I am one semester into my Bioinformatics MS, with a B.S. in Biological sciences. I was an RA in a microbiology lab, and am currently working in a cognitive neuroscience lab. I would say I am definitely strongest in the biology section, with a good amount of experience (for my age of course) in a variety of labs. My weakest point is statistics, which I never took a class in throughout my entire academic career. I will be taking it next semester, along with a computational methods course. I am excited to hear more.
Same, I literally presented a project on all the research I have done regarding tools and methodologies within the field yet I still feel like I know nothing. I think what is important is just trying to find a project to work on and trying your hand at it. for example, i am working with one of my professors to conduct a scRNA-seq analysis concerning SCAMP proteins in relation to muscular aging. It seems difficult enough for me to learn quite a bit yet easy enough for me to actually make it happen. But nevertheless it is daunting and I still have so many papers and documentation to read befpre I get started (Im a 3rd year Biology bsc undergrad and self taught programmer)
@@danielpintard7382 I am a new learner basically start bioinformatics and python what should I learn in basic python and where I learn bioinformatics from scratch suggest me UA-cam channel
Thank you for your video. I'm an Italian master's student in Industrial Biotechnologies and I'm currently learning Python and R as tools for my lab data analysis. Hence, answering your poll, I'm more interested in spreadsheets and scripting. Keep it up with your channel!
Hi Maria, i used to be a wet lab scientist for many years and switched to data analyst because there was no one to help me on this. I am now ngs analyst but remain first a biologist. I too often see or ear informaticians who claim the bio but do not have it. This leads to projects that are irrelevant for the lab and are mostly based on inflatuated interpretations of noise (and there is plenty of it luckily). I do believe that a bioinformatitian should be able to understand both worlds to be efficient. This requires hands on practice in both wet and dry labs and cannot just be learned in class. This is of course only one person's opinion. Thanks for discussing these points and being a code sharing and educating talented person.
I'm a CS major, still in college. I always was interested in Biology, but ended up switching my career paths at the last moment in high school because I liked doing CS more. Since then I have been trying to find a middle ground where I can have my feet planted in both the domains. I'll check out some of your videos and see if the field is still accessible as an outsider or do you first need a good foundation in biology (beyond high school). I'm ready to learn more biology, it's just more exciting stuff to try!
Hello, I am a biochemistry major in the USA and planning to pursue a data science minor. I want to explore and possibly pursue a career in the bioinformatics field! I am working in a lab as an undergraduate studying genes right now while doing my classes, and seeing all the technology and software that they use inspired me to consider this career. I got introduced to the field by one of my professors and it was very inspiring as well. I am not really sure what I should do from now to transition into this career from undergrad, (should I pursue a masters or phd as well?), BUT I am taking action to learn python basics before I start my data science minor next year. I have a strong biology background and some experience with R (had a class with it). I am looking forward to watching your videos and will probably go through your past ones to learn some more. Thank you so much for doing this!
Hi, I am glad I found this channel. I am finishing my first year of a MS in Bioinformatics. I have a BS in Biology and kind of self-learned r and some python. I look forward to do a PhD in Bioinformatics or a related research topic. I would like to keep on track on this channels to see my career options and development in future (Industry VS ACADEMIA) thanks for this video and sharing your knowledge and experience I look forward to see more.
Nice! I'm purely a software engineer - I haven't studied any biology since my teens, but am working at a genomics company. I'm liking learning more about the bio side so I've got a better understanding of our users, the domain, and frankly... after 10 years of just coding it's refreshing to be a beginner again and learn something completely different :)
Thank you for the informative video. I have been following your channel since my second year of college when I was majoring in AI. Your channel has helped me a lot in getting a job at a bioinformatics company. This video reminded me of when I was a beginner and knew nothing about this field. Thank you once again for all the help.
1- ive started learning R but not really making progress tbh. So ill switch to python :) 2-no idea on that 3-im actually taking biostatistics this term! Does that count? Lol I’m in group 2, second year molecular biology and genetics student!
I'm a software engineer but very interested in doing more with biology - maybe bioinformatics or more of the computational biology stuff. I've been learning more basic biology, just finished one of the Coursera Bioinformatics courses and going through ISLR to learn the statistics side. The bioinformatics course was mostly focused on algorithms like Gibbs sampling for motif finding, as you said thats not really necessary even as an engineer - we would probably use something already built in a library. But it did have some nice basics about the biology like replication, Okazaki fragments etc. There also seems to be lots of promising stuff happening with deep learning like Alphafold so thats another huge area to learn about. I considered a Masters/PhD but with my grades and lack of research experience I don't see much of a shot. So for now I'm just learning more to see if I really like this field, planning to do some kind of project soon and also applying to regular software engineering positions at biotech companies. Seems many of them have a need for running large distributed computations, so that is something easy within my wheelhouse. Hopefully experience at those companies will allow me to then transition more into bioinformatics by learning on the job or leveraging that to get into a Masters. Thanks for all your videos BTW, they have really been very helpful! I loved the one about project ideas where you walked through your college project.
Hello, I've recently completed my Masters degree in GEnomic medicine, I had a dry lab research project using R mainly. Initially i was more of a wet lab with my undergrad project in the lab as well as a year long internship. After my MSc project i've started to find the dry side very interesting and had wanted to round out my skill with the technical skill of bioinformatics. oh and I'm looking for a job as research assistant or a Lab tech, which is proving to be very difficult but I'll be pressisting.
I'm in the third group. I'm a computer engineer who started on a startup and has 3 years experience. I have mainly worked in ML (computer vision) and embedded but I also touched almost everything thanks to startup culture. I'm quite experienced in python and command line. I started following this channel because I love biology since highschool and thought bio-informatics can be the intersection of my passiong and skills. I'm not yet sure if the field is for me. Do you think it is a good idea to find a job to see I fit in? Do I need a bioinformatics master or academic background? Also are there some projects that I can try out to see if I'm good at it and like it? or should I jump in if I can find a job?
That's great you have the CS skills already! One option is always working at bio-related companies and trying to hang out with the bioinformatics pipeline folks to see how you can help while learning from them about the bio stuff. As a small step, check out my video on "bioinformatics project ideas" and see if you can do some kind of small project. You can also take some basic bio classes, but like I mentioned biology is super broad at the research cutting edge level. I tend to recommend doing a PhD instead of a masters to get the more complete research experience needed to become a scientist who has all the chops to lead a full research group. It's all depending on what you want for your career. Check out Ben Langmead's channel for some good videos on the algorithms part of bioinformatics, which would be along the lines of a good fit for your excellent CS background. If you were to do a PhD, a lab like Ben Langmead's or similar would be my recommendation, meaning a CS-heavy bioinformatics lab.
Hi Maria your videos are great! Do you know or use the Julia programming language? And could you suggest a good book about Bioinformatics but applied more to ecology and evolutionary biology, and not necessarily human/medical biology? Thanks!
Hi Maria, thank you so much for your videos. I’m an agronomist looking to learn bioinformatics to address practical agricultural challenges. I’m not interested in reinventing the wheel; I’m seeking practical knowledge. Could you suggest the best learning path for this?
I have a lot of understanding of biology and I LOVE biology and genetics. Any time I see an ATCG or AUCG I get overwhelmed with excitement. My undergrad is in Evolutionary Anthropology and Biology, but I have been learning Python and brushing up on my statistics. I recently applied to ASU in hopes of earning a master's in Biological Data Science and then working on my PhD in Biomedical Informatics with a focus on translational informatics. Whether I can pull it off or not is unknown, but that is my goal. I am late in the game and actually have my MBA in IT with a data science and business analytics emphasis, but I am a lover of science and wish I would have stayed with it. So by the time I am 47 I will have my PhD if I can pull this off. Not to bad... right? Or am I crazy for this and it is a bad idea? I don't know.
Hi, I am a medical student but I have lots of interest in bioinformatics, do think this is a path worth exploring as a medical doctor? And if yes, how can I merge medicine and bioinformatics?
I am a Medical Lab scientist, with almost 0 knowledge on languages. I got fully funded scholarship to study bioinformatics. What are your suggestions. Thank You
Hi well explained in the video Im Sanjana k. Im a currently planning to pursue msc biotechnology.i want to gain knowledge about technical knowledge that is computing biology so that it could be useful to me.can u please suggest course of bioinformatics for free .so i can get some knowledge to it
Is there a Google Health team in France? I am an international student in France studying medicine, and I hold a bachelor's degree in computer science. I have already completed an internship in a research lab focused on computer vision (PyTorch, U-Net, AUNet) applied to biology, and I am very interested in having an internship experience with the Google team next summer (2025). What advice can you give me ?
I actually for my Bachelors thesis designed a drug, and I want to pursue Masters in Bioinformatics and so I recently took a workshop on Bioinformatics. but the problem is I dont have any knowledge on coding and so while Drug designing I thought I can easily make a career in this (which I'm 90% sure I can, but in Pakistan, This field is under developing [like every other field]) and because I don't know where to start. Would you please help me with where should I should i get started from? (PYTHON OR R language) thanks for reading.
hello. I'm a person with a biological research background in field of wet lab molecular biology (i'm a student now) like so many others, I made a mistake and starting think about how to develop bikes insted of how to use it. I didn't need to write a scripts and use programs and tools. how I can get to the level of scripting and deep understanding of my work, analyse data that i have received in my lab experiments? if not a bioinformatics course, maybe just programming in python, R? what I can do to improve my lab practice with a bioinformatic expirience, what kind of expirience it should be?
I am a biochemistry graduate and really didn't enjoy the lab part of it (which is all of it lol) and wanted to switch to a remote job so I started learning programming online. How do I get from a bachelor's degree to remote bioinformatics? Do I have to get a bioinformatics master's to get a job ?
I am computer science major with an AAS in Mathematics. I just learned about bioinformatics. The school I am attending for BS degree in computer science has an option to minor in bioinformatics.
Hello; I am from Statistics background. I have earned Master degree in Biostatistics as an specialization. Now I am finding a way to study Bioinformatics; because, I am interested in studying machine learning and algorithms to analyze big biological data. I have a good knowledge of classical data analysis methodologies and R programming statistical software. However, my worry is, I have no biology background. What is your advice for me Maria?
Your background should be enough to get into some PhD program for bioinformatics if you're looking for further education, but otherwise you can also look for jobs in industry using what you have now. Doesn't your "biostatistics" specialization count as biology background?
Thank you for your reply @@OMGenomics. Biostatistics is more of the application of statistical methodologies in health. I took three health related courses (Survival Analysis, Epidemiology, and Clinical Trial) in the program of Biostatistics. However, I don't think it is enough to say I have a biology background. I want to know better about my self (human anatomy) especially, about human DNA and I want do more on how to analyze it. I hope, the Bioinformatics field can help me a lot on how to do this all. I have checked Bioinformatics program of some universities and they heavily focus on Omics Data Analysis.
Right, I do remember taking a biostatistics course once before grad school and thinking that this is medicine, nothing to do with biology as defined by the biology major I had just finished in college. Statistics is a really good starting point, covering one of those 3 circles in the Venn diagram I showed, so you got one covered and can branch out from there into the bio space more. I do agree it's almost all omics at this point in bioinformatics, especially genomics. Would you be open to doing a PhD, or are you looking for another way into the field?
@@OMGenomics I really appreciate your genuine reply. Thank you so much. I am applying for another master's degree in bioinformatics specialization, and I am thinking of doing PhD after that. Hopefully, I will be an expert in Bioinformatics. I am affirming that I am a genome scientist. I am thrilled about your service; the way you genuinely help people sharing basic information replying to their comments. Many respects 🙏
@@dg_gad19Please consider applying to some PhD programs immediately instead of doing another master's degree. A masters is not required for all PhD programs, especially in the US, so it might save you years of your life to look into PhD programs first! Good luck with everything!
I just finshed my undergrad in biologly and did a bioinformatics project for my capstone. Loved it so much decided to do my masters in bioinformatics at the University of Maryland Global in the fall.
Thank you. I am a Project Manager on a team whose work involves Bionformatics. Your video was very helpful. I am completing a qualification in Public Health Informatics
Well this is awkward. I was just searching around for possible ideas for a field in which to pursue a masters degree. I have a bachelor's in computer science and a bachelor's in biology, because those were the two biggest educational interests I wanted to pursue in my life. Until just this moment, I had no idea bioinfomatics was a thing.
5:30 i’m a college student doing medical laboratory science bachelors program, i’ve learned about bioinformatics as a part of molecular biology course although all what we studied about it was just theoretical introduction, I’ve been really interested in learning it more deeply.
Hi. First of all i thank for your wonderful video, this is so helpful. I have studied biology group in my 11th and 12th grade. I'm so interested and i love biology but some family situation I'm studying engineering in Computer science and business system. I want to get a work which satisfies my life. Then i decided to start studying bioinformatics, do you recommend any free courses in bioinformatics, that will be more helpful in collapsed situation.
Oh yay! I know I have felt many times like "there should be an easy way to do this! What am I missing? Am I the only one who doesn't understand this?" You're not alone!
Hey how's it going guys, I'm a veteran that's been out of the service for many years and used his GI bill foolishly to get an associates only, having swaping majors so many times, fast forward years later I get a temp job now salary at a bio tech company, and love everything about genetics and machine learning, and taking bioinformatics and applying that knowledge to ai, so my question finally is I have an associates and wish to get my under grad what will be a straight shot pathway to bioinformatics, or more advantageous for machine learning and genetics, and bioinformatics in terms of undergrad, and what areas will I need to focus on! Loaded question possibly but hope to hear from you!
Definitely try to go somewhere that gives you good undergraduate research opportunities, which you'll want to jump straight into as soon as you start. Given that you have industry experience, it's probably worth talking to professors who do research you're interested in to see if they will have research opportunities available to you before you actually commit to a university. Basically I'm thinking that in your case your skill level sounds like it might be far ahead of your educational background, so #1 is finding ways to catch up your education quickly, which is entirely a matter of working with transfer admissions on a plan for fast graduation, and #2 is making sure you learn a lot and don't waste your time in classes that are too easy or not relevant to your interests just to get that degree. I think this will take some research and maybe finding a go-to person to talk to in the bio department at each school you're considering, since you're such a special case they should be willing to help you navigate the system. In your shoes, I would select the major based on what classes you would need to take and how excited you are about them, as well as how many of them there are, of course. Good luck!
I'm about a year into my PhD in molecular microbiology... I'm mainly in the lab but my thesis will involve bioinformatics and in silico stuff so I need to learn command-line and feeling incredibly overwhelmed
I hear you about feeling overwhelmed. I’d love to help if I can. How about you start with the courses on sandbox.bio and then message me on LinkedIn and we can talk about how to make it less overwhelming?
This is great news! I have watched some of your R tutorials before when there was nothing on YT about bioinformatics (6y ago). I am glad that this is changing and students get realy good courses on the internet. I like to think that I am now on the right side of the spectrum where developing algorithms is very tough to get into without having a scientific question that you want to aswer. Informations and books how to start with that but specific to bioinformatics would be awsome to see!
I’m just a simple student at school, learning the school materials regarding biology, and I actually wanted to participate in international Olympiad, however I find that I’ve got to know this bioinformatics thing, the sphere, about which I know absolutely nothing, also I even have no idea how to use the computer, so python and is something very unknown to me, obviously, I’ve got a lot to work on, but just wanted to sincerely ask for help, as I can see that you’re actually involved in this thing, thanks in advance, I’ll wait for your answer impatiently.
@@OMGenomicsI have a fastq file for example.. I dont have a solid pipeline to get quality info from it. And If I ran that file on websites, I dont know which is correct, which is not? Like for taxonomic classification for example, are these websites reliable, what threshold I should to get accurate results. Etc It is all dodgy, you know what I mean.
I'm pursuing MSc in biotechnology and bioinformatics has been a amazing for me. And I want to pursue the PhD in computational biology but still feel like I don't have have knowledge about that i have a 6 month for being completed my master's degree and meanwhile I want to have a excellent command on bioinformatics what should I do give me some tips and tricks 😊
Hi, I'm in my 1st year of MS in Applied Mathematics. I have experience with ML with Python. Also, I have been studying GNNs for my research topic. I have always wanted to work in the Bio-related areas field but don't have the knowledge of Biology. I'm thinking of getting into Bioinformatics where maybe I can use the GNNs in some way. Any advice for me?
I just graduated with a BSc in Biochemistry and Chemistry. I am fascinatd about mixing physical and biological sciences with programming. I am actually learning how to code(in JavaScript but I will definitely do python) since I have found a job yet. I just want to ask about job opportunities? Do bioinformatists completely work outside the lab? The requirements seem fair me.
So what would you suggest to someone who has a bachelors degree in software engineering. (Can work with Python and CLI, but hasn't worked with Data stuff) to get into bioinformatics ( i want to do my masters in this field but i need to etablish a good understanding before proceeding). We had a bioinfo course where we learned about basics of bioinfo like local/global/multi alignment and used the tools to perform them like blast,tcoffee etc.
Wet lab PhD student here. I am spending stupid amounts of time on excel which ik for a fact can be automated. But i never get around to learning any python. I HAVE TO LEARN haha. maybe 2024 new years resolution?
I'm a web development student who has a strong passion for biology. Although I've completed my degree in bvoc software development,I didn't like to work in an IT company. I've discovered my interest in bioinformatics. I believe this is my calling, but I'm unsure about the next steps. im planning to do my masters in bioinformatics (idk what to do).Could you please help me gain more insights into this field?
This is really helpful! I've been wandering around bioinformatics for two years now and I still feel totally lost. Two questions their answers would be much help, the first, what are the python skills necessarily needed and enough to proceed the journey? and the second which field of bioinformatics suits a PharmD who aspire to work in a R&D pharmaceutical companies? I hope you see and reply to my comment. I can't thank you enough 🙏❤️
stumbled here because I was searching for help with my data analysis. Student studying Bsc Animal science, hard to find information on haplotype analysis on youtube
I just got my BSc in Biochemistry and will be starting my MSc in Bioinformatics and Systems Biology in September, so I watched this video bc I often find myself unable to explain what bioinformatics is to someone who's not in STEM. This was helpful for that. I do not have a high school background in math so numbers aren't my forte but I want to be competent and a good bioinformatician, so I look for videos that discuss statistics and bioinformatic techniques in a practical way. Often I find videos that just explain what things mean but not why we use them, or why we use a particular test or technique.
Hi! Dani from Argentina . Biotech and PhD in biological sciences . Currently enrolled in Ms in data science . My weakness is in the bioinformatics tools per se. What do you recommend ?
Thank you. You being here from 2015 or something like that, hence suggest go from deep end (developing bioinformatic algorithms, or more deeper use of quantum computing in life science scenario, (free platform out there to get hands dirty..) for the shallow end, suggest them to search this channels and few out there, in this modern llms world most are exceptionally good at clicking around menu driven options without having understanding.....sad but true, that's where most of us are heading.....my apologies for this set of thoughts, thank you
It make sense if I say I want to study a bioinformatic bachelor degree in order to understands the roots of the human brain, also adding that knowledge with technology and after that take a master degree in psychology. I wouldnt just take bachelor in psychology because it mostly emotions (generally speaking) and have nothing to do with technology and the study of atoms. I find your video today, it was very helpful I would like to your advice regarding this. Regards, Belisario.
I am a Medical Laboratory Scientist and I have been interested in databases and software for a while now. Strongly considering a career upgrade into bioinformatics. I already started learning Python and will dive into stats once I develop a solid grasp of programming.
I have a BA in biology with some computer science courses. Im interested in bioinformatics as a way of processing my own data. Currently i am only learning and dont have data to analyze that would benefit from the sequence analysis techniques ive learned from the biostar handbook. I am mostly interested in wetlab work but am interested in seeing how i could maybe do bioinformatics as a work from home job.
Microbiology prof here looking to learn bioinformatics, rather than getting postdoc or collaborators to do analyses. Would open new ways of thinking/experimenting in microbial genomics.
Thank you maria. I liked the concept of learning how to ride a bike vs actually building a bike. I'm currently in my PhD program in bioinformatics and I agree its quite a broad field and just feel overwhelmed with the loads of information I've been receiving(especially stats). I'm comfortable with the command line and currently learning python. Looking forward to more informative videos.
I totally understand the overwhelm. I feel like that too, especially about stats! It is a lot of information, but the sliver of stats you'll really use can end up being small for your project. I'm not sure I reported a single p-value in my entire PhD thesis, so it's possible to lean into your strengths and contribute to the field in a way that works for your interests and personality. Mine is all about the visualization and building useful approachable software. What do you think your favorite parts will be?
@@OMGenomics for now its applying the various tools in genomics and genetics, I think I'm leaning towards pipeline development and machine learning too. But those are still broad terms, I'm still soul searching as to what aspect of the field will fit my personality and goals.
Hello. I love your video. I have BSc in Cell Biology and Genetics but I'm also decent in python programming and data analysis. In fact, my main goal is to build machine learning models in Healthcare. I want to study bioinformatics in the USA but my grades aren't so great either. What would you recommend for me to do?
I’m a master student in applied statistics with a concentration in biostatistics. My current internship at UPenn only uses SAS and is majority longitudinal studies and clin trials. However I really want to learn bioinformatics! I’m surprised you said python and not R, I was told last summer R would be more useful in this field. Specifically the package bioconductor. Really not sure what I want to do yet and want to learn as much as possible. Do you have any textbook recommendations or other tips?
Thank you and good for me i found this channel. I just started my journey in bioinformatics from one of my lecturers so things haven't become too complex, but i would look to see more videos on computer part of bioinformatics Thank you
I am from India and doctorate in biotechnology. I love bioinformatics and I always watch your videos and I am trying to learning but it looks like somewhat tough. So suggest some books to analyse the RNA seq data and other work in bioinformatics. Thakns for your video...
Currently learning python. Worked in a wet lab for about 8 years in total. Mostly want to use bioinformatics for RNA-seq data maybe also use python to make arduino based tools to use for mouse research. (Already replicated someone's hacked kitchenscale gripstrength meter)
Helpful video. I studied biochemistry and mathematics in undergrad, then went on to be an AP Biology teacher for 5 years. I am looking for a career change and bioinformatics is where I ultimately want to go. This video has given me some nice clear steps on some of the initial skills to begin to develop, thanks!
Thank you for your video! I graduated from computer engineering and I am interested in data science. Is it a good idea that doing master degree in bioinformatics and then finding a job? Or doing master degree in data science to improve machine learning and technical skills ?
@@OMGenomics Dear Maria, my future research project will be on plant evolutionary biology. So I need to develop skills in bioinformatics to analyse large scale plant genome data in my future research, I mean with in 6 months I want to learn. I mean how to compare the genomes of plants in my study. I am starting from scratchs and I am a purely wet lab biologist. So I am looking for courses by bioinformaticians . Do you plan to make any such videos in the future? Thank you for channel.
I as an older student currently studying biology at the undergraduate level. My computer skills and knowledge are at the novice level. My career goal is to study data sets in the field of proteostasis.
I am a combined undergraduate senior / first year master's student in chemical engineering. In my research I have mainly focus doing models and simulations of very small particle systems, but recently I have been wanting to learn a bit more about biology so I applied to bioinformatic internships this summer and actually got one. Bioinformatics seems like a really cool field so I want to see if this is the potential field that I want to work and maybe go to graduate school for.
This channel is enlightening. I know you from Bio Data Format explanation video. ua-cam.com/video/MrVpn0vpIYU/v-deo.html I just wish you make more technical videos, because you have a good bird view about Bioinformatics (in general) and genomic data (specially), you can show us the right path and give us strings. We can follow them ourselves. this is a job that a university can (maybe) do in 3 or 4 years! Thanks a lot. Stay the way how you are.
I just Finnished my 2nd year of my Bachelors in botany and Microbiology, would love to get into bioinformatics in my honour's and masters... Im going to start learning python over the holidays! Love your videos they are so helpful.!
Yes, it's writing a script in python/bash and being able to run it on the command-line, so yes building a pipeline is a good example, whether that's in bash or even a workflow manager like Nextflow. I lumped all that into "scripting". Or you could say "using tools well automatically".
I am a microbiologist but recently moved to IT as SME and content editor will be moving towards deep bioinformatics as I love the subject from my master
Thanks for your videos-they are very helpful! I have a biology background, and I only ever took first year single variable calculus, so I was wondering how far into mathematics you went. Aside from statistics, is it helpful to have taken classes beyond single variable calculus (like linear algebra) in bioinformatics?
Happy to hear that! Statistics is definitely most important, and I personally found linear algebra very interesting, but I don't think I've really needed anything other than statistics. People who like math can go much deeper (and much deeper than I can follow them!), but if you are not a huge fan of math, it's not necessary to go beyond statistics.
I've been working in biotech ngs labs for 10 years. What I found is a huge gap between the wet lab and the dry lab that bioinformatics department seemed to be indifferent about what's gaining on from the wet lab side of things, as they take the data for granted without understanding how the data is processed that might have impacted the quality. On top of that they don't share their side of things as I feel we won't understand. Thus I want to break into the data science side to at least be able to understand what they are actually doing.
This is a really interesting observation. I have heard similar things from both sides that it's just hard to speak the same language. Kudos to you for working to understand the dry-lab side and learn their language!
8:12 i am at core a pathogen bench lab scientist who has a background in population genetics and epidemiology. I work in public health as an applied epidemiologist and am transitioning to work as a genomic epidemiologist. Your basic videos have been encouraging because they clearly transmit information with biological examples. I recently took a course called Bioinformatics for Biologists I have gotten my feet wet with bash and R. What I wish the class had more of are examples of say using command line arguments in bioinformatics or plotting bioinformatics data in R not just plotting sepal length and width. I have taken a brief intro course on Python but I don’t understand where that will fill gaps R and bash can’t deliver for genomic epidemiology. Can you help me understand where Python fits in for my background and needs?
Do most people use R instead of python for genomic epidemiology? I ask because I see some subfields within bioinformatics are moving from R to python starting from industry, where eventually academia follows as students read job descriptions and realize they need those python skills too. I made a Plotting in R for Biologists course, by the way, which definitely doesn't stick to sepal length :) Instead I plot genomic data like variant calls and show adjustments like ordering chromosome names correctly that are constant annoyances specific to genomic data. You can find it at marianattestad.com/blog
Hi - There are articles in press that demonstrate that large language models (ChatGPT, Gemini) can perform all R/Bioconductor routines and visualization using simple English text or voice commands instead of Unix command lines. These include Forest plots, PCA, and Circos using one's own data. See PLoS Genetics, Nature Genetics, arXiv. What do you think of this? Will Python be next? - Dr. Gerry Higgins, retired prof, Computational Medicine and Bioinformatics, Michigan.
Hi Gerry! That would be great, but I'm not sure we're quite there yet. Actually python is so much easier because there is more training data with python algorithms than with our niche bioinformatics code (regardless of language). What I've tried myself generally fails quickly when faced with real bioinformatics data beyond the simple examples. It can still be a helpful accompaniment but beginners should beware to check the output, since it's good at sounding like it makes sense while doing the wrong thing. And it's not all as easy to catch as what happened to me last time: when faced with a need to visualize explainability from a model in tensorflow, it imported a perfect-sounding library that doesn't actually exist. I have high hopes though, and it's generally exciting that some of the more repetitive parts of our work are getting replaced by AI. I'm actually just impatient that it hasn't fully happened yet. Have you tried getting LLMs to do all the coding for any of your projects?
@@OMGenomics I learned R Bioconductor at the CSHL. Otherwise it was Python and PERL, and before that, C++ and Fortran. I reviewed the PLoS Genetics paper, and the LLM could analyze the data and produce a Forest plot. For many of the other R functions, it is esentially using text or voice commands instead of UNIX line commands. It has a 5% error rate in terms of differences between results using different datasets. I think it will be a "code helper" - Google Gemini Ultra is better - but won't displace programming altogether. My son has been coding AI since 2000, at Meta and Apple, and he is graduating from Michigan with a PhD in Computer Science Engineering, and has postdoc offers at Berkeley, Stamford, and CMU. Against my advice, he he headed into academia! He created a Circos plot using Gemini Ultra...but says that LLM's are not ready for prime time for a language like Python, like you! He is not a bioinformatician, as a crack programmer, he eats them for lunch😀 - Dr. Gerry Higgins, University of Michigan Medical School (no longer retired)/Phenomics Health Inc.
I have a bachelor in Medicine and I took a 2 year program to become a fullstack developer after which I worked for a short stint at a startup. I have now started my master in Bioinformatics and I'm adding courses on the side in data analysis, machine learning and pharmaceutical bioinformatics. I want my master thesis to be coding heavy, and preferably with ML. That's what I think is fun so I think that is what will take me the furthest. If I could find a PhD afterwards that is more aimed towards coding/ML that would be amazing, but we will see what I can get once I get there. I definitely want to make the tools rather than using them.
That sounds like a great plan, and I like that you're paying attention along the way to what you find enjoyable to work on. Good luck! We need more good software engineers building easy-to-maintain tools for bioinformatics, so I'm sure you will be in high demand for a PhD with that background!
Hello Maria Nattestad, I'm a fresh graduate of Microbiology. I am highly interested in bioinformatics. What should I do to build up my next career in bioinformatics? Please give me the best suggestion for such stage. Warm regards Manotush A student from Bangladesh
If you have a degree in Biology, and you have wet lab experience in Biomedical science research. Where would you recommend starting to get into Bioinformatics? Would it be going back to get a Masters for Bioinformatics, or would you just recommend self-learning Python?
Masters degree would be ideal to be competitive. I am planning on getting mine online while working as a mech E currently. I have a bachelors of science in biomedical engineering
I generally prefer the idea of going straight to a PhD rather than a masters, simply because a PhD unlocks all the paths to being a full scientist. But it all depends on what you're trying to achieve. It's hard to say more without knowing your full background and life goals :)
Thank You SOOOO much for your time and effort on this subject! I am a MS student at CSUEB, and formally trained in molecular biology. My thesis is whole genome sequencing of many different samples so its pretty bioinformatics heavy. I fall into the first catagory for sure, the bioinformtaics course at my university gives a nice overview and a annotation project, but not much after that. I am kinda on my own as far as really understanding the data analysis part and would love more videos on how "group 1" people can advance. I am currently teaching myself python and am semi-comfortable with comman-line. excited to build this skill!!!! If you could reccomend a series of projects from intro to intermediate, that would be amazing!! again thank you for your help!
I love that you're building these great skills already as a molecular biologist, and it sounds like you have to for your project, so that's certainly a good motivator. You're doing great! I really like your idea of having a series of projects from beginner to intermediate **scribbles in notes**. Check out sandbox.bio for some useful and approachable interactive command-line tutorials -- if you've seen our podcast on this channel, that's Robert's work there :)
If you were a beginner like me at his time point, what would you do? 1. Become a generalist and learn a little bit of everything and try to get any job anywhere. 2. Look for a research lab and who is willing to take you on and then learn whatever they tell you to learn. I'm on the fence with specialization since this field is so broad and I'm worried that what I choose to devote my time to will not be the most efficient use of time and I may not get the opportunities.
What do you want from your career? If you're not sure, trying a few different courses may help expose you to different options. I was unsure and didn't know enough about the field at the beginning too, and it got resolved for me by applying to grad schools (PhD) and meeting professors during the interviews who inspired me and showed me broadly what's possible in the field. Ultimately finding a great lab can solve this problem :) I think you'll have the most options if you start going the PhD route and learn some solid Python skills in the meantime so you'll have the coding skills ready for whatever research inspires you.
@@OMGenomics I want to work in a lab that is working on an illness that I currently have. I don't really have a solid career path due to this illness derailing my previous career. I've always been averse to doing a PhD because of the time commitment and hardship involved. I'm currently doing a Masters program to transition into tech so I want to leverage these skills for scientific research. I guess my question is can I still work in a research lab without any expectation of doing a PhD?
thank you, i have been watching your videos from past one year and learnt many thing from you. Please also make a video on "How to select a research topic for my thesis" as i'm doing my masters in Bioinformatics and Genomics and i have a background of Bachelors in Biotechnology. I am interested in Cancer side on Bioinformatics.
Yay! Interesting idea! My quick advice (which I should totally do a video on **scribbles in notes**) is to go deep on reading papers in the topic area you are interested in. Here's a research prompt you can use: "What are the top 5 ways that our understanding of cancer has changed due to genomics research in the last 10 years?" And continuing from there you might now have enough background to find an answer to: "It is weird that with all the genomics research done so far, we still don't know ___________" and fill in that blank :) You can also look through papers to figure out what tools might be missing. A few things I've noticed are missing right now: Good structural variant calling evaluation tool for comparing calls to a truth set (not straightforward like it sounds), and a lightweight Rust or Python toolkit for working with pangenomes including reads aligned to pangenomes.
Back in the day, I liked Codecademy for the interactive method where you have to apply each skill instead of just reading about it and practicing it "later". That method is now pretty common across other learning websites, so you can try Codecademy's python 3 course or find something else that's interactive and feels good to you. Please let me know how it goes!
First the basics like if statements, for loops, functions. Then I'd recommend trying using the Pandas library (good for spreadsheet-like data) and doing some visualization on that with Seaborn or Altair. Numpy is also very useful. Check my video called Genes and Geography for an example where you can see me using Python on a real mini-project, just to get you an idea of how you might use it for bioinformatics.
I am one semester into my Bioinformatics MS, with a B.S. in Biological sciences. I was an RA in a microbiology lab, and am currently working in a cognitive neuroscience lab. I would say I am definitely strongest in the biology section, with a good amount of experience (for my age of course) in a variety of labs. My weakest point is statistics, which I never took a class in throughout my entire academic career. I will be taking it next semester, along with a computational methods course. I am excited to hear more.
I'm a masters student in microbiology, and I've taken so many bioinformatics courses but I still feel like a beginner.
What makes you say you still feel like a beginner? What is missing?
Same, I literally presented a project on all the research I have done regarding tools and methodologies within the field yet I still feel like I know nothing. I think what is important is just trying to find a project to work on and trying your hand at it. for example, i am working with one of my professors to conduct a scRNA-seq analysis concerning SCAMP proteins in relation to muscular aging. It seems difficult enough for me to learn quite a bit yet easy enough for me to actually make it happen. But nevertheless it is daunting and I still have so many papers and documentation to read befpre I get started (Im a 3rd year Biology bsc undergrad and self taught programmer)
Do u have a LinkedIn?
@@danielpintard7382 I am a new learner basically start bioinformatics and python what should I learn in basic python and where I learn bioinformatics from scratch suggest me UA-cam channel
This video was amazing, I can't thank you enough!!! I'm definitely gonna subscribe ^^
Thank you for your video. I'm an Italian master's student in Industrial Biotechnologies and I'm currently learning Python and R as tools for my lab data analysis. Hence, answering your poll, I'm more interested in spreadsheets and scripting. Keep it up with your channel!
Hi Maria, i used to be a wet lab scientist for many years and switched to data analyst because there was no one to help me on this. I am now ngs analyst but remain first a biologist. I too often see or ear informaticians who claim the bio but do not have it. This leads to projects that are irrelevant for the lab and are mostly based on inflatuated interpretations of noise (and there is plenty of it luckily). I do believe that a bioinformatitian should be able to understand both worlds to be efficient. This requires hands on practice in both wet and dry labs and cannot just be learned in class.
This is of course only one person's opinion. Thanks for discussing these points and being a code sharing and educating talented person.
I'm a CS major, still in college. I always was interested in Biology, but ended up switching my career paths at the last moment in high school because I liked doing CS more. Since then I have been trying to find a middle ground where I can have my feet planted in both the domains. I'll check out some of your videos and see if the field is still accessible as an outsider or do you first need a good foundation in biology (beyond high school). I'm ready to learn more biology, it's just more exciting stuff to try!
Hi! Similar story. Glad to know there are people like me
@@SugarBerry-w8mI'm also interested in bioinformatics but not sure about future🔮?
Hello, I am a biochemistry major in the USA and planning to pursue a data science minor. I want to explore and possibly pursue a career in the bioinformatics field! I am working in a lab as an undergraduate studying genes right now while doing my classes, and seeing all the technology and software that they use inspired me to consider this career. I got introduced to the field by one of my professors and it was very inspiring as well. I am not really sure what I should do from now to transition into this career from undergrad, (should I pursue a masters or phd as well?), BUT I am taking action to learn python basics before I start my data science minor next year. I have a strong biology background and some experience with R (had a class with it). I am looking forward to watching your videos and will probably go through your past ones to learn some more. Thank you so much for doing this!
Hi, I am glad I found this channel. I am finishing my first year of a MS in Bioinformatics. I have a BS in Biology and kind of self-learned r and some python. I look forward to do a PhD in Bioinformatics or a related research topic. I would like to keep on track on this channels to see my career options and development in future (Industry VS ACADEMIA) thanks for this video and sharing your knowledge and experience I look forward to see more.
Nice! I'm purely a software engineer - I haven't studied any biology since my teens, but am working at a genomics company. I'm liking learning more about the bio side so I've got a better understanding of our users, the domain, and frankly... after 10 years of just coding it's refreshing to be a beginner again and learn something completely different :)
Nice, which company you work for? If you comfortable in saying so.
@@mustafaiwritesofficial3489 Sorry, I'd rather not share that publically :)
@@SwimmingInSeas okay! Totally fine 😀.
Same here. It really excites me as a software engineer.
Thank you for the informative video. I have been following your channel since my second year of college when I was majoring in AI. Your channel has helped me a lot in getting a job at a bioinformatics company. This video reminded me of when I was a beginner and knew nothing about this field. Thank you once again for all the help.
1- ive started learning R but not really making progress tbh. So ill switch to python :)
2-no idea on that
3-im actually taking biostatistics this term! Does that count? Lol
I’m in group 2, second year molecular biology and genetics student!
I'm a software engineer but very interested in doing more with biology - maybe bioinformatics or more of the computational biology stuff. I've been learning more basic biology, just finished one of the Coursera Bioinformatics courses and going through ISLR to learn the statistics side. The bioinformatics course was mostly focused on algorithms like Gibbs sampling for motif finding, as you said thats not really necessary even as an engineer - we would probably use something already built in a library. But it did have some nice basics about the biology like replication, Okazaki fragments etc. There also seems to be lots of promising stuff happening with deep learning like Alphafold so thats another huge area to learn about.
I considered a Masters/PhD but with my grades and lack of research experience I don't see much of a shot. So for now I'm just learning more to see if I really like this field, planning to do some kind of project soon and also applying to regular software engineering positions at biotech companies. Seems many of them have a need for running large distributed computations, so that is something easy within my wheelhouse. Hopefully experience at those companies will allow me to then transition more into bioinformatics by learning on the job or leveraging that to get into a Masters.
Thanks for all your videos BTW, they have really been very helpful! I loved the one about project ideas where you walked through your college project.
Hello, I've recently completed my Masters degree in GEnomic medicine, I had a dry lab research project using R mainly. Initially i was more of a wet lab with my undergrad project in the lab as well as a year long internship. After my MSc project i've started to find the dry side very interesting and had wanted to round out my skill with the technical skill of bioinformatics.
oh and I'm looking for a job as research assistant or a Lab tech, which is proving to be very difficult but I'll be pressisting.
I'm in the third group. I'm a computer engineer who started on a startup and has 3 years experience. I have mainly worked in ML (computer vision) and embedded but I also touched almost everything thanks to startup culture. I'm quite experienced in python and command line. I started following this channel because I love biology since highschool and thought bio-informatics can be the intersection of my passiong and skills. I'm not yet sure if the field is for me. Do you think it is a good idea to find a job to see I fit in? Do I need a bioinformatics master or academic background? Also are there some projects that I can try out to see if I'm good at it and like it? or should I jump in if I can find a job?
That's great you have the CS skills already! One option is always working at bio-related companies and trying to hang out with the bioinformatics pipeline folks to see how you can help while learning from them about the bio stuff. As a small step, check out my video on "bioinformatics project ideas" and see if you can do some kind of small project. You can also take some basic bio classes, but like I mentioned biology is super broad at the research cutting edge level. I tend to recommend doing a PhD instead of a masters to get the more complete research experience needed to become a scientist who has all the chops to lead a full research group. It's all depending on what you want for your career. Check out Ben Langmead's channel for some good videos on the algorithms part of bioinformatics, which would be along the lines of a good fit for your excellent CS background. If you were to do a PhD, a lab like Ben Langmead's or similar would be my recommendation, meaning a CS-heavy bioinformatics lab.
@@OMGenomics Thank you for the great insights and the video. I will be checking your recommendations.
Hi Maria your videos are great! Do you know or use the Julia programming language? And could you suggest a good book about Bioinformatics but applied more to ecology and evolutionary biology, and not necessarily human/medical biology? Thanks!
I have the biology background, but not much CS or the programming aspect knowledge to be exact
Hi Maria, thank you so much for your videos. I’m an agronomist looking to learn bioinformatics to address practical agricultural challenges. I’m not interested in reinventing the wheel; I’m seeking practical knowledge. Could you suggest the best learning path for this?
I have a lot of understanding of biology and I LOVE biology and genetics. Any time I see an ATCG or AUCG I get overwhelmed with excitement. My undergrad is in Evolutionary Anthropology and Biology, but I have been learning Python and brushing up on my statistics. I recently applied to ASU in hopes of earning a master's in Biological Data Science and then working on my PhD in Biomedical Informatics with a focus on translational informatics. Whether I can pull it off or not is unknown, but that is my goal. I am late in the game and actually have my MBA in IT with a data science and business analytics emphasis, but I am a lover of science and wish I would have stayed with it. So by the time I am 47 I will have my PhD if I can pull this off. Not to bad... right? Or am I crazy for this and it is a bad idea? I don't know.
Go for it and Best of luck !!
Hi, I am a medical student but I have lots of interest in bioinformatics, do think this is a path worth exploring as a medical doctor? And if yes, how can I merge medicine and bioinformatics?
Hey I'm a biochemistry student, thinking that this might be an area I'd like to work in.
I am a Medical Lab scientist, with almost 0 knowledge on languages. I got fully funded scholarship to study bioinformatics. What are your suggestions. Thank You
Hi well explained in the video
Im Sanjana k.
Im a currently planning to pursue msc biotechnology.i want to gain knowledge about technical knowledge that is computing biology so that it could be useful to me.can u please suggest course of bioinformatics for free .so i can get some knowledge to it
Is there a Google Health team in France?
I am an international student in France studying medicine, and I hold a bachelor's degree in computer science. I have already completed an internship in a research lab focused on computer vision (PyTorch, U-Net, AUNet) applied to biology, and I am very interested in having an internship experience with the Google team next summer (2025).
What advice can you give me ?
I actually for my Bachelors thesis designed a drug, and I want to pursue Masters in Bioinformatics and so I recently took a workshop on Bioinformatics. but the problem is I dont have any knowledge on coding and so while Drug designing I thought I can easily make a career in this (which I'm 90% sure I can, but in Pakistan, This field is under developing [like every other field]) and because I don't know where to start. Would you please help me with where should I should i get started from? (PYTHON OR R language) thanks for reading.
hello. I'm a person with a biological research background in field of wet lab molecular biology (i'm a student now) like so many others, I made a mistake and starting think about how to develop bikes insted of how to use it. I didn't need to write a scripts and use programs and tools. how I can get to the level of scripting and deep understanding of my work, analyse data that i have received in my lab experiments? if not a bioinformatics course, maybe just programming in python, R? what I can do to improve my lab practice with a bioinformatic expirience, what kind of expirience it should be?
I am a biochemistry graduate and really didn't enjoy the lab part of it (which is all of it lol) and wanted to switch to a remote job so I started learning programming online. How do I get from a bachelor's degree to remote bioinformatics? Do I have to get a bioinformatics master's to get a job ?
I am computer science major with an AAS in Mathematics. I just learned about bioinformatics. The school I am attending for BS degree in computer science has an option to minor in bioinformatics.
Hello; I am from Statistics background. I have earned Master degree in Biostatistics as an specialization. Now I am finding a way to study Bioinformatics; because, I am interested in studying machine learning and algorithms to analyze big biological data. I have a good knowledge of classical data analysis methodologies and R programming statistical software. However, my worry is, I have no biology background. What is your advice for me Maria?
Your background should be enough to get into some PhD program for bioinformatics if you're looking for further education, but otherwise you can also look for jobs in industry using what you have now. Doesn't your "biostatistics" specialization count as biology background?
Thank you for your reply @@OMGenomics. Biostatistics is more of the application of statistical methodologies in health. I took three health related courses (Survival Analysis, Epidemiology, and Clinical Trial) in the program of Biostatistics. However, I don't think it is enough to say I have a biology background. I want to know better about my self (human anatomy) especially, about human DNA and I want do more on how to analyze it. I hope, the Bioinformatics field can help me a lot on how to do this all. I have checked Bioinformatics program of some universities and they heavily focus on Omics Data Analysis.
Right, I do remember taking a biostatistics course once before grad school and thinking that this is medicine, nothing to do with biology as defined by the biology major I had just finished in college. Statistics is a really good starting point, covering one of those 3 circles in the Venn diagram I showed, so you got one covered and can branch out from there into the bio space more. I do agree it's almost all omics at this point in bioinformatics, especially genomics. Would you be open to doing a PhD, or are you looking for another way into the field?
@@OMGenomics I really appreciate your genuine reply. Thank you so much. I am applying for another master's degree in bioinformatics specialization, and I am thinking of doing PhD after that. Hopefully, I will be an expert in Bioinformatics. I am affirming that I am a genome scientist.
I am thrilled about your service; the way you genuinely help people sharing basic information replying to their comments.
Many respects 🙏
@@dg_gad19Please consider applying to some PhD programs immediately instead of doing another master's degree. A masters is not required for all PhD programs, especially in the US, so it might save you years of your life to look into PhD programs first! Good luck with everything!
I am a final year undergraduate student i want to learn the basics of bioinformatics, kindly provide direction
I just finshed my undergrad in biologly and did a bioinformatics project for my capstone. Loved it so much decided to do my masters in bioinformatics at the University of Maryland Global in the fall.
I just finished my degree in genetic and biotechnology
I am a beginner in this course
I want to know the process
Thank you. I am a Project Manager on a team whose work involves Bionformatics. Your video was very helpful. I am completing a qualification in Public Health Informatics
Well this is awkward. I was just searching around for possible ideas for a field in which to pursue a masters degree. I have a bachelor's in computer science and a bachelor's in biology, because those were the two biggest educational interests I wanted to pursue in my life. Until just this moment, I had no idea bioinfomatics was a thing.
Amazing! At least you’re in a great position now that you know 😜
5:30 i’m a college student doing medical laboratory science bachelors program, i’ve learned about bioinformatics as a part of molecular biology course although all what we studied about it was just theoretical introduction, I’ve been really interested in learning it more deeply.
Hi. First of all i thank for your wonderful video, this is so helpful. I have studied biology group in my 11th and 12th grade. I'm so interested and i love biology but some family situation I'm studying engineering in Computer science and business system. I want to get a work which satisfies my life. Then i decided to start studying bioinformatics, do you recommend any free courses in bioinformatics, that will be more helpful in collapsed situation.
Your reassurance at the beginning is super appreciated
Oh yay! I know I have felt many times like "there should be an easy way to do this! What am I missing? Am I the only one who doesn't understand this?" You're not alone!
Hey how's it going guys, I'm a veteran that's been out of the service for many years and used his GI bill foolishly to get an associates only, having swaping majors so many times, fast forward years later I get a temp job now salary at a bio tech company, and love everything about genetics and machine learning, and taking bioinformatics and applying that knowledge to ai, so my question finally is I have an associates and wish to get my under grad what will be a straight shot pathway to bioinformatics, or more advantageous for machine learning and genetics, and bioinformatics in terms of undergrad, and what areas will I need to focus on! Loaded question possibly but hope to hear from you!
Definitely try to go somewhere that gives you good undergraduate research opportunities, which you'll want to jump straight into as soon as you start. Given that you have industry experience, it's probably worth talking to professors who do research you're interested in to see if they will have research opportunities available to you before you actually commit to a university. Basically I'm thinking that in your case your skill level sounds like it might be far ahead of your educational background, so #1 is finding ways to catch up your education quickly, which is entirely a matter of working with transfer admissions on a plan for fast graduation, and #2 is making sure you learn a lot and don't waste your time in classes that are too easy or not relevant to your interests just to get that degree. I think this will take some research and maybe finding a go-to person to talk to in the bio department at each school you're considering, since you're such a special case they should be willing to help you navigate the system. In your shoes, I would select the major based on what classes you would need to take and how excited you are about them, as well as how many of them there are, of course. Good luck!
I'm about a year into my PhD in molecular microbiology... I'm mainly in the lab but my thesis will involve bioinformatics and in silico stuff so I need to learn command-line and feeling incredibly overwhelmed
I hear you about feeling overwhelmed. I’d love to help if I can. How about you start with the courses on sandbox.bio and then message me on LinkedIn and we can talk about how to make it less overwhelming?
This is great news! I have watched some of your R tutorials before when there was nothing on YT about bioinformatics (6y ago). I am glad that this is changing and students get realy good courses on the internet. I like to think that I am now on the right side of the spectrum where developing algorithms is very tough to get into without having a scientific question that you want to aswer. Informations and books how to start with that but specific to bioinformatics would be awsome to see!
I’m just a simple student at school, learning the school materials regarding biology, and I actually wanted to participate in international Olympiad, however I find that I’ve got to know this bioinformatics thing, the sphere, about which I know absolutely nothing, also I even have no idea how to use the computer, so python and is something very unknown to me, obviously, I’ve got a lot to work on, but just wanted to sincerely ask for help, as I can see that you’re actually involved in this thing, thanks in advance, I’ll wait for your answer impatiently.
Find a course in Python as a start, and good luck!
I am a physician and I changed my career to Bioinformatics (Systems Biology). I know some python but I still feel lost.
When do you feel lost?
@@OMGenomicsI have a fastq file for example.. I dont have a solid pipeline to get quality info from it. And If I ran that file on websites, I dont know which is correct, which is not?
Like for taxonomic classification for example, are these websites reliable, what threshold I should to get accurate results. Etc
It is all dodgy, you know what I mean.
I'm pursuing MSc in biotechnology and bioinformatics has been a amazing for me. And I want to pursue the PhD in computational biology but still feel like I don't have have knowledge about that i have a 6 month for being completed my master's degree and meanwhile I want to have a excellent command on bioinformatics what should I do give me some tips and tricks 😊
Hi, I'm in my 1st year of MS in Applied Mathematics. I have experience with ML with Python. Also, I have been studying GNNs for my research topic. I have always wanted to work in the Bio-related areas field but don't have the knowledge of Biology. I'm thinking of getting into Bioinformatics where maybe I can use the GNNs in some way. Any advice for me?
I just graduated with a BSc in Biochemistry and Chemistry. I am fascinatd about mixing physical and biological sciences with programming. I am actually learning how to code(in JavaScript but I will definitely do python) since I have found a job yet. I just want to ask about job opportunities? Do bioinformatists completely work outside the lab? The requirements seem fair me.
So what would you suggest to someone who has a bachelors degree in software engineering. (Can work with Python and CLI, but hasn't worked with Data stuff) to get into bioinformatics ( i want to do my masters in this field but i need to etablish a good understanding before proceeding). We had a bioinfo course where we learned about basics of bioinfo like local/global/multi alignment and used the tools to perform them like blast,tcoffee etc.
Wet lab PhD student here. I am spending stupid amounts of time on excel which ik for a fact can be automated. But i never get around to learning any python. I HAVE TO LEARN haha. maybe 2024 new years resolution?
I'm a web development student who has a strong passion for biology. Although I've completed my degree in bvoc software development,I didn't like to work in an IT company. I've discovered my interest in bioinformatics. I believe this is my calling, but I'm unsure about the next steps. im planning to do my masters in bioinformatics (idk what to do).Could you please help me gain more insights into this field?
This is really helpful! I've been wandering around bioinformatics for two years now and I still feel totally lost. Two questions their answers would be much help, the first, what are the python skills necessarily needed and enough to proceed the journey? and the second which field of bioinformatics suits a PharmD who aspire to work in a R&D pharmaceutical companies? I hope you see and reply to my comment. I can't thank you enough 🙏❤️
stumbled here because I was searching for help with my data analysis. Student studying Bsc Animal science, hard to find information on haplotype analysis on youtube
I just got my BSc in Biochemistry and will be starting my MSc in Bioinformatics and Systems Biology in September, so I watched this video bc I often find myself unable to explain what bioinformatics is to someone who's not in STEM. This was helpful for that. I do not have a high school background in math so numbers aren't my forte but I want to be competent and a good bioinformatician, so I look for videos that discuss statistics and bioinformatic techniques in a practical way. Often I find videos that just explain what things mean but not why we use them, or why we use a particular test or technique.
Hi! Dani from Argentina . Biotech and PhD in biological sciences . Currently enrolled in Ms in data science . My weakness is in the bioinformatics tools per se. What do you recommend ?
Hey maria, could you recommend a laptop for bioinformatics phd ?
Thanks !
Thank you. You being here from 2015 or something like that, hence suggest go from deep end (developing bioinformatic algorithms, or more deeper use of quantum computing in life science scenario, (free platform out there to get hands dirty..) for the shallow end, suggest them to search this channels and few out there, in this modern llms world most are exceptionally good at clicking around menu driven options without having understanding.....sad but true, that's where most of us are heading.....my apologies for this set of thoughts, thank you
It make sense if I say I want to study a bioinformatic bachelor degree in order to understands the roots of the human brain, also adding that knowledge with technology and after that take a master degree in psychology. I wouldnt just take bachelor in psychology because it mostly emotions (generally speaking) and have nothing to do with technology and the study of atoms. I find your video today, it was very helpful I would like to your advice regarding this. Regards, Belisario.
I am a Medical Laboratory Scientist and I have been interested in databases and software for a while now. Strongly considering a career upgrade into bioinformatics. I already started learning Python and will dive into stats once I develop a solid grasp of programming.
Great Video!!😊 Your reassurance is so helpful for me as an early career bioinformatician
Thank you! So glad to hear that. Good luck and welcome :D
I have a BA in biology with some computer science courses. Im interested in bioinformatics as a way of processing my own data. Currently i am only learning and dont have data to analyze that would benefit from the sequence analysis techniques ive learned from the biostar handbook. I am mostly interested in wetlab work but am interested in seeing how i could maybe do bioinformatics as a work from home job.
Microbiology prof here looking to learn bioinformatics, rather than getting postdoc or collaborators to do analyses. Would open new ways of thinking/experimenting in microbial genomics.
Thank you maria. I liked the concept of learning how to ride a bike vs actually building a bike. I'm currently in my PhD program in bioinformatics and I agree its quite a broad field and just feel overwhelmed with the loads of information I've been receiving(especially stats). I'm comfortable with the command line and currently learning python. Looking forward to more informative videos.
I totally understand the overwhelm. I feel like that too, especially about stats! It is a lot of information, but the sliver of stats you'll really use can end up being small for your project. I'm not sure I reported a single p-value in my entire PhD thesis, so it's possible to lean into your strengths and contribute to the field in a way that works for your interests and personality. Mine is all about the visualization and building useful approachable software. What do you think your favorite parts will be?
@@OMGenomics for now its applying the various tools in genomics and genetics, I think I'm leaning towards pipeline development and machine learning too. But those are still broad terms, I'm still soul searching as to what aspect of the field will fit my personality and goals.
@OMGenomics Also please don't stop encouraging us beginners. Thank you !
Hello. I love your video. I have BSc in Cell Biology and Genetics but I'm also decent in python programming and data analysis. In fact, my main goal is to build machine learning models in Healthcare. I want to study bioinformatics in the USA but my grades aren't so great either. What would you recommend for me to do?
I’m a master student in applied statistics with a concentration in biostatistics. My current internship at UPenn only uses SAS and is majority longitudinal studies and clin trials. However I really want to learn bioinformatics!
I’m surprised you said python and not R, I was told last summer R would be more useful in this field. Specifically the package bioconductor.
Really not sure what I want to do yet and want to learn as much as possible. Do you have any textbook recommendations or other tips?
Thank you and good for me i found this channel. I just started my journey in bioinformatics from one of my lecturers so things haven't become too complex, but i would look to see more videos on computer part of bioinformatics Thank you
I just graduated this month with bsc.data science and computing and am looking for work, how do l get into the sector of BioTech
Glad you'll be able to produce new videos.
I am in my masters doing research in computational evolutionary biology. I became familiar with scripting so far.
I am from India and doctorate in biotechnology. I love bioinformatics and I always watch your videos and I am trying to learning but it looks like somewhat tough.
So suggest some books to analyse the RNA seq data and other work in bioinformatics.
Thakns for your video...
Thank you for another great video!
Thank you for the kind words! :D
Hi, sorry can you please recommend any good courses to learn python? Thank you so much
Currently learning python. Worked in a wet lab for about 8 years in total. Mostly want to use bioinformatics for RNA-seq data maybe also use python to make arduino based tools to use for mouse research. (Already replicated someone's hacked kitchenscale gripstrength meter)
Helpful video. I studied biochemistry and mathematics in undergrad, then went on to be an AP Biology teacher for 5 years. I am looking for a career change and bioinformatics is where I ultimately want to go. This video has given me some nice clear steps on some of the initial skills to begin to develop, thanks!
Thank you for your video! I graduated from computer engineering and I am interested in data science. Is it a good idea that doing master degree in bioinformatics and then finding a job? Or doing master degree in data science to improve machine learning and technical skills ?
Data Scientist here but want to learning more on the bioinformatic things , and tried to have my master on this
I am a biologist looking to achieve bioinformatics skills in the area of genomics and functional genomics.
What makes you want to learn bioinformatics skills?
@@OMGenomics Dear Maria, my future research project will be on plant evolutionary biology. So I need to develop skills in bioinformatics to analyse large scale plant genome data in my future research, I mean with in 6 months I want to learn. I mean how to compare the genomes of plants in my study. I am starting from scratchs and I am a purely wet lab biologist. So I am looking for courses by bioinformaticians . Do you plan to make any such videos in the future? Thank you for channel.
I as an older student currently studying biology at the undergraduate level. My computer skills and knowledge are at the novice level. My career goal is to study data sets in the field of proteostasis.
im a wet lab scientist looking to broaden my knowledge and learn the basics!
I am a combined undergraduate senior / first year master's student in chemical engineering. In my research I have mainly focus doing models and simulations of very small particle systems, but recently I have been wanting to learn a bit more about biology so I applied to bioinformatic internships this summer and actually got one. Bioinformatics seems like a really cool field so I want to see if this is the potential field that I want to work and maybe go to graduate school for.
amazing information. thanks for the video it clarifies a lot of things for me!
This channel is enlightening.
I know you from Bio Data Format explanation video. ua-cam.com/video/MrVpn0vpIYU/v-deo.html
I just wish you make more technical videos, because you have a good bird view about Bioinformatics (in general) and genomic data (specially), you can show us the right path and give us strings. We can follow them ourselves. this is a job that a university can (maybe) do in 3 or 4 years!
Thanks a lot.
Stay the way how you are.
But I came from chemistry field.
How do you feel those skills prepared you for different aspects of bioinformatics work?
I am a medical laboratory scientist, I work in a laboratory
I just Finnished my 2nd year of my Bachelors in botany and Microbiology, would love to get into bioinformatics in my honour's and masters... Im going to start learning python over the holidays! Love your videos they are so helpful.!
What exactly do you mean by scripting? Is it at the python side or at the bash side or both? Like writing a whole pipeline could be an example?
Yes, it's writing a script in python/bash and being able to run it on the command-line, so yes building a pipeline is a good example, whether that's in bash or even a workflow manager like Nextflow. I lumped all that into "scripting". Or you could say "using tools well automatically".
Great channel. My background is in statistics & I'm at the notebook analysis stage.
I am a microbiologist but recently moved to IT as SME and content editor will be moving towards deep bioinformatics as I love the subject from my master
Good job teaching, Maria. Making things easy is the hallmark of education in my book. Thank you!
Thanks for your videos-they are very helpful! I have a biology background, and I only ever took first year single variable calculus, so I was wondering how far into mathematics you went. Aside from statistics, is it helpful to have taken classes beyond single variable calculus (like linear algebra) in bioinformatics?
Happy to hear that! Statistics is definitely most important, and I personally found linear algebra very interesting, but I don't think I've really needed anything other than statistics. People who like math can go much deeper (and much deeper than I can follow them!), but if you are not a huge fan of math, it's not necessary to go beyond statistics.
This video is very helpful. Thank you !
Can bioinformatics work in laboratory?
I've been working in biotech ngs labs for 10 years. What I found is a huge gap between the wet lab and the dry lab that bioinformatics department seemed to be indifferent about what's gaining on from the wet lab side of things, as they take the data for granted without understanding how the data is processed that might have impacted the quality. On top of that they don't share their side of things as I feel we won't understand. Thus I want to break into the data science side to at least be able to understand what they are actually doing.
This is a really interesting observation. I have heard similar things from both sides that it's just hard to speak the same language. Kudos to you for working to understand the dry-lab side and learn their language!
8:12 i am at core a pathogen bench lab scientist who has a background in population genetics and epidemiology. I work in public health as an applied epidemiologist and am transitioning to work as a genomic epidemiologist. Your basic videos have been encouraging because they clearly transmit information with biological examples. I recently took a course called Bioinformatics for Biologists I have gotten my feet wet with bash and R. What I wish the class had more of are examples of say using command line arguments in bioinformatics or plotting bioinformatics data in R not just plotting sepal length and width. I have taken a brief intro course on Python but I don’t understand where that will fill gaps R and bash can’t deliver for genomic epidemiology. Can you help me understand where Python fits in for my background and needs?
Do most people use R instead of python for genomic epidemiology? I ask because I see some subfields within bioinformatics are moving from R to python starting from industry, where eventually academia follows as students read job descriptions and realize they need those python skills too. I made a Plotting in R for Biologists course, by the way, which definitely doesn't stick to sepal length :) Instead I plot genomic data like variant calls and show adjustments like ordering chromosome names correctly that are constant annoyances specific to genomic data. You can find it at marianattestad.com/blog
Hi - There are articles in press that demonstrate that large language models (ChatGPT, Gemini) can perform all R/Bioconductor routines and visualization using simple English text or voice commands instead of Unix command lines. These include Forest plots, PCA, and Circos using one's own data. See PLoS Genetics, Nature Genetics, arXiv. What do you think of this? Will Python be next? - Dr. Gerry Higgins, retired prof, Computational Medicine and Bioinformatics, Michigan.
Hi Gerry! That would be great, but I'm not sure we're quite there yet. Actually python is so much easier because there is more training data with python algorithms than with our niche bioinformatics code (regardless of language). What I've tried myself generally fails quickly when faced with real bioinformatics data beyond the simple examples. It can still be a helpful accompaniment but beginners should beware to check the output, since it's good at sounding like it makes sense while doing the wrong thing. And it's not all as easy to catch as what happened to me last time: when faced with a need to visualize explainability from a model in tensorflow, it imported a perfect-sounding library that doesn't actually exist. I have high hopes though, and it's generally exciting that some of the more repetitive parts of our work are getting replaced by AI. I'm actually just impatient that it hasn't fully happened yet. Have you tried getting LLMs to do all the coding for any of your projects?
@@OMGenomics I learned R Bioconductor at the CSHL. Otherwise it was Python and PERL, and before that, C++ and Fortran. I reviewed the PLoS Genetics paper, and the LLM could analyze the data and produce a Forest plot. For many of the other R functions, it is esentially using text or voice commands instead of UNIX line commands. It has a 5% error rate in terms of differences between results using different datasets. I think it will be a "code helper" - Google Gemini Ultra is better - but won't displace programming altogether. My son has been coding AI since 2000, at Meta and Apple, and he is graduating from Michigan with a PhD in Computer Science Engineering, and has postdoc offers at Berkeley, Stamford, and CMU. Against my advice, he he headed into academia! He created a Circos plot using Gemini Ultra...but says that LLM's are not ready for prime time for a language like Python, like you! He is not a bioinformatician, as a crack programmer, he eats them for lunch😀 - Dr. Gerry Higgins, University of Michigan Medical School (no longer retired)/Phenomics Health Inc.
I have a bachelor in Medicine and I took a 2 year program to become a fullstack developer after which I worked for a short stint at a startup. I have now started my master in Bioinformatics and I'm adding courses on the side in data analysis, machine learning and pharmaceutical bioinformatics. I want my master thesis to be coding heavy, and preferably with ML. That's what I think is fun so I think that is what will take me the furthest. If I could find a PhD afterwards that is more aimed towards coding/ML that would be amazing, but we will see what I can get once I get there. I definitely want to make the tools rather than using them.
That sounds like a great plan, and I like that you're paying attention along the way to what you find enjoyable to work on. Good luck! We need more good software engineers building easy-to-maintain tools for bioinformatics, so I'm sure you will be in high demand for a PhD with that background!
Hello Maria Nattestad, I'm a fresh graduate of Microbiology. I am highly interested in bioinformatics. What should I do to build up my next career in bioinformatics? Please give me the best suggestion for such stage.
Warm regards
Manotush
A student from Bangladesh
That’s a big topic! Take a look at my other videos to get started, and then ask me anything specific and I’ll try to help!
@@OMGenomics I already watched some videos of your channel. Can you suggest me sequence of videos that will help me to select specific topic!
If you have a degree in Biology, and you have wet lab experience in Biomedical science research. Where would you recommend starting to get into Bioinformatics? Would it be going back to get a Masters for Bioinformatics, or would you just recommend self-learning Python?
Masters degree would be ideal to be competitive. I am planning on getting mine online while working as a mech E currently. I have a bachelors of science in biomedical engineering
I generally prefer the idea of going straight to a PhD rather than a masters, simply because a PhD unlocks all the paths to being a full scientist. But it all depends on what you're trying to achieve. It's hard to say more without knowing your full background and life goals :)
Thank You SOOOO much for your time and effort on this subject! I am a MS student at CSUEB, and formally trained in molecular biology. My thesis is whole genome sequencing of many different samples so its pretty bioinformatics heavy. I fall into the first catagory for sure, the bioinformtaics course at my university gives a nice overview and a annotation project, but not much after that. I am kinda on my own as far as really understanding the data analysis part and would love more videos on how "group 1" people can advance. I am currently teaching myself python and am semi-comfortable with comman-line. excited to build this skill!!!! If you could reccomend a series of projects from intro to intermediate, that would be amazing!! again thank you for your help!
I love that you're building these great skills already as a molecular biologist, and it sounds like you have to for your project, so that's certainly a good motivator. You're doing great! I really like your idea of having a series of projects from beginner to intermediate **scribbles in notes**. Check out sandbox.bio for some useful and approachable interactive command-line tutorials -- if you've seen our podcast on this channel, that's Robert's work there :)
If you were a beginner like me at his time point, what would you do?
1. Become a generalist and learn a little bit of everything and try to get any job anywhere.
2. Look for a research lab and who is willing to take you on and then learn whatever they tell you to learn.
I'm on the fence with specialization since this field is so broad and I'm worried that what I choose to devote my time to will not be the most efficient use of time and I may not get the opportunities.
What do you want from your career? If you're not sure, trying a few different courses may help expose you to different options. I was unsure and didn't know enough about the field at the beginning too, and it got resolved for me by applying to grad schools (PhD) and meeting professors during the interviews who inspired me and showed me broadly what's possible in the field. Ultimately finding a great lab can solve this problem :) I think you'll have the most options if you start going the PhD route and learn some solid Python skills in the meantime so you'll have the coding skills ready for whatever research inspires you.
@@OMGenomics I want to work in a lab that is working on an illness that I currently have. I don't really have a solid career path due to this illness derailing my previous career. I've always been averse to doing a PhD because of the time commitment and hardship involved. I'm currently doing a Masters program to transition into tech so I want to leverage these skills for scientific research.
I guess my question is can I still work in a research lab without any expectation of doing a PhD?
thank you, i have been watching your videos from past one year and learnt many thing from you. Please also make a video on "How to select a research topic for my thesis" as i'm doing my masters in Bioinformatics and Genomics and i have a background of Bachelors in Biotechnology. I am interested in Cancer side on Bioinformatics.
Yay! Interesting idea! My quick advice (which I should totally do a video on **scribbles in notes**) is to go deep on reading papers in the topic area you are interested in. Here's a research prompt you can use: "What are the top 5 ways that our understanding of cancer has changed due to genomics research in the last 10 years?" And continuing from there you might now have enough background to find an answer to: "It is weird that with all the genomics research done so far, we still don't know ___________" and fill in that blank :)
You can also look through papers to figure out what tools might be missing. A few things I've noticed are missing right now: Good structural variant calling evaluation tool for comparing calls to a truth set (not straightforward like it sounds), and a lightweight Rust or Python toolkit for working with pangenomes including reads aligned to pangenomes.
@@OMGenomics Thank you so much for your guidance, means a lot to me 😇
Thanks for the info. Can you recommend a free resource to start learning Python?
Back in the day, I liked Codecademy for the interactive method where you have to apply each skill instead of just reading about it and practicing it "later". That method is now pretty common across other learning websites, so you can try Codecademy's python 3 course or find something else that's interactive and feels good to you. Please let me know how it goes!
I'll check it out! Im a big believer in learning by doing.Thanks a mil!@@OMGenomics
What topic we should cover in Python
First the basics like if statements, for loops, functions. Then I'd recommend trying using the Pandas library (good for spreadsheet-like data) and doing some visualization on that with Seaborn or Altair. Numpy is also very useful. Check my video called Genes and Geography for an example where you can see me using Python on a real mini-project, just to get you an idea of how you might use it for bioinformatics.
@@OMGenomics thanks it really help