@eneskemalergin Some things to be updated in the README

• Remove section Becoming an OSS student from TOC and also remove the content.
• In "Order of the classes" section, change the last statement for: "OBS: If the course is not open, do it with the archived resources or wait until next class is open."

https://www.edx.org/course/molecular-biology-part-1-dna-replication-mitx-7-28-1x-1

Maybe we can put an official badge in this repository, so students will be able to link back to this in their own projects.

Example:

• Markdown: [![Open Source Society University - Bioinformatics](https://img.shields.io/badge/OSSU-bioinformatics-blue.svg)](https://github.com/open-source-society/bioinformatics)
• 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>

😄

https://www.edx.org/course/introduction-statistics-inference-uc-berkeleyx-stat2-3x

https://www.youtube.com/watch?v=TUyo8NFi_3Q&list=PLHn7WmALbthnAwbJ4mWw5gk8dgqsjRL87&ab_channel=Prof.JeffreyJ.GrayatJohnsHopkinsUniversity

Issue In Brief

The bioinformatics program does not have good course alignment with OSSU's well-known, vetted, and recommended introductory courses in other OSSU programs.

Comment Period: thru 13 August 2022

Issue

Bioinformatics is one of OSSU's newer offerings and it appears to have been developed by one person in isolation, who did a great job of putting together free or nearly-free courses in bioinformatics.

One problem is this degree plan doesn't seem to merge well with OSSU's other offerings (specifically the CS/data science/mathematics courses). Curation work that has been done to provide high-quality early courses in mathematics, computer science and data science therefore needs to be duplicated.

This has already produced confusion with at least one potential learner; the COMP 1311a course which serves as an Introduction to Programming in Python has paywalled components which can't be completed without payment for the course. The mathematics courses use nonstandard wording to suggest they are providing a Calculus 1, 2, 3 sequence -- but the courses are only single variable and don't appear to extend to multivariate.

Selecting nonstandard intro courses in what is already a niche program further isolates the learners from the OSSU community, leaving us unable to help or guide the learners at the start of their journey when they need support the most.

Recommendation

Replace key introductory courses in the Bioinformatics degree path with OSSU-vetted equivalents from the Computer Science, Data Science or Math programs, where available and acceptable.

In part, replace:

• COMP 1311a/b with Py4E
• COMP 1311c with MIT 6.00.1x
• COMP 1311d with MIT 6.00.2x
• MATH 1311 with ALEKS College Algebra + Khan Academy/Professor Leonard supplement
• MATH 1312 with ALEKS Pre-Calculus + Khan Academy/Professor Leonard supplement
• MATH 1313 with MIT Calculus A
• MATH 1314 with MIT Calculus B
• MATH 2311 with MIT Calculus C
• MATH 2312 with MIT Math for CS 6.042J
• MATH 2313 with MIT Linear Algebra 18.06

Consider other replacements as appropriate.

Alternatives

Source and vet each of the currently recommended courses for OSSU quality and free accessibility; if found suitable, consider using these as alternative courses in the other degree programs.

https://www.edx.org/course/useful-genetics-part-2-genes-genetic-ubcx-usegen-2x-0

Current MATH 1313, MATH 1314, MATH 2311 courses by Robert Ghrist requires familiarity with limits, derivatives as stated in the beginning of that course. I tried to take that course but I could not do that as a beginner. All three course should be replaces by Calculus 1A: Differentiation, Calculus 1B: Integration, Calculus 1C: Coordinate Systems & Infinite Series respectively. Otherwise most people would stuck or even give up at calculus section of curriculum

This should be mentioned

• https://www.edx.org/micromasters/bioinformatics

BIO 4312c | Molecular Biology 3 | 8 Weeks | 4-8 Hours/Week

https://www.edx.org/course/useful-genetics-part-1-how-genes-shape-ubcx-usegen-1x-0

Would it be ok to add some of the short but owesome youtube videos on the list? such as Thermo Fisher Scientific 's "Seq it out" , and a list of that would be great.

The projects of all students will be listed in this file. Submit your project's information in that file after you conclude it.

The link to the file leads to an 404 error.
Also the forum link is not working...

MIT recently started offering a Pre-7.01 course titled "Getting Up To Speed In Biology" (https://openlearninglibrary.mit.edu/courses/course-v1:OCW+Pre-7.01+1T2020/about). The course was designed for students incoming to MIT who did not have the necessary background in biology from previous education.

I wanted to get some thoughts on the group before creating a PR to merge this into the baseline Bioinformatics program.

according to the first 9 pages of the PDF in this link https://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie1.pdf
I want the answer to this:-

https://www.coursera.org/learn/advanced-calculus

In order to maintain this curriculum, OSSU should identify a curricular guideline. Such a document can aid in comparing different course offerings and guide conversations about coverage and rigor.

The International Society for Computational Biology has a task force to create such guidelines. That work can be found here:

https://www.iscb.org/curriculum-guidelines-colleges-universities

The course COMP 2312 is now moved into another site (edX) and it is segmented into 5 2-week courses. I guess 😸 , didn't take the course yet

Edit:
The link from the curriculum is this
And if you follow the link to the edX page and search there for "introduction database" it will show the 5 courses from Stanford that I am guessing where in the original link.

The vital part of the bioinformatics is a good knowledge of biology. It's very important for fundamental introductory courses to be in a very good quality. In my opinion it is impossible to learn biology without reading textbook. Of course lectures are important but text is far more. I'm currently learning my first "fundamental" course in Biology - it's not easy. To get a good grasp of every topic I'm taking three courses and reading two textbooks concurrently, and it does not feels overwhelming but instead helps a lot with understanding.
So BIO 1311 "Introductory to Biology" fails to be a good fundamental course in a various aspects.

1. No textbook readings
2. No solutions to problem sets
3. No detailed explanation (this gap should filled with textbook). Many students cannot solve the problems given in the course, which would lead to frustration and anxiety. Students would think that they are not "good" enough to study biology.

Overall BIO1311 is a good course for non biology major. I think to be a good curriculum in bioinformatics either one of this should be done with OSSU's curriculum:
a) replace Introduction to Biology - The Secret of Life with Introductory Biology 7.016
b) just add Introductory Biology 7.016 to the curriculum

Fundamentals of Biology is a course offered in MIT campus in Fall 2018 (which means it's relatively new). It's based on a good textbook (which I'm using), even if something won't be clear from lecture there's always a required reading where you will understand what you want.
7.016 contains detailed calendar when to read and when to solve problem sets in case you need one.
It has good quality problem sets and recitations (which are basically summaries and problems).
And recorded lectures which are also not bad.
Students will get a deeper understanding of each topic from 7.016 which would make them love and appreaciate biology.
The proposed course is much more rigorous but it's worth time spent.

The link

1. https://lagunita.stanford.edu/courses/Engineering/db/2014_1/about
   is no longer available.

This one should be the right one:
2) https://online.stanford.edu/courses/soe-ydatabases-databases

Stanford Online retired the Lagunita online learning platform on March 31, 2020 and moved most of the courses that were offered on Lagunita to edx.org, come to that links on page 2) points to edx.

Is it intentional that the link points to the 2008 class rather than the 2014 class? It kinda sounds like 2008 has more bio examples but it's also missing problem sets (unless I just suck at finding them).

https://www.edx.org/course/molecular-biology-part-2-transcription-and-transposition

https://www.coursera.org/learn/calculus1

This course here is no longer available:
https://www.edx.org/course/introduction-differential-equations-bux-math226-1x-1

An alternative is available here:
https://ocw.mit.edu/courses/mathematics/18-03sc-differential-equations-fall-2011/
I've found it quite well organized, and the course videos are straight out of MIT's intro ODE class.