Join Us in a Top 50 MOOC of All Time! How do we sequence and compare genomes? How do we identify the genetic basis for disease? How do we construct an evolutionary Tree of Life for all species on Earth? When you complete this Specialization, you will learn how to answer many questions in modern bi...
Whole Genome Sequencing Viterbi Algorithm Suffix Tree Python Programming Algorithms Unweighted Pair Group Method with Arithmetic Mean (UPGMA) Bioinformatics Bioinformatics Algorithms Dynamic Programming Graph Theory
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University of California San Diego
This specialization includes these 7 courses.
Reddit Posts and Comments
1 posts • 92 mentions • top 44 shown below
18 points • arosa09
Which of coursera specialization is better to get into bioinformatics?
I am a medical graduate and I have interest in data science and bioinformatics. I started applying data science technique to my current work. However I am looking for Phd position in a lab in bioinformatics. I will self-study bioinformatics but I feel the amount is too huge to get started so I want an outline to a track to follow before I start applying. I found those 2 specializations on Coursera
I don't know which one is better to help me get a position in a lab would you please suggest me a track to start on ?
6 points • Naturedrag
Help in selecting a viable topic for a 4 month project
Hi, I am going into my final year of undergraduate study in biotechnology and have decided to do a sort of mega-project in the field of bioinformatics since I wish to peruse my masters in that field and this project would really help me in the application process for my further studies. I currently have done: * A variety of biotechnology based courses (Drug Design and Delivery, Genetics, Recombinant DNA Technology, Microbiology, Immunology, Bio Chemistry, etc.) * A Bioinformatics course in university, it was however mostly theoretical. * I am currently doing the 7 part bioinformatics course of coursera Link. (Finished the first 3 parts) * I am also reading through the Essential Bioinformatics textbook by Jin Xiong
I, however, only have very basic coding knowledge and skill (only done a basic C programing course).
Based on this would anyone be able to guide me on what kind of topic I should base my project on, that would be possible to complete in 4 to 4 and a half months, including the time i would need to study or pick up new skills? If you wish for more information regarding this, please do ask. I would be grateful for whatever guidance you may be able to provide.
4 points • kyleekol
Hello r/bioinformatics, I need some help
recently graduated from Queen's University Belfast with a BSc in Biomedical Science and have decided that my next step is to undertake a masters degree in bioinformatics and computational genomics. I've been looking at a number of online courses in the field in order to try and help my application (such as coursera's 'Bioinformatics Specialization' https://www.coursera.org/specializations/bioinformatics) and have run into some problems. Whilst I have a reasonable understanding of bioinformatics (my final year dissertation was on current DNAseq landscape in NGS-driven clinical decisions in cancer), my study has always been on the biological/clinical side of bioinformatics. I feel like doing this course would require a level of programming knowledge that I don't have and I'm wondering if there is anybody who was in a similar situation to myself (coming from a purely biological/medical background and not a computer science background) who could help me out with some courses or reading. I understand it would be advantageous to learn 'R' or python before commencing a course in bioinformatics but I'm very lost!
TL;DR what is the best way to get into the programming side of bioinformatics for somebody with no programming experience
17 points • seifeldin122
I am lost and I need guidance
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"
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.
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"
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 !
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... "
I don't want spoon feeding, I want guidance and answers, I will do the digging... just point out on where !
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 !
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 !"
After reading all of this, do you still think Bioinformatics can help me achieve my goal if so then How ?
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"
- 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 !
3 points • johnlavolpe
https://www.coursera.org/specializations/bioinformatics made at UCSD
3 points • makeswell2
Is an understanding of bioinformatics algorithms important for a job?
I'm trying to wrap my head around what skills are necessary for a 'bioinformatics job'. Or if there are different jobs within bioinformatics that require different skill sets.
I love the algorithmic side of bioinformatics, and these courses that teach that side, but I wonder if all bioinformaticians need an understanding of algorithms, or how algorithms fit into the bigger picture. Further, I am two semesters shy of graduating with a Bachelor's in Computer Science, and this summer is my time to take just one (or two) courses in bioinformatics, along with help in a lab building a pipeline. I don't know if the algorithms course I linked would be the one to chose to position myself to get a job in bioinformatics, or if there is a better choice to accomplish that. Is the algorithms background truly essential, or is there more important stuff.
6 points • niemasd
The Bioinformatics specialization track on Coursera and the accompanying textbook, Bioinformatics Algorithms: An Active Learning Approach
2 points • NullTheFool
Here you go! You can audit those courses individually :) have fun!
2 points • runhigher
Thanks, I'll check those out. I've never used coursera before, it looks like I'd have to wait until the 18th- I can't jump right into it?(https://www.coursera.org/specializations/bioinformatics?action=enroll).
2 points • being87
apart from googling and reading tons of great content online, you can also find a bit more curated and structured online courses on coursera https://www.coursera.org/specializations/bioinformatics
1 points • Thalrador
Its this one: https://www.coursera.org/specializations/bioinformatics
I really recommend it if you want to delve further into algorithms!
1 points • genomedr
I recommend most professional resumes have bulleted or highlighted skills at the top, then relevant work experience and education last. As long as you can demonstrate proficiency with the requested skills in the job posting you'll be fine. Now a days bioinformatics pipelines are pretty much commoditized- many labs just "order one up" from DNANexus or Illumina, but the bioinformatician is needed to spot when things aren't working, do data analysis, help with the assay validation and maintain QC. Here's the info on the Coursera bioinformatics program https://www.coursera.org/specializations/bioinformatics
1 points • kiwiboy94
For courses, you can try the bioinformatics specialisation on Coursera .
In your free time get yourself familiar with at least one programming language. Python is a low-barrier entry language and a good one to start with. Once you are familiar with Python, start on R programming, a statistic language that is essential for data analysis. While picking up these languages, start reading more about this field. Look up on bioinformatics topic on twitter and follow researchers that have projects that interest you. Then start reading more papers, constantly ask yourself questions on how you can get involve in that topic. If you have doubt, reach out to our bioinformatics community, we are super friendly.
1 points • lammnub
Check out some courseras, this one for example https://www.coursera.org/specializations/bioinformatics
A lot of courses/books are going to give you theory which IMO doesn't help much when analyzing actually data. I suggest looking up papers that have deposited data sets and try to mimic their workflow from their methods. When you get comfortable with that, then try taking related data sets from ENCODE and do your own analysis.
1 points • CoalCrackerKid
Have fun! https://www.coursera.org/specializations/bioinformatics
1 points • cannedleech
I'm also in a 2nd post doc, and currently taking this series of courses:
They assume you already know how to program, which I didn't but its not too hard to pick up as you go along. Some of their assignments are a little incomplete or vague in their descriptions, but the comments from other students help with that.
1 points • Tempojack
Hi there. I was considering taking the Coursera intro to bioinformatics. You can find it here. You get a 7 day free trial and then it's $50 a month after that until you complete the specialization. I haven't started it nor know anyone who has completed it.
I don't think they teach anything python or R related, but if you can tether the course with some basic programming (either by book or free resource) then it may be worthwhile at least in terms of focusing problem solving on bioinformatics with programming concepts?
You could also try searching EDX for some structured programming classes (I haven't seen any bioinformatics things on their end, but also haven't looked in depth). You don't have to pay anything for the class if you audit it. If you want a certificate, then it will cost $$. Could be another resource to help you with the programming side that's free.
Note - sorry if I'm advertising and that isn't allowed. I've just had a good experience with one of their classes and I think $50 is relatively cheap compared to blindly taking college level courses which cost a few hundred $$.
1 points • fkautz
This answer is correct.
Go sign up for the bioinformatics course on Coursera and go see if you like it.
1 points • Nimkolp
If you want a literal curriculum might as well start here
1 points • MIKParadox
Oh great! Thanks for your opinion. How long it took you to complete:
and apart from that if I would like to focus more on the applied side (ML/DL) of bioinformatics rather than core algorithms what suggestion or direction will you have for me?
Thanks in advance.
8 points • niemasd
No clue about your transfer situation nor retaking classes, but I'm pretty knowledgeable about Bioinformatics at UCSD as well as Bioinformatics education in general. Rest assured that, even if you're unable to switch into the Biology: Bioinformatics major, you can still get the proper Bioinformatics training you need. The only main classes you need to take are Pavel Pevzner's CSE 181 course (Bioinformatics Algorithms, which has an online equivalent you can take through Coursera for free instead of for UCSD credit) and Vineet Bafna's CSE 182 course (Biological Databases, but this is a misnomer and it's pretty much an extension of CSE 181). Glenn Tesler's MATH 186 is also useful if you don't have a solid statistics background, but not as much as the other two. Even if you're not in the major, I'd imagine you can ask them directly to give you enrollment permission. CSE 181 and MATH 186 are offered every winter, and CSE 182 is offered every spring
I would also 100% recommend looking into Terry Gaasterland's SIO 242C course, which is pretty much an intro to all types of real bioinformatics analyses. It was the single most practical Bioinformatics course I took: given a real biological dataset and a real biological question, what are the proper workflows to run and how do you run them? Plus she's super chill and will definitely clear you to enroll in her class
Aside from those 3 or 4 courses, I strongly suggest just trying to jump into research. SIO actually has a lot of cool Bioinformatics projects (e.g. Greg Rouse collaborates with my lab, Terry Gaasterland is over at SIO, I know there's some cool ocean metagenomics projects, etc.), but you can also look into faculty members in the other departments (e.g. CSE, BENG, School of Medicine, etc.; check the faculty list for professors who work on stuff that interests you). You actually don't learn very much real Bioinformatics in the courses of the major (it's all very theoretical); the vast majority of your learning needs to come from research
Then the last thing to address: "But my major won't say Bioinformatics!" As it turns out, pretty much no other schools across the country have a "Bioinformatics" major. Some schools have been recently creating "Bioinformatics" or "Computational Biology" or w/e majors, but not many and very recently for the ones that have. No matter what your aspirations are for after undergrad (e.g. Ph.D., industry, research, etc.), if you want to do Bioinformatics work, nobody cares about the title of your major because people in the field come from such randomly titled majors. What matters is the specific skillset and knowledge base you have, which is what you will gain from research and from these classes I mentioned
TL;DR: Hopefully you can transfer, but even if you can't, you're totally chillin. Your immediate plan of action should be the following:
Join the Undergraduate Bioinformatics Club to network with other Bioinformatics-interested students as well as to go to their events (e.g. workshops, research panels, professor talks, etc.)
Take Pavel's course, either as CSE 181 at UCSD, or if they don't let you enroll in it, the online Coursera version is literally 100% identical (I personally helped create the course). Try to get the online course series done over the span of the next few months
Find a lab to join. Go through the Bioinformatics faculty list and find professors whose research interests you on two fronts: (i) the biological question they're tackling (e.g. cancer, or autism, or evolution, or marine animals, etc.), and (ii) the computational methods they use to tackle the problem (e.g. traditional sequence alignment stuff, or machine learning algorithms, or network algorithms, etc.). Once you have a list of professors who interest you, literally go down your list and email them asking "to meet to discuss potential research projects" (those exact words). Many will probably ignore you, but all you need is one
Figure out what exactly your post-graduation goals are, and work towards setting yourself up for those. You can feel free to PM me if you ever need advice on this front (or on any of the previous things)
> I love computers but im a junior and I fee like I screwed up my early years
Don't stress, you have plenty of time to get into Bioinformatics :-)
5 points • TebbaVonMathenstein
I'm in the same boat -- trying to go back for a Masters in genomics/bioinformatics/bio-engineering in the next year after working as a software engineer. My sister-in-law just got a Ph.D in molecular biology and she (and her peers) echo what others here are saying: your quantitative background will be an advantage. You'll be able to collaborate with people who understand the bio and chem stuff more than you do, but it won't hurt to go back-fill some of that knowledge.
If scheduling is the main problem for taking the class at your university, you can find a lot of good general level information online. Checkout Khan Acadamy's biology section, for example: https://www.khanacademy.org/science/biology (consider the chemistry section too). Since my background is programming, I'm also considering this bioinformatics class on Coursera to help me prepare: https://www.coursera.org/specializations/bioinformatics.
Having papers that you want to understand, but can't yet, is a great starting point. Read the paper until you find something you don't get -- then start your research there. I hope it helps, and good luck to you.
2 points • hamtaroismyhomie
2 points • divineartist
I'm not sure how good this is and have also been considering taking this. It seems like a reasonable course. If anyone has experience with it, I would appreciate any critiques/feedback.
3 points • smash_teh_hamsta
given your phd I'd suggest you focus on research/data science roles over and above web development.
Python is also a really good choice in language; flexible, easy to learn and have lots of science/data libraries to have fun with.
If I where you, I'd check out websites such as Coursera, Edx and be on the look out for anything that seems to merge your interests.
For what it is worth, I think you may struggle to get a coding job without at least something on the CV that suggests you can (a) do it and (b) are willing. One or two online courses should probably help you figure out a path.
7 points • niemasd
> Phase 4: Electives i) Algorithms - Grokking Algorithms Book + Bioinformatics Algorithms Book/Course ii) Statistics ?
Electives? Algorithms and statistics are most definitely required, not electives. Once you know how to program in Python, I would recommend going through my Data Structures text before attempting to learn about algorithms, and then once you're ready, I always recommend Bioinformatics Algorithms: An Active Learning Approach (and its accompanying online courses, 1 2) for Bioinformatics algorithms, and I strongly recommend Algorithms, by Sanjoy Dasgupta for a general Algorithms book. The Data Structures and Algorithms series on Coursera is great if you need a MOOC for general algorithms. Once you have a solid understanding of data structures and algorithms, you should be solid on the computer science theory side of things
Useful statistics includes the theory behind various hypothesis tests (e.g. Wilcoxon, Mann-Whitney, Student's t-test, Chi-Square, Fisher's exact, etc.), various probability distributions (what a random variable of each distribution means, their relationships with one another, their properties, etc.) (e.g. uniform, gaussian, exponential, poisson, log-normal, gamma, etc.), fundamental probability theory, and combinatorics. I don't know what a good resource would be to learn these things
1 points • VirtualCell
I think the BioPython tutorial and cookbook, especially the first few sections, might be great: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc8 -- they go over how to load/parse (SeqIO.parse()), transform (Seq.translate, etc), and format (SeqIO.write(my_record, "fasta")), etc, for DNA, RNA, and amino acid sequences.
Or, for a more programming/algorithms-centric view, the Bioinformatics courses on Coursera are challenging and fantastic: https://www.coursera.org/specializations/bioinformatics
There's not really a one-page "hello world" equivalent because th
1 points • Turin_Martell
5 points • martasetzer
First of all, congrats for your choice ;) I'm doing bioinformatics right now and is important to have a minimum knowledge on programming, even for running someone's else software. You can be a basic bioinformatician and perform analysis using available software (it's okay and they're necessary too because sometimes it's hard to do it and to interpret the results) or you can be develope your own software and analysis. In this case, you really have to know how to program.
It's weird that your university doesn't teach you basic programming, maybe it's not specified but you will do. If not, maybe you should think about going to another university.
In bioinformatics the most used programming languages are Python and R (most for the statistics part), and you should also be used to work with the Linux command line. There's a lot of online courses on coursera to learn this.
Python: https://www.coursera.org/learn/python (I did this one when I started) https://www.coursera.org/learn/python-genomics? https://www.coursera.org/learn/bioinformatics https://www.coursera.org/specializations/bioinformatics
Enjoy the journey! Programming could be really frustrating sometimes, but hold on! And the end it's really fulfilling. Hope it helped :)
1 points • orenmn
1 points • 7LayerMagikCookieBar
I'm currently taking this bioinformatics algorithm course from UCSD: https://www.coursera.org/specializations/bioinformatics
You can create your algorithms using any programming language, just need to submit the correct answers. I've been enjoying it a lot. The instructors are also involved in the kaggle-esque bioinformatics website called Rosalind: http://rosalind.info/problems/locations/
1 points • Dynev
If you're just beginning learning bioinformatics, I strongly suggest starting with free online course on coursera from San Diego Uni (https://www.coursera.org/specializations/bioinformatics). It is possible to get access to courses' materials for free using audit option. This course is a great starting point. Pavel Pevzner, the main author, also has a few decent books for people new to bioinformatics.
If you have a more specific task in your mind, there are good reviews that cover tools/skills commonly used in that area, for example, genome annotation. I can't personally recommend any related to genomics since my area of interest is far away, but I'm sure they are easily findable.
Hope to be helpful. Good luck!
1 points • niemasd
It's great that you're learning this! Quick note, though: it's not clear to me why you're searching for suffix trees if you're working on LCS. The LCS problem is solved (most efficiently) via Dynamic Programming
I would suggest the following learning materials for data structures and algorithms:
My own Data Structures MOOC
The Bioinformatics Specialization Track on Coursera, which accompanies the textbook
5 points • proozywoozy
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.
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.
1 points • mam288
Thoughts on switching from Biology to Bioinformatics
I'm looking to get some thoughts on what it would take for me to switch fields. I have been away from science for 6-7 years and am considering going back to school for Bioinformatics. I have a Ph.D. in Genetics and limited programming experience (some online courses in Java, a couple basic CS courses years ago in undergrad). My question is, what would I need in order to get hired for a bioinformatics job? My options are: 1) Master's Degree in Bioinformatics from a local University (North Carolina State University) 2) Online Master's Degree (Johns Hopkins, NYU, Brandeis, etc) 3) Cousera Specialization (https://www.coursera.org/specializations/bioinformatics?utm_medium=courseDescripTop, https://www.coursera.org/specializations/genomic-data-science, https://www.coursera.org/specializations/systems-biology)
Of course, a Master's Degree would be ideal but they are pricey and a full-time program would be difficult for my family (I have 2 young kids) as for 2 years I would not be bringing in any income and would be paying tuition. I could potentially work part time at least if I did an online Master's but I'm not sure if they hold the same amount of weight? The Coursera Specialization would be the easiest from a logistics perspective but I don't know if it would hold enough weight when applying for jobs to be worth the time investment. Does anybody have any thoughts on this?
Thanks in advance for any advice!!
3 points • paarulakan
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.
8 points • drdhuv
My (long-term) learning plan
I’ve browsed the sidebar curriculum, David Venturi’s Data Science recommendations, OSSU’s bioinformatics curriculum, the Bioinformatics Career Guide and countless number of posts here, to come up with the below plan. I’m keen to read thoughts/critiques/opinions. The italics are maybes depending on how comfortable I'm feeling at moving forwards.
|Title|Platform|Provider| |:-|:-|:-| |CS50's Introduction to Computer Science |edX|Harvard| |Learn to Program: The Fundamentals|Coursera|University of Toronto| |Learn to Program: Crafting Quality Code|Coursera|University of Toronto| |Complete Python Bootcamp|Udemy|Jose Portilla| |Data Scientist with R Career Track|DataCamp |DataCamp | |Data Structures and Algorithms Specialization|Coursera |UCSD | |Statistics in Medicine |Stanford OpenEdx |Stanford| |Foundations of Data Analysis - Part 1: Statistics Using R |edX| UTAustin | |Foundations of Data Analysis - Part 2: Inferential Statistics|edX| UTAustin | |Statistical Learning|Stanford OpenEdx |Stanford| |Bioinformatics Specialization|Coursera|UCSD| |Machine Learning|Coursera|Stanford|
This is will accompanied by Rosalind.info towards the back end.
I’m a clinical haematology/haematopathology registrar (US equivalent of resident/fellow) in Australia looking for an employment and research ‘niche’. My programming experience consists of dabbling with BASIC when I was about 7 years old; I can do a wicked conditional colour formatting in Excel for what that’s worth. My stats knowledge is limited (clinical research and some laboratory applications), though really high school maths is probably a better baseline. In summary, I’m green.
My target is Cambridge MPhil in Computational Biology in 2021/22. Not having a computer science or mathematical undergrad background, I'm aiming to have a solid foundation so this is a 2 year project.
My biggest concern is stats- the OSSU curriculum has college level intro units like algebra and calculus- would these be advisable?
Thanks for all input.
1 points • AlchemicalAle
I was actually in your shoes a little while back (starting my PhD with no real coding experience). Funnily enough, I also wanted to learn about coding with an emphasis on bioinformatics (Python & R). For that, I've been working through a couple of Coursera specializations. The main reason I chose Coursera was so that I could put the completion certificates on my LinkedIn, which I'm hoping gives me at least some minor legitimacy over someone just *claiming* to have experience.
If you're looking for specifics, here is a list of the specializations I'm using:
1 points • mqmareq
I am coming from exactly opposite direction: software engineer being fascinated by biology trying to get into biotech industry - so my comment may be skewed that way.
That being said, I tried the aforementioned courses by Johns Hopkins and while they were not bad, they did not really stand out - maybe it's me, but it was just dry enumeration of basic facts, click here, load data there, without much of the deeper reasoning/explanation, to the point that I had trouble to keep my concentration.
I enjoyed much more the Bioinformatics specialization by UC San Diego: https://www.coursera.org/specializations/bioinformatics
It also has a version bit more accessible to people w/o lots of computer science experience: https://www.coursera.org/learn/bioinformatics?
As well as external support website with tons of extra exercises and nice hands-on introduction to Python that may get you started: http://rosalind.info/problems/locations/
I also started the specialisation by Uni of Toronto, but at that time, I was lacking needed biology background, so I dropped off. Still, it looked like something definitely worth of checking out: https://www.coursera.org/learn/bioinformatics-methods-1
Are these going the direction you had in mind or are they going too much into programming?
1 points • my_password_is______
how much money can you spend ?
this online course was offered last fall
if its offered again this fall I'm thinking of taking it -- but it fills up FAST
there are also this non-credit specializations from coursera to help get you up to speed with your math
and this for bioinformatics
^ this is one recommended for beginners before doing the speciallization below
maybe those + the BS in data analytics would be a good start to get your where you want to go
1 points • pawan12394
Please mention what bioinformatics topics have you covered. Do you have a programming background? What are the research areas you are interested in? Have you covered mathematics/statistics courses ?
However I will try to answer your question to the best of my knowledge and give a an overall idea of what you could do.
For a bioinformatician or computational biologist, you can contribute in research through,
1. A new method/algorithm/insight (bioinformatics advance)
2. Novel biological insight (computational biology)
3. A tool for others to use (public goods contribution)
And these constitute different paths in your skill set development.
There are two types of skill sets in my opinion:
1) A general skill set ( bread and butter for a computational biologist ) : Basic linear algebra, calculus, data structures, working with command line, SQL, molecular biology, genetics, protein structure.
You could strengthen your programming skills by solving these problems in Rosalind , which is a learning my doing platform.
2) A specific skill set ( this takes time to develop and requires a specific area of interest )
A general skill set is a must have, and below I have listed few of the many areas you could work in.
If you wish to build your skills as a software engineer and develop tools that researchers can use, you could learn C++, SQL, cloud computing, web development. I don't know much about software but this is a must have skill set.
If you have a strong background in biology (which I am assuming you do), you could learn bio-statistics and learn programming in R. Knowledge of data structures is a must. This way you could do good research projects in omics. Along with this, knowledge of basic machine learning techniques will be very very useful.
Mathematical modelling in systems biology is also an interesting area of research now and has many projects in understanding disease progression. That requires you to have a good mathematics background in writing differential equations.
Since my background is in genomics I can suggest some online courses and video links where you can start from
1) Bioinformatics Coursera - This is a complete course which will familiarize you with the core concepts in bioinformatics
2) Genomic data analysis X series - This course is also a great starting point if you wish to learn data analysis in genomics
3) What is bioinformatics? - Please go through this playlist by Maria Nattestad. Her channel covers more videos which give an idea of what you could do as a biologist in bioinformatics.
You could message me if you have any more questions. I would be happy to have a chat with you and provide you with relevant study material or ideas.
1 points • advanced_dreams
Fellow newbie programmer here that just started to dive into Python a few months back. Here are a few additional python learning resources you might want to take a look at:
- Learn Python the Hard Way: https://learncodethehardway.org/python/
Decent "from scratch" set of lessons. The $30 price tag is a bit steep, but I'd be happy to share the PDF with you if you'd like.
- Python for Everybody: https://www.py4e.com/
Another beginner tutorial. Part of a broader coursera course and specialization. Totally free. A bit short on practical exercises.
- DataCamp: https://www.datacamp.com/
Killer resource for Python and R programming lessons focused on data science. Really solid learning platform. Good for getting an intro to various Python packages (pandas/numpy/matplotlib/seaborn are essentials). The lessons are very "fill-in-the-blank" but there are tons of extra practice questions and more open-ended "projects". Monthly sub is worth every penny (and you can pause it as needed).
Also, since this is the bioinformatics subreddit, I'd be remiss if I didn't mention:
- Algorithms for DNA sequencing Coursera course: https://www.coursera.org/learn/dna-sequencing/home/welcome
Fairly short and sweet, and a good intro to some basic bioinformatics algorithms and programming exercises in Python.
- Bioinformatics Coursera specialization: https://www.coursera.org/specializations/bioinformatics
A much longer sequence of courses. As a newbie to Python, I found the programming exercises VERY challenging. Course does a great job of pulling in plenty of foundational genetics/biology as well.
Hope you find these suggestions helpful! Let me know if you have any questions, and good luck!
1 points • ElephantSpirit
https://www.biostarhandbook.com/ (Not free but worth the money, good for beginners and intermediates)
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/specializations/genomic-data-science (intermediate level, not the best instruction for beginners)
https://www.edx.org/micromasters/bioinformatics (I can't comment much about it, haven't looked at material)
https://software.broadinstitute.org/gatk/ This is from the Broad, and gives an idea of current best practices in clinical bioinformatic analysis.