├── ARCHIVED.md
├── README.md
├── Subject_Domains.md
├── To-Do.md
└── extras
├── articles.md
├── free-books.md
├── free-courses.md
├── other-resources.md
├── paid-books.md
├── paid-courses.md
└── softwares.md
/ARCHIVED.md:
--------------------------------------------------------------------------------
1 | # Archived
2 | This curriculum has been archived.
3 | No issues will be addressed and no pull requests merged in.
4 | No changes will be made to the curriculum going forward.
5 |
6 | ## Reason
7 | OSSU relies on a community of experts and learners to develop our curricula.
8 | This is ongoing work, which requires evaluating new course offerings,
9 | replacing courses that are discontinued,
10 | and responding to updated learning expectations of the field.
11 |
12 | Unfortunately, OSSU no longer has volunteers to undertake that work for this curriculum.
13 |
14 | ## Unarchiving Criteria
15 | This curriculum can be unarchived by a volunteer for curriculum maintainer.
16 | Such a volunteer should contact the directors with:
17 |
18 | 1. A proposed curricular guide.
19 | A stranger who reads the guide should have a clear idea of how to evaluate if a course will fit in the curriculum.
20 | It is generally easier to make such judgements if there is one curricular guide, a reason that the OSSU CS curriculum changed from having two to one a number of years ago.
21 | [This open issue](https://github.com/ossu/bioinformatics/issues/28) may be of assistance.
22 | 2. An explanation of personal expertise.
23 | The maintainer must have demonstrated more than familiarity with bioinformatics.
24 | 3. A pledge to be involved for at least 2 years.
25 | Maintaining the curriculum is a rewarding and long term commitment.
26 | 4. A transition plan for the end-of-tenure.
27 | The last job of a great leader is to establish another great leader in their place.
28 | What steps will you take when you decide to step down to ensure that another maintainer is prepared to take over?
29 |
30 | You can reach out to the directors by sending a message in the [server suggestions](https://discord.gg/ZQ2KRzU44D)
31 | channel of the OSSU discord.
32 | Use `@directors` in your message.
33 | A director will start a private thread with you.
34 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 | <div align="center">
2 | <img src="http://i.imgur.com/kYYCXtC.png" alt="Open Source Society logo"/>
3 | <h3>Open Source Society University</h3>
4 | <p>
5 | :microscope: Path to a free self-taught education in <strong>Bioinformatics!</strong>
6 | </p>
7 | <p>
8 | <a href="https://github.com/open-source-society/bioinformatics">
9 | <img alt="Open Source Society University - Bioinformatics" src="https://img.shields.io/badge/OSSU-bioinformatics-blue.svg">
10 | </a>
11 | </p>
12 | <p>
13 | <h3>
14 | Archived
15 | </h3>
16 | </p>
17 | </div>
18 |
19 | Note: this curriculum is not under active development and may be out of date. Read more [here](./ARCHIVED.md).
20 |
21 | ## Contents
22 |
23 | - [About](#about)
24 | - [Motivation & Preparation](#motivation--preparation)
25 | - [Curriculum](#curriculum)
26 | - [How to use this guide](#how-to-use-this-guide)
27 | - [Prerequisite](#prerequisite)
28 | - [How to collaborate](#how-to-collaborate)
29 | - [Code of Conduct](#code-of-conduct)
30 | - [Community](#community)
31 | - [Team](#team)
32 | - [References](#references)
33 |
34 | ## About
35 |
36 | This 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.
37 |
38 | In 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.
39 |
40 | To become a bioinformatician, you have to learn quite a lot of science, so be ready for subjects like; Biology, Chemistry, etc...
41 |
42 | ## Motivation & Preparation
43 |
44 | Here are two interesting links that can make **all** the difference in your journey.
45 |
46 | The 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**.
47 |
48 | - [MIT Challenge](https://www.scotthyoung.com/blog/myprojects/mit-challenge-2/)
49 |
50 | The 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.
51 |
52 | - [Learning How to Learn](https://www.coursera.org/learn/learning-how-to-learn)
53 |
54 | **Are you ready to get started?**
55 |
56 | ## Curriculum
57 |
58 | ### 1st Year
59 |
60 | Code | Course | Duration | Effort
61 | :-- | :--: | :--: | :--:
62 | BIO 1311 | [Fundamentals of Biology](https://ocw.mit.edu/courses/7-01sc-fundamentals-of-biology-fall-2011/) | 12 weeks | 7-14 Hours/Week
63 | CHEM 1311 | [Principles of Chemical Science](https://ocw.mit.edu/courses/5-111sc-principles-of-chemical-science-fall-2014/) | 15 Weeks | 4-6 Hours/Week
64 | Py4E | [Python for Everybody](https://www.py4e.com/lessons) | 10 weeks | 10 hours/week
65 | 6.00.1x | [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
66 | MATH 1311 | [College Algebra and Problem Solving](https://www.edx.org/course/college-algebra-problem-solving-asux-mat117x) | 4 Weeks | 6 Hours/Week
67 | MATH 1312 | [Pre-calculus](https://www.edx.org/course/precalculus-asux-mat170x) | 4 Weeks | 6 Hours/Week
68 | 18.01.1x | [Calculus 1A: Differentiation](https://openlearninglibrary.mit.edu/courses/course-v1:MITx+18.01.1x+2T2019/about) | 13 weeks | 6-10 hours/week
69 | 18.01.2x | [Calculus 1B: Integration](https://openlearninglibrary.mit.edu/courses/course-v1:MITx+18.01.2x+3T2019/about) | 13 weeks | 5-10 hours/week
70 | MATH 1315 | [Introduction to Probability and Data (with R)](https://www.coursera.org/learn/probability-intro) | 5 Weeks | 6 Hours/Week
71 |
72 |
73 | ### 2nd Year
74 |
75 | Code | Course | Duration | Effort
76 | :-- | :--: | :--: | :--:
77 | BIO 2311 | [Biochemistry](https://www.edx.org/course/principles-of-biochemistry) | 15 Weeks | 4-6 Hours/Week
78 | CHEM 2311 | [Organic Chemistry](http://ocw.mit.edu/courses/chemistry/5-12-organic-chemistry-i-spring-2005/) | 15 Weeks | 4-6 Hours/Week
79 | COMP 2311 | [CS 2 - Object Oriented Java](https://www.coursera.org/learn/object-oriented-java) | 6 Weeks | 4-6 Hours/Week
80 | 18.01.3x | [Calculus 1C: Coordinate Systems & Infinite Series](https://openlearninglibrary.mit.edu/courses/course-v1:MITx+18.01.3x+1T2020/about) | 6 weeks | 5-10 hours/week
81 | 6.042J | [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
82 | COMP 2312 | [Databases](https://online.stanford.edu/courses/soe-ydatabases-databases) | 10 Weeks | 8-12 Hours/Week
83 | 18.06 | [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
84 | COMP 2313 | [Introduction to Linux](https://www.edx.org/course/introduction-linux-linuxfoundationx-lfs101x-0) | 8 Weeks | 5-7 Hours/Week
85 | MATH 2314 | [Inferential Statistics (with R)](https://www.coursera.org/learn/inferential-statistics-intro) | 5 Weeks | 6 Hours/Week
86 |
87 | ### 3rd Year
88 |
89 | Code | Course | Duration | Effort
90 | :-- | :--: | :--: | :--:
91 | BIO 3311 | [Proteins' Biology](https://www.edx.org/course/proteins-biologys-workforce) | 5 Weeks | 4-6 Hours/Week
92 | COMP 3311a | [Algorithmic Thinking 1 ](https://www.coursera.org/learn/algorithmic-thinking-1) | 4 Weeks | 6 Hours/Week
93 | COMP 3311b | [Algorithmic Thinking 2 ](https://www.coursera.org/learn/algorithmic-thinking-2) | 4 Weeks | 6 Hours/Week
94 | MATH 3311 | [Linear Regression and Modeling (with R)](https://www.coursera.org/learn/linear-regression-model)| 4 Weeks | 6 Hours/Week
95 | MATH 3312 | [Bayesian Statistics (with R)](https://www.coursera.org/learn/bayesian) | 5 Weeks | 6 Hours/Week
96 | BIO 3312 | [Cell Biology ](http://ocw.mit.edu/courses/biology/7-06-cell-biology-spring-2007/) | - Weeks | - Hours/Week
97 | MATH 3313 | [Differential Equations](https://ocw.mit.edu/courses/mathematics/18-03sc-differential-equations-fall-2011/) | 7 Weeks | 8-10 Hours/Week
98 | BIO 3313a | [Biostatistics 1](https://www.coursera.org/learn/biostatistics) | 4 Weeks | 3-5 Hours/Week
99 | BIO 3313b | [Biostatistics 2](https://www.coursera.org/learn/biostatistics-2) | 4 Weeks | 3-5 Hours/Week
100 |
101 |
102 | ### 4th Year
103 |
104 | Code | Course | Duration | Effort
105 | :-- | :--: | :--: | :--:
106 | BIO 4311 | [DNA: Biology's Genetic Code](https://www.edx.org/course/dna-biologys-genetic-code) | 6 Weeks | 4-6 Hours/Week
107 | COMP 4311 | [Data Science ](http://cs109.github.io/2015/) | 13 Week | 10 Hours/Week
108 | BIO 4312a | [Molecular Biology](https://ocw.mit.edu/courses/biology/7-28-molecular-biology-spring-2005/) | 16 Weeks | 4-8 Hours/Week
109 | BIO 4312d | [Bioinformatics 1](https://www.coursera.org/learn/dna-analysis) | 4 Weeks | 4-10 Hours/Week
110 | COMP 4312a | [Bioinformatics 2](https://www.coursera.org/learn/genome-sequencing) | 4 Week | 6 Hours/Week
111 | COMP 4312b | [Bioinformatics 3](https://www.coursera.org/learn/comparing-genomes) | 4 Week | 6 Hours/Week
112 | COMP 4312c | [Bioinformatics 4](https://www.coursera.org/learn/molecular-evolution) | 4 Week | 6 Hours/Week
113 | COMP 4312d | [Bioinformatics 5](https://www.coursera.org/learn/genomic-data) | 4 Week | 6 Hours/Week
114 | COMP 4312e | [Bioinformatics 6](https://www.coursera.org/learn/dna-mutations) | 4 Week | 6 Hours/Week
115 | COMP 4312f | [Bioinformatics 7 (Capstone)](https://www.coursera.org/learn/bioinformatics-project) | 3 Week | 3-4 Hours/Week
116 | BIO 4313 | [Evolution](https://www.coursera.org/learn/genetics-evolution) | 11 Weeks | 4-6 Hours/Week
117 |
118 |
119 | ### Extra Year
120 |
121 | Code | Course | Duration | Effort
122 | :-- | :--: | :--: | :--:
123 | COMP 5311 | [Introduction to Machine Learning](https://www.udacity.com/course/intro-to-machine-learning--ud120) | 10 Weeks | 6 Hours/Week
124 | COMP 5312 | [Deep Learning](https://www.udacity.com/course/deep-learning--ud730) | 8 Weeks | 6 Hours/Week
125 | Extension | [Genomic Data Science Specialization](https://www.coursera.org/specializations/genomic-data-science) | 32 Week | 6 Hours/Week
126 |
127 |
128 | > Will continue with Master's in Bioinformatics
129 |
130 |
131 | ---
132 |
133 | 
134 |
135 | ## How to use this guide
136 |
137 | ### Order of the classes
138 |
139 | This guide was developed to be consumed in a linear approach. What does this mean? That you should complete one course at a time.
140 |
141 | The 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.
142 |
143 | **If the course is not open, do it with the archived resources or wait until next class is open.**
144 |
145 | ### How to track and show your progress
146 |
147 | 1. Create an account in [Trello](https://trello.com/).
148 | 1. 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/).
149 |
150 | Now 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.
151 |
152 | We also have **labels** to help you have more control through the process. The meaning of each of these labels is:
153 |
154 | - `Main Curriculum`: cards with that label represent courses that are listed in our curriculum.
155 | - `Extra Courses`: cards with that label represent courses that was added by the student.
156 | - `Doing`: cards with that label represent courses the student is current doing.
157 | - `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.
158 | - `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*.
159 | - `Extra Sections`: cards with that label represent sections that was added by the student.
160 |
161 | The 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**.
162 |
163 |
164 |
165 | ### Should I take all courses?
166 |
167 | **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.
168 |
169 | ### Duration of the course
170 |
171 | It 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**!
172 |
173 | You 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.
174 |
175 | > See more about "Commit to a process, not a goal" [here](http://jamesclear.com/goals-systems).
176 |
177 | ### Project Based
178 |
179 | Here in **OSS University**, you do **not** need to take exams, because we are focused on **real projects**!
180 |
181 | In 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.
182 |
183 | > "What does it mean?"
184 |
185 | After 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.
186 |
187 | Put the OSSU-Bioinformatics badge in the README of your repository! [](https://github.com/open-source-society/bioinformatics)
188 |
189 | - Markdown: `[](https://github.com/open-source-society/bioinformatics)`
190 | - HTML: `<a href="https://github.com/open-source-society/bioinformatics"><img alt="Open Source Society University - Bioinformatics" src="https://img.shields.io/badge/OSSU-bioinformatics-blue.svg"></a>`
191 |
192 | **You can create this project alone or with other students!**
193 |
194 | ### Be creative!
195 |
196 | This is a **crucial** part of your journey through all those courses.
197 |
198 | You **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**!
199 |
200 | In order to show that you **really** learned those things, you need to be **creative**!
201 |
202 | Here are some tips about how you can do that:
203 |
204 | - **Articles**: create blog posts to synthesize/summarize what you learned.
205 | - **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.
206 |
207 | ### Cooperative work
208 |
209 | **We love cooperative work**! Use our [channels](#community) to communicate with other fellows to combine and create new projects!
210 |
211 | ### Which programming languages should I use?
212 |
213 | List of skills:
214 | - C/C++
215 | - Unix System
216 | - Python/Perl
217 | - R
218 | - Algorithms
219 |
220 | These skills mentioned above are the very essential tool set that bioinformatician and computational biologist depends on.
221 |
222 | The **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.
223 |
224 | ### Content Policy
225 |
226 | You 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.
227 |
228 | [Be creative](#be-creative) in order to show your progress! :smile:
229 |
230 | ### Stay tuned
231 |
232 | [Watch](https://help.github.com/articles/watching-repositories/) this repository for futures improvements and general information.
233 |
234 | ## Prerequisite
235 |
236 | Students 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).
237 |
238 | Understanding 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.
239 |
240 | ## How to collaborate
241 |
242 | You 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.
243 |
244 | You 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.
245 |
246 | TODO:
247 | If 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.
248 |
249 | The **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*.
250 |
251 | **Let's do it together! =)**
252 |
253 | ## Code of conduct
254 |
255 | [OSSU's code of conduct](https://github.com/ossu/code-of-conduct).
256 |
257 | ## Community
258 |
259 | We 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)
260 |
261 | Subscribe to our [newsletter](https://tinyletter.com/OpenSourceSocietyUniversity)
262 |
263 | You can also interact through [GitHub issues](https://github.com/open-source-society/bioinformatics/issues).
264 |
265 | Add **Open Source Society University** to your [Linkedin](https://www.linkedin.com/school/11272443/) and join our [Facebook](https://www.facebook.com/groups/opensourcesocietyu/) group!
266 |
267 | ## Team
268 |
269 | * **Curriculum Founder**: [Enes Kemal Ergin](https://github.com/eneskemalergin)
270 | * **Curriculum Maintainer**: [Enes Kemal Ergin](https://github.com/eneskemalergin)
271 | * **Contributors**: [contributors](https://github.com/open-source-society/bioinformatics/graphs/contributors)
272 |
273 | ## References
274 |
--------------------------------------------------------------------------------
/Subject_Domains.md:
--------------------------------------------------------------------------------
1 | ## Subject Domains for Bioinformatics Education
2 |
3 | ### Biology
4 | Code | Course | Duration | Effort
5 | :-- | :--: | :--: | :--:
6 | BIO 1311 | [Introduction to Biology](https://www.edx.org/course/introduction-biology-secret-life-mitx-7-00x-2) | 12 weeks | 7-14 Hours/Week
7 | BIO 2311 | [Biochemistry](https://www.edx.org/course/principles-biochemistry-harvardx-mcb63x) | 15 Weeks | 4-6 Hours/Week
8 | BIO 3311 | [Genetics 1 ](https://www.edx.org/course/useful-genetics-part-1-how-genes-shape-ubcx-usegen-1x-0) | 7 Weeks | 6-8 Hours/Week
9 | BIO 3312 | [Cell Biology ](http://ocw.mit.edu/courses/biology/7-06-cell-biology-spring-2007/) | - Weeks | - Hours/Week
10 | BIO 3313a | [Biostatistics 1](https://www.coursera.org/learn/biostatistics) | 4 Weeks | 3-5 Hours/Week
11 | BIO 3313b | [Biostatistics 2](https://www.coursera.org/learn/biostatistics-2) | 4 Weeks | 3-5 Hours/Week
12 | BIO 4311 | [Genetics 2](https://www.edx.org/course/useful-genetics-part-2-genes-genetic-ubcx-usegen-2x-0) | 5 Weeks | 6-8 Hours/Week
13 | BIO 4312a | [Molecular Biology 1 ](https://www.edx.org/course/molecular-biology-part-1-dna-replication-mitx-7-28-1x1-0) | 8 Weeks | 4-8 Hours/Week
14 | BIO 4312b | [Molecular Biology 2 ](https://www.edx.org/course/molecular-biology-part-2-transcription-mitx-7-28-2x-0) | 6 Weeks | 4-8 Hours/Week
15 | BIO 4312c | [Molecular Biology 3](https://www.edx.org/course/molecular-biology-part-3-rna-processing-mitx-7-28-3x-0) | 8 Weeks | 4-8 Hours/Week
16 | BIO 4312d | [Basic Bioinformatics (Bioinformatics 1)](https://www.coursera.org/learn/bioinformatics) | 4 Weeks | 4-6 Hours/Week
17 | BIO 4313a | [Evolution](https://www.coursera.org/learn/genetics-evolution) | 11 Weeks | 4-6 Hours/Week
18 |
19 | ### Chemistry
20 | Code | Course | Duration | Effort
21 | :-- | :--: | :--: | :--:
22 | CHEM 1311 | [Principles of Chemistry](http://ocw.mit.edu/courses/chemistry/5-111-principles-of-chemical-science-fall-2008/) | 15 Weeks | 4-6 Hours/Week
23 | CHEM 2311 | [Organic Chemistry](http://ocw.mit.edu/courses/chemistry/5-12-organic-chemistry-i-spring-2005/) | 15 Weeks | 4-6 Hours/Week
24 |
25 | ### Computer Science
26 | Code | Course | Duration | Effort
27 | :-- | :--: | :--: | :--:
28 | COMP 1311a | [CS 1 - Python 1 ](https://www.coursera.org/learn/interactive-python-1) | 5 Weeks | 6 Hours/Week
29 | COMP 1311b | [CS 1 - Python 2 ](https://www.coursera.org/learn/interactive-python-2) | 4 Weeks | 6 Hours/Week
30 | COMP 1311c | [CS 1 - Principles of Computing 1 ](https://www.coursera.org/learn/principles-of-computing-1) | 4 Weeks | 6 Hours/Week
31 | COMP 1311d | [CS 1 - Principles of Computing 2 ](https://www.coursera.org/learn/principles-of-computing-2) | 4 Weeks | 6 Hours/Week
32 | COMP 2311 | [CS 2 - Object Oriented Java](https://www.coursera.org/learn/object-oriented-java) | 6 Weeks | 4-6 Hours/Week
33 | COMP 2312 | [Introduction to Databases](https://lagunita.stanford.edu/courses/Engineering/db/2014_1/about) | 10 Weeks | 8-12 Hours/Week
34 | COMP 2313 | [Introduction to Linux](https://www.edx.org/course/introduction-linux-linuxfoundationx-lfs101x-0) | 8 Weeks | 5-7 Hours/Week
35 | COMP 3311a | [Algorithmic Thinking 1 ](https://www.coursera.org/learn/algorithmic-thinking-1) | 4 Weeks | 6 Hours/Week
36 | COMP 3311b | [Algorithmic Thinking 2 ](https://www.coursera.org/learn/algorithmic-thinking-2) | 4 Weeks | 6 Hours/Week
37 | COMP 3312 | [High Performance (?)]() | ? | ?
38 | COMP 4311 | [Data Science ](http://cs109.github.io/2015/) | 13 Week | 10 Hours/Week
39 | COMP 4312a | [Bioinformatics 2](https://www.coursera.org/learn/genome-sequencing) | 4 Week | 6 Hours/Week
40 | COMP 4312b | [Bioinformatics 3](https://www.coursera.org/learn/comparing-genomes) | 4 Week | 6 Hours/Week
41 | COMP 4312c | [Bioinformatics 4](https://www.coursera.org/learn/molecular-evolution) | 4 Week | 6 Hours/Week
42 | COMP 4312d | [Bioinformatics 5](https://www.coursera.org/learn/genomic-data) | 4 Week | 6 Hours/Week
43 | COMP 4312e | [Bioinformatics 6](https://www.coursera.org/learn/dna-mutations) | 4 Week | 6 Hours/Week
44 | COMP 5311 | [Introduction to Machine Learning](https://www.udacity.com/course/intro-to-machine-learning--ud120) | 10 Weeks | 6 Hours/Week
45 | COMP 5312 | [Deep Learning](https://www.udacity.com/course/deep-learning--ud730) | 8 Weeks | 6 Hours/Week
46 | Extension | [Genomic Data Science Specialization](https://www.coursera.org/specializations/genomic-data-science) | 32 Week | 6 Hours/Week
47 |
48 | ### Math
49 | Code | Course | Duration | Effort
50 | :-- | :--: | :--: | :--:
51 | MATH 1311 | [Calculus 1](https://www.coursera.org/learn/calculus1) | 16 Weeks | 6 Hours/Week
52 | MATH 1312 | [Mathematics for CS](http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-042j-mathematics-for-computer-science-fall-2010/index.htm) | 13 Weeks | 6 Hours/Week
53 | MATH 2311 | [Calculus 2](https://www.coursera.org/learn/advanced-calculus) | 8 Weeks | 6 Hours/Week
54 | MATH 2312 | [Linear Algebra](https://www.edx.org/course/linear-algebra-foundations-frontiers-utaustinx-ut-5-04x) | 15 Weeks | 8 Hours/Week
55 | MATH 2313 | [Descriptive Statistics](https://www.edx.org/course/introduction-statistics-descriptive-uc-berkeleyx-stat2-1x#!) | 5 Weeks | 8 Hours/Week
56 | MATH 3311 | [Probability](https://www.edx.org/course/introduction-statistics-probability-uc-berkeleyx-stat2-2x)| 5 Weeks | 8 Hours/Week
57 | MATH 3312 | [Differential Equations](https://www.edx.org/course/introduction-differential-equations-bux-math226-1x-0) | 7 Weeks | 8-10 Hours/Week
58 | MATH 4311 | [Inferential Statistics](https://www.edx.org/course/introduction-statistics-inference-uc-berkeleyx-stat2-3x) | 5 Weeks | 8 Hours/Week
59 |
60 |
61 | ### Master Courses
62 | - Choose your Path
63 | - Systems Biology
64 | - Computational Biology
65 | - Bioinformatics
66 | - Computational Neuroscience
67 | - Biomedical Engineering
68 | > More here...
69 |
--------------------------------------------------------------------------------
/To-Do.md:
--------------------------------------------------------------------------------
1 | # To-Do List for Bioinformatics
2 |
3 | - [x] Read the papers about online bioinformatics
4 | - [x] Itemize the topic requirements
5 | - [x] Search for other schools curriculum
6 | - [x] Search for the online education platforms
7 | - [x] Itemize the courses
8 | - [x] Order the courses
9 | - [ ] Prepare a reading list of textbooks
10 | - [ ] Extra reading, most recent papers on bioinformatics technologies
11 | - [ ] Search for all possible fields of studies (For mastery)
12 | - [ ] Find a domain of your interest, do your own research while learning ;-)
13 |
--------------------------------------------------------------------------------
/extras/articles.md:
--------------------------------------------------------------------------------
1 | # Bioinformatics - Extra Resources
2 |
3 | # Articles
4 | 1. [So you want to be a computational biologist?](http://www.nature.com/nbt/journal/v31/n11/full/nbt.2740.html) by Nick Loman and Mick Watson (2013).
5 | 1. [A Quick Guide for Developing Effective Bioinformatics Programming Skills](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000589) by Joel Dudley and Atul Butte (2009).
6 | 1. [Unix Philosophy](https://en.wikipedia.org/wiki/Unix_philosophy)
7 |
--------------------------------------------------------------------------------
/extras/free-books.md:
--------------------------------------------------------------------------------
1 | # Bioinformatics - Extra Resources
2 |
3 | # Free Books
4 | * [Molecular Biology of the Cell](https://www.ncbi.nlm.nih.gov/books/NBK21054/)
5 | * [An Introduction to Genetic Analysis](https://www.ncbi.nlm.nih.gov/books/NBK21766/)
6 | * [The GNU/Linux Command Line Interface (CLI)](http://linuxcommand.org/tlcl.php)
7 | * [Unix Grymoire](http://www.grymoire.com/)
8 | * [Algorithms and Data Structures](http://interactivepython.org/runestone/static/pythonds/index.html)
9 | * [Think like a Computer Scientist](http://interactivepython.org/runestone/static/thinkcspy/index.html)
10 | * [Data Analysis for the Life Sciences](https://leanpub.com/dataanalysisforthelifesciences)
11 |
12 | ## Language Books
13 | * [Python](http://scipy.org/topical-software.html)
14 | * [Interactive Py](http://interactivepython.org/runestone/static/pythonds/index.html)
15 | * [Py For Biologists](http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/)
16 | * Quick applied language overview in [this workshop](https://swcarpentry.github.io/python-novice-inflammation/index.html)
17 | * Perl
18 | * [Perl 6](http://perl6intro.com/)
19 | * [Unix and Perl for Biologists](http://korflab.ucdavis.edu/Unix_and_Perl/index.html)
20 | * [Haskell](http://learnyouahaskell.com/chapters)
21 | * [Julia](http://julialang.org/learning/) ([book](https://en.wikibooks.org/wiki/Introducing_Julia))
22 | * [Make](http://www.oreilly.com/openbook/make3/book/index.csp) pipelines
23 | * R
24 | * [Data Analysis and Visualizations](http://varianceexplained.org/RData/)
25 | * Coursera JHU's [course notes](http://sux13.github.io/DataScienceSpCourseNotes/2_RPROG/R_Programming_Course_Notes.html)
26 | * Nail [lexical scoping](http://adv-r.had.co.nz/Functions.html#lexical-scoping)
27 |
--------------------------------------------------------------------------------
/extras/free-courses.md:
--------------------------------------------------------------------------------
1 | # Bioinformatics - Extra Resources
2 |
3 | # Free Courses
4 |
5 | PH525.1x: Statistics and R for the Life Sciences
6 |
7 | PH525.2x: Introduction to Linear Models and Matrix Algebra
8 |
9 | PH525.3x: Statistical Inference and Modeling for High-throughput Experiments
10 |
11 | PH525.4x: High-Dimensional Data Analysis
12 |
13 | PH525.5x: Introduction to Bioconductor: annotation and analysis of genomes and genomic assays
14 |
15 | PH525.6x: High-performance computing for reproducible genomics
16 |
17 | PH525.7x: Case studies in functional genomics
18 |
19 | ## Workshops and tutorials mostly:
20 | * [Data Carpentry](http://www.datacarpentry.org/lessons/)
21 | * [OpenHelix](http://www.openhelix.com/freeTutorials.cgi)
22 | * [BioStars](https://www.biostars.org/t/Tutorials/)
23 | * [GenomeSpace Recipes](http://recipes.genomespace.org/home)
24 | * [EMBL-EBI](https://www.ebi.ac.uk/training/online/course-list)
25 | * [UC SantaCruz Training](https://genome.ucsc.edu/training/index.html)
26 | * [UC Davis Workshops](http://bioinformatics.ucdavis.edu/training/documentation/)
27 | * [InsideDNA Tutorials](https://insidedna.me/tutorials)
28 | * [Stephen Turner's list](http://stephenturner.us/edu.html)
29 | * [Griffith's RNA-seq](https://github.com/griffithlab/rnaseq_tutorial/wiki)
30 | * [NCBI Tutorials](http://www.ncbi.nlm.nih.gov/home/learn.shtml)
31 | * [Homolog.us Tutorials](http://homolog.us/Tutorials/)
32 | * [Broad Institute Medical and Population Genetics Primers](https://www.youtube.com/playlist?list=PLEEE2A91B09B77B4A)
33 |
34 |
35 | Try searching keywords like bioinformatics, biology, genomic, genetic, data analysis, data science, computer science, life science... in these websites:
36 | * [Coursera](https://www.coursera.org/)
37 | * [edX](https://www.edx.org/)
38 | * [MIT](http://ocw.mit.edu/courses)
39 | * [eBiomics](http://ebiomics.sdcinfo.com/)
40 | * [Khan Academy](http://www.khanacademy.org/)
41 | * [Udemy](http://www.udemy.com/)
42 |
43 |
44 | ## Coding Courses and Tutorials
45 | * [Code Academy](https://www.codecademy.com/#!/exercises/0)
46 | * [Software Carpentry](http://software-carpentry.org/lessons/)
47 | * [Code Snipcademy](http://code.snipcademy.com)
48 | * [Udacity](https://www.udacity.com/)
49 | * [FreeCodeCamp](https://www.freecodecamp.com/)
50 | * Python
51 | * [Matplotlib](http://www.loria.fr/~rougier/teaching/matplotlib/) - Plotting
52 | * [Seaborn](https://web.stanford.edu/~mwaskom/software/seaborn/tutorial.html) - Plotting
53 | * [Pandas](http://pandas.pydata.org/pandas-docs/stable/) - Data Analysis
54 | * [Machine Learning](http://scikit-learn.org/stable/documentation.html) - Library
55 | * [HTSeq](http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) - Library
56 | * R
57 | * [Quick-R](http://www.statmethods.net/)
58 | * [Swirl](http://swirlstats.com/students.html)
59 | * [ggplot2](http://ggplot2.org/)
60 | * [R & NGS](http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-SOAP)
61 | * [Bioconductor Lib](http://bioconductor.org/help/workflows/)
62 | * [RSeek Lib Search](http://www.rseek.org/)
63 | * Data Analysis Pipelines
64 | * GNU Make
65 | * [Dave Tang](http://davetang.org/muse/2015/05/31/learning-about-makefiles/)
66 | * [Stat545](http://stat545.com/automation04_make-activity.html)
67 | * [ZMJones](http://zmjones.com/make/)
68 | * [NextFlow](http://www.nextflow.io/docs/latest/index.html)
69 | * [SnakeMake](http://snakemake.bitbucket.org/snakemake-tutorial.html)
70 |
--------------------------------------------------------------------------------
/extras/other-resources.md:
--------------------------------------------------------------------------------
1 | # Handy Stuff
2 | * [UCSC FAQ](https://genome.ucsc.edu/FAQ/)
3 | * Rosalind [Glossary](http://rosalind.info/glossary/)
4 | * [Cheatsheets](http://overapi.com/)
5 | * [File Format Specifications](https://github.com/samtools/hts-specs)
6 | * [GATK](http://gatkforums.broadinstitute.org/gatk/categories)
7 | * [Genome Space](https://www.broadinstitute.org/scientific-community/science/projects/genomespace/genomespace)
8 | * [Writing your first academic paper](https://github.com/jtleek/firstpaper)
9 | * [Statistics for Biologists](http://www.nature.com/collections/qghhqm)
10 | * [another DS career, apart from the one of OSS](https://github.com/datasciencemasters/go)
11 | * [don't be a luser](http://www.catb.org/esr/faqs/smart-questions.html)
12 | * [here's the future](https://biojulia.github.io/Bio.jl/latest/)
13 |
14 | # Forums Q&A
15 | * [BioStars](https://www.biostars.org/)
16 | * [SEQAnswers](http://seqanswers.com/)
17 | * [SEQanswers - Bioinformatics](http://seqanswers.com/forums/external.php?type=RSS2&forumids=18)
18 | * [Bioinformatics subreddit](https://www.reddit.com/r/bioinformatics/)
19 | * [Bio Databases subreddit](http://www.reddit.com/r/BioDatasets)
20 | * [Genomic subreddit](http://www.reddit.com/r/genomics)
21 | * [Biology Q&A](https://biology.stackexchange.com/)
22 | * [Unix and GNU/Linux Q&A](https://unix.stackexchange.com/)
23 | * [Code Q&A](http://stackoverflow.com/)
24 | * [Ion Community](http://ioncommunity.lifetechnologies.com/community/)
25 | * [LinuxQuestions](http://www.linuxquestions.org/questions/)
26 | * [Bioconductor Q&A](https://support.bioconductor.org/)
27 | * [Statistics Q&A](http://stats.stackexchange.com/)
28 | * [Data Science Q&A](http://datascience.stackexchange.com/)
29 |
30 | # Wikis
31 | * [SEQAnswers](http://seqanswers.com/wiki/SEQanswers)
32 | * [GNU/Linux (Arch)Wiki](https://wiki.archlinux.org/)
33 |
34 | # Puzzles and Code Golf
35 | * [Code Golf](https://codegolf.stackexchange.com/)
36 | * [Project Euler](https://projecteuler.net/)
37 | * [Rosalind](http://rosalind.info/)
38 | * [Hacker Rank](https://www.hackerrank.com/domains/algorithms/warmup)
39 |
40 | # Other lists
41 | * [Bioinformatics Jobs](http://www.indeed.com/q-Bioinformatics-jobs.html)
42 | * [Biological Databases](https://en.wikipedia.org/wiki/List_of_biological_databases) (can't be up-to-date)
43 | * [Genomics Class](http://genomicsclass.github.io/book/pages/resources.html)
44 | * [HTS training materials repository](http://bioinformatics.upsc.se/htmr)
45 | * [Genomics Papers](https://github.com/jtleek/genomicspapers) by Leek Group
46 | * [Bioinformatics.org Educational Services](http://www.bioinformatics.org/wiki/Educational_services)
47 | * [ISCB courses](http://www.iscb.org/iscb-degree-certificate-programs)
48 | * Learning Programming Languages [[1]](http://hackr.io/) [[2]](https://github.com/vhf/free-programming-books)
49 | * Software
50 | * [bio-tools.org](https://bio-tools.org/)
51 | * [CCB at JHU](http://ccb.jhu.edu/software.shtml)
52 | * [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/)
53 | * [OMICtools](http://omictools.com/about)
54 | * [Sanger's Isntitute list](http://www.sanger.ac.uk/science/tools)
55 |
56 | # Illegal resources [you should avoid](http://www.sciencemag.org/news/2016/04/whos-downloading-pirated-papers-everyone)
57 | * Sci-Hub
58 | * LibGen
59 | * Bookfi
60 |
61 | **And always, enjoy [open culture](http://www.openculture.com/)**
62 |
--------------------------------------------------------------------------------
/extras/paid-books.md:
--------------------------------------------------------------------------------
1 | # Bioinformatics - Extra Resources
2 |
3 | # Paid Books
4 | * Biological Sequence Analysis (R. Durbin et al)
5 | * Bioinformatics and Functional Genomics (J. Pevsner)
6 | * BioInfoBook [Figures](http://bioinfbook.org/php/powerpoints)
7 | * [Bioinformatic Algorithms](http://bioinformaticsalgorithms.com/)
8 |
--------------------------------------------------------------------------------
/extras/paid-courses.md:
--------------------------------------------------------------------------------
1 | # Bioinformatics - Extra Resources
2 |
3 | # Paid Courses
4 | [Micro-masters in Bioinformatics from University of Maryland](https://www.edx.org/micromasters/bioinformatics)
5 |
--------------------------------------------------------------------------------
/extras/softwares.md:
--------------------------------------------------------------------------------
1 | # Bioinformatics - Extra Resources
2 |
3 | # Software Documentation
4 | * Install CLI tools with [BioConda](https://bioconda.github.io/) package manager
5 | * [Circos](http://circos.ca/documentation/course/)
6 | * [OpenGene Libraries](https://github.com/OpenGene)
7 | * [GATK Tools](https://www.broadinstitute.org/gatk/guide/tooldocs/index)
8 | * [ADAM](http://bdgenomics.org/) Big-Data Genomics
9 | * [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
10 | * samtools 1:[BioBits'](http://biobits.org/samtools_primer.html) 2:[DaveTang's](https://github.com/davetang/learning_bam_file) 3:[YanhuiFan's](https://felixfan.github.io/bam-sam/) 4:[BinaryFlags](https://broadinstitute.github.io/picard/explain-flags.html)
11 | * [bcftools](https://samtools.github.io/bcftools/howtos/variant-calling.html) 1:[GATK](http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it) 2:[DaveTang's](https://github.com/davetang/learning_vcf_file) 3:[Paper](https://www.researchgate.net/publication/230658044_A_beginners_guide_to_SNP_calling_from_high-Throughput_DNA-sequencing_data)
12 | * bedtools 1:[Quinlan](http://quinlanlab.org/tutorials/bedtools/bedtools.html) 2:[YanhuiFan's](https://felixfan.github.io/bedtools/)
13 | * BWA
14 | * bowtie2
15 | * [Tuxedo Suite](http://cole-trapnell-lab.github.io/cufflinks/) 1:[YanhuiFan's](http://felixfan.github.io/tophat-cufflinks/)
16 | * [bedops](https://bedops.readthedocs.org/en/latest/content/usage-examples.html)
17 | * [picard](http://broadinstitute.github.io/picard/)
18 | * [jvarkit](https://github.com/lindenb/jvarkit)
19 | * [Exomiser](http://www.sanger.ac.uk/science/tools/exomiser) disease causing variants
20 | * [PopSV](https://github.com/jmonlong/PopSV) structural variants
21 | * [Silva](http://compbio.cs.toronto.edu/silva/) silent mutations
22 | * [Variant Effect Predictor](http://www.ensembl.org/info/docs/tools/vep/index.html)
23 | * [ANNOVAR](http://annovar.openbioinformatics.org/en/latest/)
24 | * [BioGPS](http://biogps.org/help/)
25 | * [ABySS](http://sjackman.ca/abyss-activity/)
26 | * [GEMINI](https://gemini.readthedocs.io/en/latest/) annotation db
27 | * Graphical User Interface (GUI) apps
28 | * [Integrative Genomics Viewer (IGV)](https://www.broadinstitute.org/software/igv/)
29 | * [NCBI Genome Workbench](https://www.ncbi.nlm.nih.gov/tools/gbench/)
30 | * [Savant](http://genomesavant.com/p/savant/index)
31 | * [JBrowse](http://jbrowse.org/)
32 |
33 | # Other Non-specific Tools
34 | * [Atom](http://atom.io/) modern text editor
35 | * [Reference Manager](https://en.wikipedia.org/wiki/Comparison_of_reference_management_software)
36 | * [Git](https://git-scm.com/) Version Control
37 | * [HowTo Guide](https://githowto.com/)
38 | * [Try Online](https://try.github.io/)
39 | * [Pro Book](https://progit.org/)
40 | * [Short Videos](https://git-scm.com/videos)
41 | * [Start Contributing Guide](https://about.gitlab.com/2016/06/16/fearless-contribution-a-guide-for-first-timers/)
42 | * [LaTeX](https://latex-project.org/intro.html)
43 | * [Overleaf](http://www.overleaf.com/) write collaboratively
44 | * [Markdown](http://daringfireball.net/projects/markdown/)
45 | * [Here](http://markdown-here.com/)
46 | * [RegEx Generator](http://www.regexr.com/)
47 | * [RegEx 101](https://regex101.com/)
48 | * [RegEx Debugger](https://www.debuggex.com/)
49 | * [Plotly](https://plot.ly/)
50 | * [Small (bioinformatic) Tools Manifesto](https://github.com/pjotrp/bioinformatics)
51 | * [Terminal Multiplexer](https://robots.thoughtbot.com/a-tmux-crash-course)
52 | * [ZSH](http://ohmyz.sh/)
53 | * [VIM](http://vim.rtorr.com/) o rather run 'vimtutor' :P
54 | * [ShellCheck your scripts](http://www.shellcheck.net/)
55 | * Writing
56 | * [Correct your Grammar](https://www.grammarly.com/)
57 | * [Look-up word by its meaning](http://www.onelook.com/reverse-dictionary.shtml)
58 | * [LanguageTool](https://languagetool.org/)
59 | * google translate, obviusly.
60 | * [Introduction to HTML](https://developer.mozilla.org/en-US/docs/Web/Guide/HTML/Introduction)
61 |
--------------------------------------------------------------------------------