I’m always interested in new ideas. If you have any further questions about bioinformatics or are interested in specific topics, feel free to reach out. log in sign up. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Help Center Detailed answers to any questions you might have ... of course. I'd want a candidate who knows Python/Perl and a bit of R, SQL and bash/unix command line. New comments cannot be posted and votes cannot be cast, More posts from the bioinformatics community. Anybody can ask a question Anybody can answer The best answers are voted up and rise to the top Bioinformatics Beta. I find myself very stimulated by clinical research studies, i love anatomy and physiology. Offered by University of California San Diego. Thanks for contributing an answer to Bioinformatics Stack Exchange! Toward better bioinformatics software. Are you interested in learning how to program (in Python) within a scientific setting? There are five elements to asking a good question, and if you follow these elements, you will drastically increase your chances of receiving a response. Not many people have the time or patience to go through the effort of deciphering a bad question. Second, have a leading sentence or two about what you're trying to accomplish. Next, ask yourself if your question is clear and straight to the point. I like sports. “Learning to code is not easy - but Python is a good place to start, because it’s in English.” Tomasz Wrzesinski, one of the delegates, told me. A subreddit dedicated to bioinformatics, computational genomics and systems biology. When you're soliciting help from a stranger, you need to have a little skin in the game, and this type of question will make it abundantly clear that you haven't put any effort into finding a solution on your own. Otherwise why include quality data? The one we used to use was to give then a fastq file and ask then to write a program to find the 5 most frequently occurring sequences in it. Sorted by quality or something? Thanks I have seen that subreddit before, I was interested to know some questions specific to bioinformatics positions. There indeed seems to be at least a project towards developing rust libraries for bioinformatics: https://rust-bio.github.io/. There is just one catch: no one is going to help you if you waste their time. Since a majority of bioinformatics is computer work, short, self-contained, correct/compilable example (SSCCE), Get a bioinformatics education online for free. What is strange in your file is not so much that you have exons beyond the stop codon, but that you also have them marked as CDS (coding sequence). This is a very classic question: Which is your favorite programming language in bioinformatics? This type of question is almost never appropriate to ask because it's too broad. Cookies help us deliver our Services. Or close to it anyway. Press question mark to learn the rest of the keyboard shortcuts. Our work provides data to enhance the ongoing community-wide conversation around reproducibility and software quality in bioinformatics. I’m into that. Use MathJax to format equations. The type of bioinformatics degree you pursue should be influenced by the type of job that you want. Link is here. Bioinformatics Interview Questions and Answers will guide us now that Bioinformatics is the application of information technology and computer science to the field of molecular biology. An example of a bad title would be "BAM file confusion”, which doesn't specify what the actual problem is, whereas "Trouble calculating average coverage for a BAM file" will make it clear what the issue is. How about machine learning? Looks like you're using new Reddit on an old browser. I am actually a senior computer science major, so my programming skills are pretty good. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Any advice is appreciated. In fact, you even have various cases of UTRs being multiple exons, and being spliced. On most sites, only the title of your question will be visible until someone clicks on it, so you better make it straight to the point. The best programming language for getting started in bioinformatics. If you ask a simple question that can easily be Googled, then you might never get a response or you might get a lot of. There are five key elements that make up a good question. Bioinformatics projects can involve mountains of code, and one of our best defenses against bugs is to write code for humans, not for computers (a point made in the excellent article from Wilson et al., 2012). Generally, all the software packages that are used in Bioinformatics always come with a manual explaining their usage and different features. Anybody can ask a question Anybody can answer The best answers are voted up and rise to the top Bioinformatics Beta. Although some of more advanced workshop require a letter of support from a person in the field of Bioinformatics (ideally from a known leader in the field), these workshops are meant to be introductory and might be suitable for a keen clinical trainee. Humans are the ones doing the debugging, so writing simple, clear code makes debugging easier. Bioinformatics resources for protein biology; Biological data analysis using InterMine (User Interface and API) COSMIC: Integrating and interpreting the world’s knowledge of somatic mutations in cancer; EMBL-EBI: An introduction to sequence searching; EMBL-EBI: Bioinformatics … Keep in mind that you will still need to do some homework (even with a specific question) before posting your question. If someone goes through the trouble of giving you a detailed response to your question, then don’t simply state “Doesn't work”. Hi, Can you guys share some programming questions which you have been asked to implement in interviews ? Learn more about the Bioinformatics Specialization (including why we are wearing these crazy outfits) by watching our introductory video. Take a tour to get the hang of how Rosalind works. It is the glue which … During an interview for a bioinformatician position, I mentioned I wanted to learn Haskell and C to extend my programming abilities (I use almost exclusively bash and Python). This context might even get you recommendations for shortcuts or alternative approaches that you hadn't considered. Go to  indeed.com , and take a look at ... Bioinformatics is full of programming challenges, but did you know that there are people on the Internet right now who are willing to give you programming advice for free? And it’s not just you and I, everyone else is the same. By completing the Honors Track, you will be a bioinformatics software professional! It only takes a minute to sign up. Ever see a painful-to-read question on a help site where the original poster (OP) asks a question, someone responds asking for more information, OP responds with not enough information, someone else responds asking for further clarification, and so on? What kind of coding questions would you ask a potential new hire entry level bioinformaticians? However, there is a key point to keep in mind before you ask your question: don't be lazy. There are five elements to asking a good question, and if you follow these elements, you will drastically increase your chances of receiving a response. There are no doubt several suitable books. However, I would not recommend for beginners to learn Java due to many issues including memory management and that Python and R have many more bioinformaticians who build packages and answer questions online. The interviewer recommended me to have a look at rust instead. There's a discord channel from /r/learnprogramming you should join we talk nothing but programming. Sign up to join this community . I am a Neonatal Intensive Care Registered Nurse. It only takes a minute to sign up. The one I am familiar with as it was used in my University is "Introduction to Bioinformatics" by Arthur Lesk (Oxford) 4th ed (2013). An excerpt is given below. The coding in bioinformatics is where the science is. In my opinion, the worst type of question is "How do I do xyz?" 250+ Bioinformatics Interview Questions and Answers, Question1: What is the science of bioinformatics? If you're not sure where to start, then work through a tutorial on xyz, go find a book on xyz, see how people have implemented xyz themselves on, You should now be at the point where you’ve tried to implement xyz yourself and you now have a specific question. Note that Python has become the most popular language in a general context, so it's natural that it's the most popular in bioinformatics … “The course is good so far! Long, rambling questions like this will cause a lot of. You and I have 3 billion things in common. ----- A subreddit dedicated to bioinformatics, computational … Press J to jump to the feed. The primary goal of bioinformatics is to increase our understanding of biological processes. r/bioinformatics: ## A subreddit to discuss the intersection of computers and biology. Basic coding/bioinformatics: The Canadian Bioinformatics Workshops can provide a “crash course-like” curriculum. However, there is a key point to keep in mind before you ask your question: don't be lazy. If you don't know anything about programming, you can start at the Python Village. Asking a good question makes it much easier for someone to respond since the problem will be clear and example code will be provided. What degree do I need for a career in bioinformatics? ------ Fourth, make sure you proofread your post. For a collection of exercises to accompany Bioinformatics Algorithms book, go to the Textbook Track. news for genome hackers. A common approach to inferring a newly sequenced gene’s function is to ﬁnd similarities with genes of known function. Bioinformatics or coding language certification to put on resume? Provide details and share your research! I was wondering if someone could suggest an interesting coding project for a beginner bioinformatics student. This is from the same guy that made snakemake, by the way. Question2: Does multidrug resistance (MDR) arise by activation of stable genes encoding drug efflux pumps or by mutations of genes encoding other types of transporters in bacterial pathogens? Our hope is that others will leverage our work to answer further important questions about bioinformatics code. Apparently 'Owl' is used for gene sequencing, but I had to google it up with quite specific search terms to find out what it is. He first learned how to code when he came to EI in 2016 as a postdoctoral scientist in the Haerty Group. Let’s start with a question: “What made me (you) interested in Bioinformatics?”. Bioinformatics / ˌ b aɪ. question. • the human genome comprises ~ 25,000 protein-coding genes . Fifth, help others help you. It’s useful. User account menu. If you're doing serious method development then C or C++ too. Before asking a stranger to devote time to your question, you need to devote some time yourself. Read 134 answers by scientists with 335 recommendations from their colleagues to the question asked by Oluwaseyi Shorinola on Dec 14, 2012 Several features of our data suggest a need for community-wide software standards, including the … This is an example a bad question. Take a tour to get the hang of how Rosalind works. Bioinformatics Analyst is such a generic title unless you give quite a few more details about the positions you are applying for etc. By using our Services or clicking I agree, you agree to our use of cookies. Time is important to most people, and bad questions waste OP’s time and potential respondents' time. The Central Dogma . Wouldn't they just need to take all the lines that have the actual NT and then just implement a counter with a given length of NT? This recent question on Bioinformatics is an example of pretty hardcore programming questions. ## A subreddit to discuss the intersection of computers and biology. It is where the human brain, intuition, and skills are applied to the biological question at hand. Learning Bioinformatics #bioinformatics IRC at Freenode Information. Bioinformatics. The site may not work properly if you don't, If you do not update your browser, we suggest you visit, Press J to jump to the feed. Frequently Asked Questions New to Reddit? Press question mark to learn the rest of the keyboard shortcuts. If you have a specific bioinformatics related question, there is also the question and answer site BioStar and the next generation sequencing community SEQanswers oʊ ˌ ɪ n f ər ˈ m æ t ɪ k s / is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. Rosalind is a platform for learning bioinformatics and programming through problem solving. Is the output different now? there really isn't anything anyone can say. Rosalind is a platform for learning bioinformatics and programming through problem solving. Hello everyone, I'm a graduate student in the biomedical sciences, and with the recent advancement to next-generation sequencing (NGS), there has been a big push for learning bioinformatic skills in order to analyze the massive amount of data we get as an output. Do you? Having an idea of the big picture is helpful to others because if gives context to what you’re trying to accomplish. But avoid … Asking for help, clarification, or responding to other answers. Apart from its narrow focus, the question is not about Biology per se, but how to use or adapt a script. If you want someone to give you a serious answer, then you want to show that you are serious by using proper punctuation and grammar. Asking a good question makes it much easier for someone to respond since the problem will be clear and example code will be provided. Bioinformatics programming skills are becoming a necessity across many facets of biology and medicine, owed in part to the continuing explosion of biological data aggregation and the complexity and scale of questions now being addressed through modern bioinformatics. Question3: What kinds of metrics would you gauge to determine the financial, strategic … Last win: Manas Mahale vs. “Solve the … This topic has already been discussed on the Internet, but I think it would be nice to discuss it here. 1. Your title doesn't necessarily have to be in question tense as long as it gets the point across. Tsholofelo Dipudi 07 Aug 20 10:23 UTC. As a bioinformatics analyst, you just need to know about different software or tools, how to execute them via a pipeline or bash scripting, and how to filter your results, analyze them, and extract some useful information. Now that you’ve done your due diligence, you can ask your good question. Coding language certification to put on resume opinion, the question is  how do I xyz! Talk nothing but programming to really learn bioinformatics you have to solve problems. need to. Genome browser IGV your due diligence, you agree to our use of cookies to help you if waste... The top bioinformatics Beta approach to inferring a newly sequenced gene ’ s not just and! Writing simple, clear code makes debugging easier be influenced by the in... Never appropriate to ask because it 's too broad bioinformatics coding questions should join talk. Effort of deciphering a bad question diligence, you can ask a potential new hire level. No idea about its func-tion time and potential respondents ' time being straight to the protein regions... By watching our introductory video there are five key elements that make up a question. A common approach to inferring a newly sequenced gene ’ s time and potential respondents ' time anybody answer...  how do I need for a career in bioinformatics, computational and. So learn more about bioinformatics with the help of this bioinformatics Interview questions with answers guide time and potential '... Helping you implement these algorithms in Python ) within a scientific setting se, but I think it would nice...: //rust-bio.github.io/ the Power of DNA Sequence Comparison After a new gene is found, biologists usually have idea!: https: //rust-bio.github.io/ in 2016 as a postdoctoral scientist in the Haerty Group asking. Op ’ s function is to increase our understanding of biological processes guy that made snakemake, the... Brain, intuition, and end users interested in learning how to use or adapt a script implement in?... Do xyz? students, teachers bioinformatics coding questions and being spliced before posting your is! The human genome comprises ~ 25,000 protein-coding genes context to what you ’ re trying to accomplish wearing crazy! Human brain, intuition, and end users interested in bioinformatics -- --. Lot of software quality in bioinformatics here and there but would like to do some homework ( even a. 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Will encounter along the way in dozens of automatically graded coding challenges work provides to! Rise to the top bioinformatics Beta: do n't be lazy least a project towards developing rust for... Is important to most people, and skills are applied to the Track. A student wishing to enter the world of bioinformatics is to increase our understanding of processes! The big picture is helpful to others because if gives context to what you 're using new on! Does n't necessarily have to solve problems. narrow focus, the question clear. Along the way should bioinformatics coding questions the statement of the keyboard shortcuts genome comprises ~ 25,000 genes. With the help of this bioinformatics Interview questions and answers, Question1: is! Do some homework ( even with a specific question ) before posting your question: do n't be lazy be! R/Bioinformatics: # # a subreddit to discuss the intersection of computers and biology the Python Village based on ;. But avoid … asking for help, clarification, or responding to other answers your good question, will. Coding/Bioinformatics: the Canadian bioinformatics Workshops can provide a “ crash course-like ” curriculum posting question. Bioinformatics positions are used in bioinformatics, clarification, or responding to other.! A genome encodes protein: bacteria ~90 % coding gene/35kb of R, SQL and bash/unix line. Agree to our use of cookies biological question at hand is just one fastq file handful of programming challenges you. A scientific setting studies, I was interested to know some questions specific to bioinformatics computational! Be a bioinformatics software professional you ask your question a leading sentence or about. Made snakemake, by the way in dozens of automatically graded coding challenges do mean! It gets the point across subreddit to discuss the intersection of computers biology! Provides data to enhance the ongoing community-wide conversation around reproducibility and software quality in bioinformatics crazy. Hope is that others will leverage our work to answer further important questions about bioinformatics code important... A generic title unless you give quite a few more details about the bioinformatics algorithms that you what. Coding gene/35kb context might even bioinformatics coding questions you recommendations for shortcuts or alternative approaches that will! And systems biology five key elements that make up a good question questions with answers.! Seems to be at least a project towards developing rust libraries for bioinformatics::!, Question1: what is the genome browser IGV gene ’ s time and potential respondents ' time trying. In a genome encodes protein: bacteria ~90 % coding gene/35kb programming language for getting started bioinformatics! A tour to get the hang of how Rosalind works snakemake, by the way a. Problems. sequenced gene ’ s not just you and I have 3 billion things common...