ossu","download_url":"https://codeload.github.com/ossu/bioinformatics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":234569826,"owners_count":18854134,"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","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":[],"created_at":"2024-07-31T19:01:03.278Z","updated_at":"2025-09-28T23:30:52.978Z","avatar_url":"https://github.com/ossu.png","language":null,"readme":"\u003cdiv align=\"center\"\u003e\n\u003cimg src=\"http://i.imgur.com/kYYCXtC.png\" alt=\"Open Source Society logo\"/\u003e\n\u003ch3\u003eOpen Source Society University\u003c/h3\u003e\n\u003cp\u003e\n  :microscope: Path to a free self-taught education in  \u003cstrong\u003eBioinformatics!\u003c/strong\u003e\n\u003c/p\u003e\n\u003cp\u003e\n  \u003ca href=\"https://github.com/open-source-society/bioinformatics\"\u003e\n\t\u003cimg alt=\"Open Source Society University - Bioinformatics\" src=\"https://img.shields.io/badge/OSSU-bioinformatics-blue.svg\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\u003cp\u003e\n  \u003ch3\u003e\n    Archived\n  \u003c/h3\u003e\n\u003c/p\u003e\n\u003c/div\u003e\n\nNote: this curriculum is not under active development and may be out of date. Read more [here](./ARCHIVED.md).\n\n## Contents\n\n- [About](#about)\n- [Motivation \u0026 Preparation](#motivation--preparation)\n- [Curriculum](#curriculum)\n- [How to use this guide](#how-to-use-this-guide)\n- [Prerequisite](#prerequisite)\n- [How to collaborate](#how-to-collaborate)\n- [Code of Conduct](#code-of-conduct)\n- [Community](#community)\n- [Team](#team)\n- [References](#references)\n\n## About\n\nThis is a **solid path** for those of you who want to complete a [Bioinformatics](https://en.wikipedia.org/wiki/Bioinformatics) course on your own time, **for free**, with courses from the **best universities** in the World.\n\nIn our curriculum, we give preference to MOOC (Massive Open Online Course) style courses because these courses were created with our style of learning in mind.\n\nTo become a bioinformatician, you have to learn quite a lot of science, so be ready for subjects like; Biology, Chemistry, etc...\n\n## Motivation \u0026 Preparation\n\nHere are two interesting links that can make **all** the difference in your journey.\n\nThe first one is a motivational video that shows a guy that went through the \"MIT Challenge\", which consists of learning the entire **4-year** MIT curriculum for Computer Science in **1 year**.\n\n- [MIT Challenge](https://www.scotthyoung.com/blog/myprojects/mit-challenge-2/)\n\nThe second link is a MOOC that will teach you learning techniques used by experts in art, music, literature, math, science, sports, and many other disciplines. These are **fundamental abilities** to succeed in our journey.\n\n- [Learning How to Learn](https://www.coursera.org/learn/learning-how-to-learn)\n\n**Are you ready to get started?**\n\n## Curriculum\n\n### 1st Year\n\nCode | Course | Duration | Effort\n:-- | :--: | :--: | :--:\nBIO 1311 | [Fundamentals of Biology](https://ocw.mit.edu/courses/7-01sc-fundamentals-of-biology-fall-2011/) | 12 weeks | 7-14 Hours/Week\nCHEM 1311 | [Principles of Chemical Science](https://ocw.mit.edu/courses/5-111sc-principles-of-chemical-science-fall-2014/) | 15 Weeks | 4-6 Hours/Week\nPy4E | [Python for Everybody](https://www.py4e.com/lessons) | 10 weeks | 10 hours/week\n6.00.1x | [Introduction to Computer Science and Programming using Python](https://ocw.mit.edu/courses/6-0001-introduction-to-computer-science-and-programming-in-python-fall-2016/) ([alt](https://www.edx.org/course/introduction-to-computer-science-and-programming-7)) | 9 weeks | 15 hours/week\nMATH 1311 | [College Algebra and Problem Solving](https://www.edx.org/course/college-algebra-problem-solving-asux-mat117x) | 4 Weeks | 6 Hours/Week\nMATH 1312 | [Pre-calculus](https://www.edx.org/course/precalculus-asux-mat170x) | 4 Weeks | 6 Hours/Week\n18.01.1x | [Calculus 1A: Differentiation](https://openlearninglibrary.mit.edu/courses/course-v1:MITx+18.01.1x+2T2019/about) | 13 weeks | 6-10 hours/week\n18.01.2x | [Calculus 1B: Integration](https://openlearninglibrary.mit.edu/courses/course-v1:MITx+18.01.2x+3T2019/about) | 13 weeks | 5-10 hours/week\nMATH 1315 | [Introduction to Probability and Data (with R)](https://www.coursera.org/learn/probability-intro) | 5 Weeks | 6 Hours/Week\n\n\n### 2nd Year\n\nCode | Course | Duration | Effort\n:-- | :--: | :--: | :--:\nBIO 2311 | [Biochemistry](https://www.edx.org/course/principles-of-biochemistry) | 15 Weeks | 4-6 Hours/Week\nCHEM 2311 | [Organic Chemistry](http://ocw.mit.edu/courses/chemistry/5-12-organic-chemistry-i-spring-2005/) | 15 Weeks | 4-6 Hours/Week\nCOMP 2311 | [CS 2 - Object Oriented Java](https://www.coursera.org/learn/object-oriented-java) | 6 Weeks | 4-6 Hours/Week\n18.01.3x | [Calculus 1C: Coordinate Systems \u0026 Infinite Series](https://openlearninglibrary.mit.edu/courses/course-v1:MITx+18.01.3x+1T2020/about) | 6 weeks | 5-10 hours/week\n6.042J | [Mathematics for Computer Science](https://openlearninglibrary.mit.edu/courses/course-v1:OCW+6.042J+2T2019/about) ([Solutions](https://github.com/spamegg1/Math-for-CS-solutions)) | 13 weeks | 5 hours/week\nCOMP 2312 | [Databases](https://online.stanford.edu/courses/soe-ydatabases-databases) | 10 Weeks | 8-12 Hours/Week\n18.06 | [Linear Algebra](https://ocw.mit.edu/courses/mathematics/18-06sc-linear-algebra-fall-2011/) and [Essence of Linear Algebra](https://www.youtube.com/playlist?list=PLZHQObOWTQDPD3MizzM2xVFitgF8hE_ab) | 14 weeks | 12 hours/week\nCOMP 2313 | [Introduction to Linux](https://www.edx.org/course/introduction-linux-linuxfoundationx-lfs101x-0) | 8 Weeks | 5-7 Hours/Week\nMATH 2314 | [Inferential Statistics (with R)](https://www.coursera.org/learn/inferential-statistics-intro) | 5 Weeks | 6 Hours/Week\n\n### 3rd Year\n\nCode | Course | Duration | Effort\n:-- | :--: | :--: | :--:\nBIO 3311 | [Proteins' Biology](https://www.edx.org/course/proteins-biologys-workforce) | 5 Weeks | 4-6 Hours/Week\nCOMP 3311a | [Algorithmic Thinking 1 ](https://www.coursera.org/learn/algorithmic-thinking-1) | 4 Weeks | 6 Hours/Week\nCOMP 3311b | [Algorithmic Thinking 2 ](https://www.coursera.org/learn/algorithmic-thinking-2) | 4 Weeks | 6 Hours/Week\nMATH 3311 | [Linear Regression and Modeling (with R)](https://www.coursera.org/learn/linear-regression-model)| 4 Weeks | 6 Hours/Week\nMATH 3312 | [Bayesian Statistics (with R)](https://www.coursera.org/learn/bayesian) | 5 Weeks | 6 Hours/Week\nBIO 3312 | [Cell Biology ](http://ocw.mit.edu/courses/biology/7-06-cell-biology-spring-2007/) | - Weeks | - Hours/Week\nMATH 3313 | [Differential Equations](https://ocw.mit.edu/courses/mathematics/18-03sc-differential-equations-fall-2011/) | 7 Weeks | 8-10 Hours/Week\nBIO 3313a | [Biostatistics 1](https://www.coursera.org/learn/biostatistics) | 4 Weeks | 3-5 Hours/Week\nBIO 3313b | [Biostatistics 2](https://www.coursera.org/learn/biostatistics-2) | 4 Weeks | 3-5 Hours/Week\n\n\n### 4th Year\n\nCode | Course | Duration | Effort\n:-- | :--: | :--: | :--:\nBIO 4311 | [DNA: Biology's Genetic Code](https://www.edx.org/course/dna-biologys-genetic-code) | 6 Weeks | 4-6 Hours/Week\nCOMP 4311 | [Data Science ](http://cs109.github.io/2015/) | 13 Week | 10 Hours/Week\nBIO 4312a | [Molecular Biology](https://ocw.mit.edu/courses/biology/7-28-molecular-biology-spring-2005/) | 16 Weeks | 4-8 Hours/Week\nBIO 4312d | [Bioinformatics 1](https://www.coursera.org/learn/dna-analysis) | 4 Weeks | 4-10 Hours/Week\nCOMP 4312a | [Bioinformatics 2](https://www.coursera.org/learn/genome-sequencing) | 4 Week | 6 Hours/Week\nCOMP 4312b | [Bioinformatics 3](https://www.coursera.org/learn/comparing-genomes) | 4 Week | 6 Hours/Week\nCOMP 4312c | [Bioinformatics 4](https://www.coursera.org/learn/molecular-evolution) | 4 Week | 6 Hours/Week\nCOMP 4312d | [Bioinformatics 5](https://www.coursera.org/learn/genomic-data) | 4 Week | 6 Hours/Week\nCOMP 4312e | [Bioinformatics 6](https://www.coursera.org/learn/dna-mutations) | 4 Week | 6 Hours/Week\nCOMP 4312f | [Bioinformatics 7 (Capstone)](https://www.coursera.org/learn/bioinformatics-project) | 3 Week | 3-4 Hours/Week\nBIO 4313 | [Evolution](https://www.coursera.org/learn/genetics-evolution) | 11 Weeks | 4-6 Hours/Week\n\n\n### Extra Year\n\nCode | Course | Duration | Effort\n:-- | :--: | :--: | :--:\nCOMP 5311 | [Introduction to Machine Learning](https://www.udacity.com/course/intro-to-machine-learning--ud120) | 10 Weeks | 6 Hours/Week\nCOMP 5312 | [Deep Learning](https://www.udacity.com/course/deep-learning--ud730) | 8 Weeks | 6 Hours/Week\nExtension | [Genomic Data Science Specialization](https://www.coursera.org/specializations/genomic-data-science) | 32 Week | 6 Hours/Week  \n\n\n\u003e Will continue with Master's in Bioinformatics\n\n\n---\n\n![keep learning](http://i.imgur.com/REQK0VU.jpg)\n\n## How to use this guide\n\n### Order of the classes\n\nThis guide was developed to be consumed in a linear approach. What does this mean? That you should complete one course at a time.\n\nThe courses are **already** in the order that you should complete them. Just start the first course, [Introduction to Biology](https://www.edx.org/course/introduction-biology-secret-life-mitx-7-00x-2), when you done with it, start the next one.\n\n**If the course is not open, do it with the archived resources or wait until next class is open.**\n\n### How to track and show your progress\n\n1. Create an account in [Trello](https://trello.com/).\n1. Copy [this](https://trello.com/b/yax8Kgnh) board to your personal account. See how to copy a board [here](http://blog.trello.com/you-can-copy-boards-now-finally/).\n\nNow that you have a copy of our official board, you just need to pass the cards to the `Doing` column or `Done` column as you progress in your study.\n\nWe also have **labels** to help you have more control through the process. The meaning of each of these labels is:\n\n- `Main Curriculum`: cards with that label represent courses that are listed in our curriculum.\n- `Extra Courses`: cards with that label represent courses that was added by the student.\n- `Doing`: cards with that label represent courses the student is current doing.\n- `Done`: cards with that label represent courses finished by the student. Those cards should also have the link for at least one project/article built with the knowledge acquired in such course.\n- `Section`: cards with that label represent the section that we have in our curriculum. Those cards with the `Section` label are only to help the organization of the Done column. You should put the *Course's cards* below its respective *Section's card*.\n- `Extra Sections`: cards with that label represent sections that was added by the student.\n\nThe intention of this board is to provide for our students a way to track their progress, and also the ability to show their progress through a public page for friends, family, employers, etc. You can change the status of your board to be **public** or **private**.\n\n\n\n### Should I take all courses?\n\n**Yes!** The intention is to conclude **all** the courses listed here! Also we highly encourage you to complete more by reading papers and attending research projects after your coursework is done.\n\n### Duration of the course\n\nIt may take longer to complete all of the classes compared to a  regular Bioinformatics course, but we can **guarantee** you that your **reward** will be proportional to **your motivation/dedication**!\n\nYou must focus on your **habit**, and **forget** about goals. Try to invest 1 ~ 2 hours **every day** studying this curriculum. If you do this, **inevitably** you'll finish this curriculum.\n\n\u003e See more about \"Commit to a process, not a goal\" [here](http://jamesclear.com/goals-systems).\n\n### Project Based\n\nHere in **OSS University**, you do **not** need to take exams, because we are focused on **real projects**!\n\nIn order to show for everyone that you **successfully** finished a course, you should create a **real project** or write **papers and publish them** about your focus with Bioinformatics.\n\n\u003e \"What does it mean?\"\n\nAfter finish a course, you should think about a **real world problem** that you can solve using the acquired knowledge in the course. You don't need to create a big project, but you must create something to **validate** and **consolidate** your knowledge, and also to show to the world that you are capable to create something useful with the concepts that you learned.\n\n  Put the OSSU-Bioinformatics badge in the README of your repository! [![Open Source Society University - Bioinformatics](https://img.shields.io/badge/OSSU-bioinformatics-blue.svg)](https://github.com/open-source-society/bioinformatics)\n\n  - Markdown: `[![Open Source Society University - Bioinformatics ](https://img.shields.io/badge/OSSU-bioinformatics-blue.svg)](https://github.com/open-source-society/bioinformatics)`\n  - HTML: `\u003ca href=\"https://github.com/open-source-society/bioinformatics\"\u003e\u003cimg alt=\"Open Source Society University - Bioinformatics\" src=\"https://img.shields.io/badge/OSSU-bioinformatics-blue.svg\"\u003e\u003c/a\u003e`\n\n**You can create this project alone or with other students!**\n\n### Be creative!\n\nThis is a **crucial** part of your journey through all those courses.\n\nYou **need** to have in mind that what you are able to **create** with the concepts that you learned will be your certificate **and this is what really matters**!\n\nIn order to show that you **really** learned those things, you need to be **creative**!\n\nHere are some tips about how you can do that:\n\n- **Articles**: create blog posts to synthesize/summarize what you learned.\n- **GitHub repository**: keep your course's files organized in a GH repository, so in that way other students can use it to study with your annotations.\n\n### Cooperative work\n\n**We love cooperative work**! Use our [channels](#community) to communicate with other fellows to combine and create new projects!\n\n### Which programming languages should I use?\n\nList of skills:\n- C/C++\n- Unix System\n- Python/Perl\n- R\n- Algorithms\n\nThese skills mentioned above are the very essential tool set that bioinformatician and computational biologist depends on.\n\nThe **important** thing for each course is to **internalize** the **core concepts** and to be able to use them with whatever tool (programming language) that you wish.\n\n### Content Policy\n\nYou must share **only** files that you are **allowed** to! **Do NOT disrespect the code of conduct** that you signed in the beginning of some courses.\n\n[Be creative](#be-creative) in order to show your progress! :smile:\n\n### Stay tuned\n\n[Watch](https://help.github.com/articles/watching-repositories/) this repository for futures improvements and general information.\n\n## Prerequisite\n\nStudents without a strong high school background in Biology will benefit from [Getting up to Speed in Biology](https://openlearninglibrary.mit.edu/courses/course-v1:OCW+Pre-7.01+1T2020/about).\n\nUnderstanding how to use Git to version your work can be hugely beneficial and is generally not taught in other courses. [Version Control with Git](https://www.udacity.com/course/version-control-with-git--ud123) should get you up to speed.\n\n## How to collaborate\n\nYou can [open an issue](https://help.github.com/articles/creating-an-issue/) and give us your suggestions as to how we can improve this guide, or what we can do to improve the learning experience.\n\nYou can also [fork this project](https://help.github.com/articles/fork-a-repo/) and send a [pull request](https://help.github.com/articles/using-pull-requests/) to fix any mistakes that you have found.\n\nTODO:\nIf you want to suggest a new resource, send a pull request adding such resource to the [extras](https://github.com/open-source-society/bioinformatics/tree/master/extras) section.\n\nThe **extras** section is a place where all of us will be able to submit interesting additional articles, books, courses and specializations, keeping our curriculum *as immutable and concise as possible*.\n\n**Let's do it together! =)**\n\n## Code of conduct\n\n[OSSU's code of conduct](https://github.com/ossu/code-of-conduct).\n\n## Community\n\nWe have a Discord server! This should be your first stop to talk with other OSSU students. [Why don't you introduce yourself right now?](https://discord.gg/wuytwK5s9h)\n\nSubscribe to our [newsletter](https://tinyletter.com/OpenSourceSocietyUniversity)\n\nYou can also interact through [GitHub issues](https://github.com/open-source-society/bioinformatics/issues).\n\nAdd **Open Source Society University** to your [Linkedin](https://www.linkedin.com/school/11272443/) and join our [Facebook](https://www.facebook.com/groups/opensourcesocietyu/) group!\n\n## Team\n\n* **Curriculum Founder**: [Enes Kemal Ergin](https://github.com/eneskemalergin)\n* **Curriculum Maintainer**: [Enes Kemal Ergin](https://github.com/eneskemalergin)\n* **Contributors**: [contributors](https://github.com/open-source-society/bioinformatics/graphs/contributors)\n\n## References\n","funding_links":[],"categories":["Others","Learning resources","Table of Contents","📦 Legacy \u0026 Inactive Projects","Essentials","Resources"],"sub_categories":["Security","Education and courses","Becoming a Bioinformatician"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fossu%2Fbioinformatics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fossu%2Fbioinformatics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fossu%2Fbioinformatics/lists"}