Genomic Data Science

I want to improve my bioinformatics skills, Genomic Data Science from Coursera?

I have a lot of background in biology/genetics (currently a postdoc), I'm fairly comfortable using the Linux command line and Perl, and I have experience analyzing ChIP-, RNA-, and WGBS-sequencing using several of the commonly used command line programs plus some R/Bioconductor packages. I want to learn/improve my knowledge of Python, statistics, and R. The Genomic Data Science Specialization at Coursera seems to cover the relevant topics, at least as a way to get started. I would skip the material I'm already familiar with (courses 1/2/5 = Intro/Galaxy/commandLineTools) and do the other ones (3/4/6/7 = Python/Algorithms/Bioconductor/Statistics). Does this seem like a good idea? Are there other courses that would be better? Any advice or feedback is appreciated.

I am lost and I need guidance

Hi everyone,

There is no short way to say this other than the subject above.

Please if you have time, do read ! do help me ! I am a student and I seriously need guidance !

I will get right to it,

I have always wanted to be a psychiatrist and a game developer, I never accepted the fact that in order for us to truly feel better and survive our emotional depressions and such, we are forced to meet addicting medications. I have always thought about an alternative, something I can reach that will make people feel better and in the same way addiction-free.

Why a game developer ? In the past I loved programming, till I discontinued multiple games due to the amount of frustrating courses that I have followed, I never had the breath to continue a course that never explains stuff fully.. The moment I felt stupid and incapable I directly stopped, which made me hate programming a bit, I never had anyone to guide me or a decent courses to hop along. When I grew up I realized this was just a big excuse for my failure and that I have to start programming from scratch again but this time without giving up and not for gaming but for something more meaningful towards my goal.

In Egypt which is where I am, according to our High school score "Final year only" also called "Thanawia Amma" we get to choose what fields we can apply to and in what universities.

Psychiatry wasn't there because I got 89,% and it was from 98,5%, I then came to realize that there is another field called Biotechnology. I have realized how close this can be towards my actual goals, since I don't want to spend the rest of my life listening to people's verbal issues more than actually solving them from a lab by eliminating the root cause, Biotechnology had all my wishes. I am meeting face to face with the conductors of hormones, of our behavior maps... DNA !

I get to work closely against the enemy, however the only part of biotechnology that is accessible to me was and which I am in at the moment is "Agriculture Biotechnology"

Now

The thing is in Egypt, we have no quality labs, no quality courses, no Quality teaching. Whoever succeeds either by enrolling in very expensive colleges or intensive online courses. I slacked in my first two years in my Cairo university, I never took what I am doing seriously... I felt hopeless that I am never gonna reach my goal, barely got out with score B of accumulative semesters.

But then recently I came to also realize that there is a field that gets in touch with both biological side and programming side, this is where I am stuck at.

All I want is to help our world become much easier to be in and live happily, I am not a programmer, I am not anything special yet. However my goal is to become something, someone that will change this world.

Every time I ask someone about bioinformatics, they either say

(A)you can either be a biologist mainly with some programming knowledge to help you process the data "This has a flaw !"

I haven't done a practical thing other than stand in labs and do some pi-petting to detect some enzymes, I don't know what type of biological data I would work on and to detect what exactly, so I feel super lost !

(B) You can do software to assist biologists "Sounds cool but not the way I really wanted to live my dream"

Also it is flawed for me in a way because they say you have to be an experienced programmer as for example a graduate from a computer science field, Which I am not and my experience if there will be any in the future will be 1-2 programming language, I am still scared to start... I am afraid that I will get stuck again.

Now both A and B doesn't seem like they would lead me to my goal, or anywhere close to it... so before I start asking questions and end this topic from my side Here are some things you need to know about me.

1. I have self taught my self English. "So this large text wouldn't be here if we are talking about Egyptian Education, I know it's not perfect but it is good enough That I got to use my language to work for multiple companies from Egypt here like : Vodafone UK and Ring company that sell security cams"

2. I am a very stubborn and determined person, If I just come to realize I want something, I would push my self to it everyday because I just don't accept not getting what I want ! That's why I am here, because I want something but I don't know where to start my path in it !

3. I know I look skill less and so on, but if you were to just help me... a little bit of guidance, Iam sure I will appear to be something. (I have tried E-mailing multiple people to assist me or guide, none of them agreed... I even tried contacting MIT where Professor Eric lander taught his courses on Edx, no luck. I tried the professors in my university, but they are more interested in working with students from abroad with actual education than me... "

4. I don't want spoon feeding, I want guidance and answers, I will do the digging... just point out on where !

5. One of the main reasons I am picking bioinformatics, It requires very little to no wet lab, because that is very expensive in Egypt if any was to be found, Besides I am really interested in programming, I even started an Excel course from Microsoft and got my certificate at 95% score, I just love stuff like Excel "I know Excel doesn't relate much to actual programming", where analyzing data,Understanding what is underlying there and figuring out a way to fix it !... That's how I generally love to work !

6. I am with very limited time, I have 4 semesters left, Then I will have to join an obligatory military service (1-3 years) and I am 20 years old soon at next Jan to be 21.

My options are either (A)

I continue my 4 semesters with both good grades at university and side studying bioinformatics.

OR (B) I find my self a scholarship where I can repeat all semesters but in a place that would guide me right and prepare me truly to the working environment.

OR (C) Same as (A)but I would find my self side projects to work on while studying, and right after the obligatory military service I would just bump out to do my master's and so on !... I am still planning to continue studying either way as a researcher mainly.

NOTE : ( I was accepted in Turkish scholarship2018 fully funded, But the university was in Samsun had a worse education than Cairo "That's what my Turkish friends told me.", So I felt like It's not worth repeating a full year for the same level of education and also in Turkish.. Which is not the language I would want to study in.")

Now my questions "I really appreciate whomever is still reading all of this !"

1. After reading all of this, do you still think Bioinformatics can help me achieve my goal if so then How ?

2. After reading all of this, where do you think I should start ? "I will put some links where one of the professors thought it's a good idea to start (For anyone, not me specifically! Which sounds odd, maybe it's not the best for me to start, as I mentioned above I have very limited time, No place to add something that wouldn't benefit me in anyway"

3. https://www.coursera.org/specializations/genomic-data-science?ranMID=40328&ranEAID=mRETjYz*mIw&ranSiteID=mRETjYz.mIw-cSkOe8kEvUlzng8yXLxJJg&siteID=mRETjYz.mIw-cSkOe8kEvUlzng8yXLxJJg&utm_content=2&utm_medium=partners&utm_source=linkshare&utm_campaign=mRETjYz*mIw

https://www.coursera.org/specializations/bioinformatics?ranMID=40328&ranEAID=mRETjYz*mIw&ranSiteID=mRETjYz.mIw-MiGHStCIh1tiQrJsRynSvQ&siteID=mRETjYz.mIw-MiGHStCIh1tiQrJsRynSvQ&utm_content=2&utm_medium=partners&utm_source=linkshare&utm_campaign=mRETjYz*mIw

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1. Talk to me, tell me what you think generally ! and What would you do if you were me.

LAST QUESTION : Do you think I can change the world from Agricultural biotechnology + Bioinformatics ? If so how would I change my goal ? " we study genetics, Microbiology, Biochemistry in details with examples on plants"

Final Note : I am currently trying to apply to Holland Korean Universities maybe I can repeat it all somewhere else, with just a better shot.

All will change depending on just an answer that can guide me !

Thank you !

What course would be best to take?

I'm a biotech student trying to learn some programming to help me stand out to employers. Does anyone have any advice on which of these two courses would be better to take if I was trying to get into the programming aspect of the biotech field? Would it be better to go for a broader course before trying to get into the specifics of the field or should I just go for the directly applicable course? Thank you!

https://www.coursera.org/specializations/data-analysis?action=enroll

https://www.coursera.org/specializations/genomic-data-science

I think there are coursera courses that take you through the steps of quality control and analyzing NGS data.

https://www.coursera.org/specializations/genomic-data-science

This one’s pretty good, there are others too

Which course would be the best to take? [xpost r/biology and r/datascience]

I'm a biotech student trying to learn some programming to help me stand out to employers. Does anyone have any advice on which of these two courses would be better to take if I was trying to get into the programming aspect of the biotech field? Would it be better to go for a broader course before trying to get into the specifics of the field or should I just go for the directly applicable course? Thank you! https://www.coursera.org/specializations/data-analysis?action=enroll https://www.coursera.org/specializations/genomic-data-science

You’re right, it looks like the Bioinf courses I remember aren’t currently offered (last time I saw them it was a few years ago). I looked through what’s currently available and if evolutional studies is more what you’re looking for this course from JHU is probably your best bet to get started:

https://www.coursera.org/specializations/genomic-data-science

It’s going to walk you through using the command line and biocunductor tools in R for NGS. This seems to be a good starting point to get you coding and working with NGS data off the bat.

I found Genomic Data Science specialization offered by John's Hopkins University in Coursera very helpful. You can audit the courses as well. Especially the course #5 deals with next gen sequencing data which is what you're looking for! https://www.coursera.org/specializations/genomic-data-science

John Hopkins offers an excellent Genomic Data Science course through Coursera that covers R, python, command line, bioconductor, and other stats in the context of genomics. It's a great starting point for learning these tools, but it does cost something like $50 per month and they say it takes about 7 months to finish (the person I know who completed it took longer). You can bargain down the subscription cost on the grounds of being a student. I'm not affiliated with them in any way :)

https://www.coursera.org/specializations/genomic-data-science

Recommendations for free MOOC on genetics please?

Hi,

I'm currently studying for a masters in computer science, and have recently developed an interest in genetics. I don't have much of a background in either biology or chemistry, but enjoy learning :)

Are there any MOOCs that are broadly recommended by the genetics community?

I am currently considering starting with one of:

Genomics: Decoding the Universal Language of Life

Introduction to Genetics and Evolution

...and then possibly following with:

Become a next generation sequencing data scientist

...Or a selection from

Genomic Data Science Specialization (John Hopkins Uni)

Can anyone share their experiences with these, or other genetics MOOCs? Any other courses or learning resource recommendations would also be much appreciated!

Thanks :)

Genomic Data Science course

I am a software engineer looking to explore bioinformatics. Have you taken the Coursera's course Geniomic Data Science (https://www.coursera.org/specializations/genomic-data-science#about). Would you share your experience? Thanks in advance.

I was able to enroll in some for free because my Uni had partnerships with Coursera. You should check out your Uni’s Learning Resource Center if they offer a simular thing!

If that’s not an option however, some courses offer financial support and would range from about 20-80USD iirc depending on the depth and difficulty of the coverage.

I would suggest the Johns Hopkins Genomic Data Science Specialization here. Some of the profs there were the actual dudes who created famous aligners like Bowtie and BWA, so it’s cool that they teach you firsthand how to operate the programs. It would certainly help if you’ve already got a background in one of BS Biology/biotech/microbio though.

Best of luck to you!

https://www.coursera.org/specializations/genomic-data-science?= It is a long program (approximately 7 months) and has everything in it( for a beginner) But I am more willing to do some research so want to focus more on projects and stuff.

I come from a Comp. Sci. background and Bioinformatics is a different world for me.

However, I did come across these courses:

https://www.coursera.org/specializations/bioinformatics

https://www.coursera.org/specializations/genomic-data-science

Currently, I am studying the bioinformatics course provided by UC San Diego(the first link).

Maybe these might help you so do check out the material that they provide.

Absolutely! I just finished the online data science boot camp through Flatiron school, although there are many others that probably accomplish the same thing. Coursera classes:

https://www.coursera.org/specializations/genomic-data-science?

https://www.coursera.org/specializations/bioinformatics?

There’s a lot of overlap between those 2 specializations so I did first one fully and only worked on some independent projects that came up in the second link. I also used Rosalind to find and showcase little projects that probably seem so basic to an actual bioinfo PhD lol but since my background is all wet lab molecular bio, I figured it would at least be a good start and hopefully I can build on this in grad school! Good luck with everything!!

Actually these:

UC San Diego Bioinformatics

Johns Hopkins Genomic Data Science

I think the JH one is higher level and more current, and the UCSD one hasn't been updated in some time. So I guess I would say the JH one.

For the concepts, I love the 8 course specialisation offered by Johns Hopkins on coursera. https://www.coursera.org/specializations/genomic-data-science I also like the UCSD specialization too https://www.coursera.org/specializations/bioinformatics#courses

For practicing and getting the hang of the concepts, Rosalind Rosalind Rosalind!! Start with Bioinformatics stronghold track and move your way up to the advanced ones. http://rosalind.info/problems/locations/

That's understandable. I can't say much as I'm still a student. But if its worth anything, the program I'm in doesn't have an online part for its Masters bioinformatics program. I imaginge this it because the topic is so multidisciplinary that it helps to have an on-compus learning experience. So unfortunately, I figure this might be similar to other programs around the country. There may be great online bioinformatics programs I'm not aware of.

If you're looking for cost-effective ways of gaining knowledge, you could consider taking the Genomic Data Science Specialization on Coursera. You can audit the individual courses for free.

A quick Google search does show that Johns Hopkins (the same institution that teaches that specialization I linked above) has a 100% online bioinformatics program.

https://www.coursera.org/specializations/genomic-data-science

Good for starting out imo.

need help choosing

Hi I am an engineer who mostly works with machine learning. I want to develop domain expertise and biology has been always my love(why I am an engineer, circumstances). I want to take course as a starting point. There seems to lot of overlapping between the courses. I want to learn core ideas and processes of biological aspects mainly as opposed to computational aspects.

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Genomic Data Science Specialization[1]

Bioinformatics Specialization[2]

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[1] https://www.coursera.org/specializations/genomic-data-science#courses

[2] https://www.coursera.org/specializations/bioinformatics#courses

Let's see how you can connect your interests to your degree:

• genetics - goes without saying
• medicine - goes without saying
• learning languages - nope, keep this as a hobby
• geography - spatial epidemiology? Quite a narrow field, requiring statistical knowledge and coding skills. Other than that, environmental science, ecology, possibly geology..?
• math - yes - depending on how inclined on math you are, as some fields of biology are very math-heavy. However, I believe such fields of study consist of mathematicians entering the field of biology rather than biologists entering the field of mathematics. They're also very academical/theoretical.
• coding - absolutely - and it's becoming an in-demand skill for biologists!

Why not bioinformatics? You like to code and you have your degree, it might be the best way to use the knowledge you already have. It also pays quite well, especially compared to other Biology jobs. You can probably easily go for an MSc in bioinformatics, but to give you a taste in order to decide here's some (carefully structured :)) advice:

• Learn some Python if you haven't (Codecademy is really not enough, and I can recommend the following books as they'll all give you plenty of practice and practical knowledge: Introduction to Programming Using Python (try to solve as many exercises as you can), Dive Into Python and Automate the Boring Stuff With Python in that order.)

• Learn how to use Jupyter notebooks as well (free, easy, popular and useful tool to code in - all you need to begin is here). You can do this as step one and use it to solve book exercises in.

• Practice a bit on Codewars - even when you know how to solve some problem, you will improve much faster if you inspect other people's code and learn from them.

• This is where the real fun begins - try and solve some Rosalind problems, see if you like it.

• If you do like it, there's an entire series of Bioinformatics and Genomic Data Science courses on Coursera to give you a taste of the "real" stuff.

Here's some more advice from people in the field: https://www.biostars.org/p/188038/ (the op is considering switching fields, but you might find something useful to yourself)

Even if you find you don't like bioinformatics you'll end up with enhanced programming skills which will likely be a plus in whatever other career path you choose.

I don't know your academic background, but I'm a neuroscience major with little coding background. I'm currently taking some courses as part of a Genomic Data Science "Specialization" through JHU:

https://www.coursera.org/specializations/genomic-data-science?=

I've had pretty decent success with these courses so far, and everything's been very intuitive despite my lack of experience in programming. You can take the courses as seriously and rapidly as you want (which leaves room for being able to slack off), but this means that if you're motivated you can tackle a ton of information/skills in a short amount of time.

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If you're looking for something more general, I'd suggest looking at the "Data Science Specialization" through JHU:

https://www.coursera.org/specializations/genomic-data-science?=

I don't have any experience with this one, but if its anything like their Genomic-based specialization it should be a great way to learn some fundamentals. Again, not sure about your previous experience, so if you already have some programming under your belt these courses may be a bit too basic.

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Good Luck!

> udacity is by far the best provider of MOOCs

nope, not even close

> Which course would be best for that, especially the bioinformatics part?

https://www.edx.org/micromasters/usmx-umgc-bioinformatics

https://www.coursera.org/specializations/bioinformatics#courses

https://www.coursera.org/specializations/genomic-data-science#courses

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

https://www.edx.org/course/essentials-of-genomics-and-biomedical-informatics

https://www.udemy.com/courses/search/?src=ukw&q=bioinformatics

https://www.extension.harvard.edu/course-catalog/courses-by-certificate/Bioinformatics-Certificate?certificate_required=Bioinformatics%20%28choose%201%29

First congratulations on getting the internship. Secondly, as others said, no one however exalted they maybe should ever insult you! And finally, to add another resource check out: Biostars forum (https://www.biostars.org/). It's a resource that folk like me (final year PhD student in statistical genetics) heavily use. It has wealth of info on handling different file types, analysis methods, troubleshooting and the forum members are so darn awesomely knowledgeable that I always get to learn something. Ohh also stackoverflow as usual for any programming help!

Some books/courses to help out:

1. Biostars Handbook (https://www.biostarhandbook.com/) - This includes a wealth of info curated from Biosatrs intro articles etc, and has a separate book on Bioinformatics Scripting. Because most likely you would use shell scripts to do QA/QC and analysis.
2. Primer to Analysis of Genomic Data Using R (https://www.springer.com/gp/book/9783319144740) - If they use R instead of Python
3. Bioinformatics with Python Cookbook (https://www.oreilly.com/library/view/bioinformatics-with-python/9781782175117/) - If they use Python instead of R
4. Bioinformatics Data Skills (https://www.oreilly.com/library/view/bioinformatics-data-skills/9781449367480/) - Similar to Biostars Handbook
5. And finally, Coursera has a nice specialization on Genomic Data Science and you can easily access individual courses within it for free: https://www.coursera.org/specializations/genomic-data-science

Best of luck with your internship!

You sound exactly like me. 24, similar interests, and didn't learn jack in college, except I went to a business school so that's a given.

Harvard, Johns Hopkins, and MIT are at the forefront of these fields, imo. Harvard has a good series on Data Analysis for Life Science that I'm taking ( https://www.edx.org/professional-certificate/harvardx-data-analysis-for-life-sciences), and I know MIT has a lot on edX and ocw.mit.edu. Here's a class specifically for synthetic biology: https://www.edx.org/course/principles-of-synthetic-biology

Haven't taken that one yet, but I liked the lectures for their Business of Biotech class.

And JHU's Genomics series: https://www.coursera.org/specializations/genomic-data-science

JHU also has a lot of online Master's programs. I don't know how good that'd be for doing the hands-on engineering or fabrication, though.

For AI, deeplearning.ai's Coursera series is considered the best place to start: https://www.coursera.org/specializations/deep-learning

I have a library of textbooks and MOOCs that I finally have time to go through, so hopefully this is helpful. Wish you great luck. Once you figure the applied side of things, I hope you can share that wisdom with me.

https://www.biostarhandbook.com/ (Not free but worth the money, good for beginners and intermediates)

Coursera:

https://www.coursera.org/specializations/bioinformatics (more algorithmic, comp sci approach, this might be what you're most interested in)

https://www.coursera.org/learn/bioinformatics-methods-1 Very beginner level

https://www.coursera.org/learn/bioinformatics-methods-2

https://www.coursera.org/specializations/genomic-data-science (intermediate level, not the best instruction for beginners)

Edx:

https://www.edx.org/micromasters/bioinformatics (I can't comment much about it, haven't looked at material)

Other:

https://software.broadinstitute.org/gatk/ This is from the Broad, and gives an idea of current best practices in clinical bioinformatic analysis.

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Good luck!

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